User Operation Manual

Edition 3
Nov-2015
 Trademark Acknowledgments

The FEI logo, AutoLoader are trademarks of FEI Company.

FEI is a registered trademark of FEI Company.
Microsoft® and Windows 7 are registered trademarks of Microsoft Corporation.
This manual was produced using FrameMaker™ document publishing software.
FrameMaker™ and Adobe are registered trademarks of Adobe Systems Incorporated.
Other product and company names mentioned herein may be the trademarks of their respective owners.

Copyright © 2015 by FEI Company

The information and materials contained herein are confidential and proprietary to FEI Company.
They are provided for your organization's internal use on a need-to-know basis.
They cannot be duplicated or disseminated for any third party without the express consent of FEI Company.

Limited Rights

The following notice applies to the U.S. Government and other purchases with federal funds:
Contractor Name:
FEI Company
Contractor Address:
5350 NE Dawson Creek Drive, Hillsboro, OR 97124
The Government's rights to use, modify, reproduce, release, perform, display, or disclose these technical data
are restricted to those rights specified in:
DFARS 252.227-7015(b)(2), FAR 52.227-14(g)(2) (Alternate II) and FAR 12.211.
Any reproduction of technical data or portions thereof marked with this legend
must also reproduce the markings.
Any person, other than the Government, who has been provided access to such data,
must promptly notify the above named Contractor.

Technical Writer

Martin Dufek
TABLE OF CONTENTS

Chapter 1 System Overview

User Manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
FEI Microscope Systems Safety Manual . . . . . . . . . . . . . . . . . . . . 1-1
User Operation Manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
System Capabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
System Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
Computer Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
Vacuum System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
Stage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Image Viewing and Capture . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Analysis Capability. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4

Chapter 2 System Control

System Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Interface Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Power Button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Vacuum System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
Vacuum Status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
Pump button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
Vent button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
Vacuum Modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
Environmental Backing Valve (EBV) . . . . . . . . . . . . . . . . . . . . . . 2-5
High Vacuum (HiVac) Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
Low Vacuum (LoVac) / ESEM Mode . . . . . . . . . . . . . . . . . . . . . . 2-5
Pressure Limiting Aperture (PLA) . . . . . . . . . . . . . . . . . . . . . . . . 2-6
Using Gas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
System States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
System Startup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
Overnight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
System Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Password Policy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Power Failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12
Emergency Off. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12
Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
Detector Types and Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
Stages and Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
Quanta 250 (50 × 50 mm) Stage . . . . . . . . . . . . . . . . . . . . . . . . 2-14
Quanta 450 / 650 (100 × 100 / 150 × 100 mm) Stage . . . . . . . . 2-15
Stage movement Limits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16

Chapter 3 Software Control

Software Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Other Software and Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Software Interface Elements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

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Tool-Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Pull-down Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Using the Mouse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Using the Keyboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Command Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
List Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
Property Editors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
Edit Boxes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
Radio Buttons / Check Boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
Adjusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Exponential Adjuster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Linear Adjuster. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Preset Adjuster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Spinners. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
2D Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Dialogues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Progress bars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
xT microscope Server Software . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
xT microscope Control Software . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
Title Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
Menu Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
File Menu (Alt + F) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
The Edit Menu (Alt + E) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10
The Detectors Menu (Alt + D) . . . . . . . . . . . . . . . . . . . . . . . . . . 3-10
The Scan Menu (Alt + S) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-11
The Beam Menu (Alt + B) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-14
The Stage Menu (Alt + S) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-14
The Tools Menu (Alt + T) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-17
The Window Menu (Alt + W) . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18
The Help Menu (Alt + H) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-20
Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-21
Magnification (HFW) / High Voltage / 
Spot Size (Beam current) List Boxes . . . . . . . . . . . . . . . . . . . . . 3-21
Degauss (F8) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-21
Imaging Pixel Resolution List Box . . . . . . . . . . . . . . . . . . . . . . . 3-21
Direct Measurement. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-21
Image Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-22
The Databar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-22
Pages and Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-23
1. The Vacuum module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-23
2. The Column Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-24
3. Magnification / HFW Module . . . . . . . . . . . . . . . . . . . . . . . . . 3-24
4. Beam Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-24
5. The Tuning Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-25
6. Detectors Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-25
7. Status Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-26
8. Stage Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-27
9. Stage Z Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-27
10. Scan Rotation Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-28
11. Measurement / Annotation Module . . . . . . . . . . . . . . . . . . . 3-28
12. Digital Zoom Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-28
13. Enhanced Image Module . . . . . . . . . . . . . . . . . . . . . . . . . . 3-29
14. Beam Deceleration Module . . . . . . . . . . . . . . . . . . . . . . . . . 3-29
15. Detector Settings Module . . . . . . . . . . . . . . . . . . . . . . . . . . 3-29
16. Quad Presets Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-30
17. Alignments Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-30

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Preferences… Dialogue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-31

The Units Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-31
The DataBar Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-32
The Presets Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-33
The Scanning Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-34
The Movie Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-35
Sensitivity Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-35
The ESEM™ Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-36
Magnification Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-37
General Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-38
FEI User Management Software . . . . . . . . . . . . . . . . . . . . . . . . . . 3-41
Control possibilities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-41
FEI Account Administrators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-41
File Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-42
Account Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-42
Userdata menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-43
Help Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-43
Account Logging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-43
Entering Commands in Summary . . . . . . . . . . . . . . . . . . . . . . . . 3-44
Using Mouse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-44
Using Keyboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-45

Chapter 4 Alignments
Common Rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
Buttons and Control Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
Alignment list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
Recommendation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
1 - Source Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
Filament Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
Particular Control Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
3 - Gun Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4 - Condenser Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5
5 - Final Lens Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6
Particular Control Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-6
6 - Stigmator Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7
Particular Control Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7
7 - Stage Rotation Centre . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-8
8 - PLA Centering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9
9 - Filament Exchange . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-10
Particular Control Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-10
94 - CCD Camera Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-12
154 - Water Bottle Venting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-13

Chapter 5 Operating Procedures

Specimen Preparation and Handling . . . . . . . . . . . . . . . . . . . . . . . 5-2
Needed items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Natural specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Coated Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Mounting Specimen to Holder. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Microscope Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
Operation Pre-Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
Inserting / Exchanging Specimen 

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and / or Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4

Selecting Vacuum Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4
Obtaining ImagING on Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
Imaging Optimising . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
Principles of SEM imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
Magnification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Changing Magnification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Scan Speed and Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Contrast and Brightness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Using Videoscope (F3) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Focusing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Focusing with MUI (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Correcting Astigmatism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Digital Imaging Enhancement / Imaging Mixing / Coloring . . . . . . . 5-9
Accelerating Voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Beam Spot size / Beam Current . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Adjusting Spotsize for Imaging . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Standard Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
Detector Settings Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
Gaseous Detectors image Procedure. . . . . . . . . . . . . . . . . . . . . . 5-12
Discharges between Gaseous Detectors and Sample . . . . . . . 5-12
Infrared CCD Camera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
Everhart Thornley Detector (ETD) . . . . . . . . . . . . . . . . . . . . . . . . 5-13
ETD Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-13
Large Field Detector (LFD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-13
Installing and Setting the LFD . . . . . . . . . . . . . . . . . . . . . . . . . . 5-13
Gaseous Secondary Electron Detector (GSED) . . . . . . . . . . . . . . 5-14
Installing and setting the GSED . . . . . . . . . . . . . . . . . . . . . . . . . 5-14
Capturing and Handling Single Image . . . . . . . . . . . . . . . . . . . . . 5-16
Image types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
Digital File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Saving / Opening / Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Image Capturing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Image Saving . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Image Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Recording Movies (Saving Multiple Images) . . . . . . . . . . . . . . . . 5-18
Movie TAB Preferences Dialogue . . . . . . . . . . . . . . . . . . . . . . . . . 5-18
Timer module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
File module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
Movie Procedure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
Record Movie Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
FEI Movie Creator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
File Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
Databar Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-22
Preview (tab) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
Playing a Movie. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
Stage Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-24
Eucentric Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-24
Sample Top Surface Positioning . . . . . . . . . . . . . . . . . . . . . . . . 5-25
Eucentric Position Setting Procedure . . . . . . . . . . . . . . . . . . . . 5-25
Software Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26
Map tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26
Coordinates tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-28
Tilt tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-29
Navigation Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-30
Stage Related Functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-30
Stage Movements – Keyboard Shift . . . . . . . . . . . . . . . . . . . . . 5-30

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Stage Movements – Track Mode. . . . . . . . . . . . . . . . . . . . . . . . 5-30

Stage Movements – Get Mode . . . . . . . . . . . . . . . . . . . . . . . . . 5-30
xT Align Feature…. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-31
Scan Rotation Align Feature . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-32
Compucentric Rotation (F12). . . . . . . . . . . . . . . . . . . . . . . . . . . 5-32
User Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-33
Sample Navigation (Ctrl + N). . . . . . . . . . . . . . . . . . . . . . . . . . . 5-34
Scan Rotation (Shift + F12) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-36
Measurement and Annotation Functions . . . . . . . . . . . . . . . . . . 5-37
Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-37
Property Editor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-37
Shape Creating . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-37
Shape Editing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-38

Chapter 6 Maintenance
Cleaning Procedures Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
List of Applied Cleaners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Cleaning Column Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Materials and Technique. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Cleaning Tips. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Accessing the Column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Opening the column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Closing the column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Wehnelt cap and Filament . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
Removing the Wehnelt Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
Removing the filament . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
Cleaning the Wehnelt Cap and Filament securing ring . . . . . . . . . 6-6
Installing filament, Wehnelt cap . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-7
Setting the filament position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-8
Installing the Wehnelt Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-8
The Anode Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-9
Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-9
Removing the Extractor Electrode . . . . . . . . . . . . . . . . . . . . . . . . . 6-9
Cleaning the Extractor Electrode . . . . . . . . . . . . . . . . . . . . . . . . . . 6-9
Replacing the Extractor Electrode . . . . . . . . . . . . . . . . . . . . . . . . 6-10
Removing the Anode assembly . . . . . . . . . . . . . . . . . . . . . . . . . . 6-10
Anode Body . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-10
Installing the Anode Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-11
The Column Liner and Apertures . . . . . . . . . . . . . . . . . . . . . . . . . 6-12
Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-12
Removing the Liner Tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-13
Removing Apertures from the Liner. . . . . . . . . . . . . . . . . . . . . . 6-13
Removing Aperture (A) from Holder . . . . . . . . . . . . . . . . . . . . . 6-13
Platinum Apertures Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-14
Installing Aperture (A) in Holder . . . . . . . . . . . . . . . . . . . . . . . . . . 6-15
Aperture positioning in the Liner . . . . . . . . . . . . . . . . . . . . . . . . . . 6-16
Cleaning the Liner Tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-17
Installing the Liner Tube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-17
The Standard Insert . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-18
Removing and Disassembling . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-18
Housing Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-19
Gaseous Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-20
Cleaning the GSED / LFD. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-20
Cleaning the GBSD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-20

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Stage Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-21

Stage mechanics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-21
Cleaning Stage parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-21
Specimen Holders. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-21
Cleaning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-21
Refilling Water Bottle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-22
Pre-Vacuum Pump Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . 6-23
Periodic check. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-23
Topping-Up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-23
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-24
Diagnostics Auto Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-26
Simple TAD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-27
Old Pump maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-28
Periodic check. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-28

Chapter 7 System Options

Manual User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3
Joystick . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3
Uninterruptible Power Supply (UPS) . . . . . . . . . . . . . . . . . . . . . . . 7-4
Nav-Cam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
Capturing Navigation Image Procedure . . . . . . . . . . . . . . . . . . . . . 7-5
403 - Nav-Cam Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-6
Optional Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-7
Optional Detectors Connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-7
Installing / Removing Lens Mounted Detectors . . . . . . . . . . . . . . . 7-7
Gaseous Back scattered Electron Detector (GBSD) . . . . . . . . . . . 7-8
Installing and Settings the GBSD. . . . . . . . . . . . . . . . . . . . . . . . . 7-8
Obtaining an images with the GBSD . . . . . . . . . . . . . . . . . . . . . . 7-9
Retractable Detectors Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-9
Low-voltage High-contrast Detector Lens Mounted / 
Retractable (vCD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-10
Installing / Removing Lens Mounted vCD Detector . . . . . . . . . . 7-10
Inserting and Retracting vCD Detector . . . . . . . . . . . . . . . . . . . 7-10
Directional Backscattered Detector – Concentric 
Backscattered Detector Lens Mounted / Retractable (CBS). . . . . 7-11
Detector Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-11
Installing / Removing Lens Mounted CBS Detector. . . . . . . . . . 7-11
Inserting and Retracting vCD / CBS Detector . . . . . . . . . . . . . . 7-11
ESEM GAD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
Installing / Removing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
Detector Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
Obtaining Image in BSE Mode. . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
Scanning Transmission Electrons Microscopy Detector (STEM I) 7-14
Settings for STEM I Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-14
Loading samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-15
Obtaining Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-15
Retractable Annular Scanning Transmission Electrons Microscopy De-
tector (STEM II). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-16
Holder Arm Installation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-16
Load In Row Holder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-17
Inserting and Retracting STEM II Detector . . . . . . . . . . . . . . . . 7-17
Settings for STEM II Detector . . . . . . . . . . . . . . . . . . . . . . . . . . 7-18
Photo Multiplier Tube / Backscattered Electron Detector 
Autrata, Centaurus (PMT-BSE). . . . . . . . . . . . . . . . . . . . . . . . . . . 7-19

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Obsolete Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-20

Quad Backscattered Electrons Detector (Quad BSED). . . . . . . 7-20
Dual BSED / Dual GAD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-21
Energy Dispersive X-ray (EDX) Analysis . . . . . . . . . . . . . . . . . . . 7-23
High Vacuum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-23
LFD EDX Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-24
GSED EDX Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-24
GAD EDX Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-25
STEM EDX Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-25
Cooling Stage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-26
Cooling Stage Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-26
Cooling Stage Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-26
Chamber feed-through Plate . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28
Cooling Stage Controller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28
Water Chiller, Flow Box and Cooling Water Hoses . . . . . . . . . . 7-29
Cooling Stage Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30
Cables and Water Hoses connection . . . . . . . . . . . . . . . . . . . . 7-30
Water Flow Box installation and operation . . . . . . . . . . . . . . . . 7-30
WetSTEM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-31
WetSTEM Basic operations. . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-31
WetSTEM II . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-32
WetSTEM Basic operations. . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-33
WetSTEM II vibration suppression . . . . . . . . . . . . . . . . . . . . . . 7-34
Cooling Stage Consumable . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-35
Software Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-36
Temperature Stage Control Module . . . . . . . . . . . . . . . . . . . . . 7-36
Temperature tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-36
Humidity tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-37
Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-37
153 - Cooling Stage Calibration. . . . . . . . . . . . . . . . . . . . . . . . . 7-38
Cooling Stages Basic Operations . . . . . . . . . . . . . . . . . . . . . . . . . 7-39
Condensation Point . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-39
Using bulk samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-40
High magnification imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-40
Cooling below Ice Point . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-40
Water Cooled Temperature Stage Operation Termination . . . . . . 7-41
Heating Stage 1 000 °C / 1 400 °C. . . . . . . . . . . . . . . . . . . . . . . . . 7-42
Heating Stages Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-42
Heating Stages Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-42
Chamber Feed-through Plate . . . . . . . . . . . . . . . . . . . . . . . . . . 7-43
Water Chiller, Flow Box and Cooling Water Hoses . . . . . . . . . . 7-43
Heating Stage Controller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-43
High Temperature GSED. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-44
1 000 °C Heating Stage variances . . . . . . . . . . . . . . . . . . . . . . 7-45
1 400 °C Heating Stage variance . . . . . . . . . . . . . . . . . . . . . . . 7-45
Heating Stage Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-47
Software Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-48
Temperature tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-48
Advanced tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-48
150 - Heating Stage Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . 7-49
151 - Temperature Calibration. . . . . . . . . . . . . . . . . . . . . . . . . . 7-50
Heating Stages Basic Operations . . . . . . . . . . . . . . . . . . . . . . . . . 7-51
Setting up Temperature Profile . . . . . . . . . . . . . . . . . . . . . . . . . 7-51
Temperature Conductivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-51
Outgassing Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-52
Using HS with EDX Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . 7-52
Water Cooled Temperature Stage Operation Termination . . . . 7-54

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HS Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-54
Cleaning. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-54
HS Consumables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-55
Remote Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-56
Connection to Microscope PC . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-56
Microscope PC’s desktop Sharing . . . . . . . . . . . . . . . . . . . . . . . . 7-57
Controlling microscope remotely. . . . . . . . . . . . . . . . . . . . . . . . . . 7-57
Beam Deceleration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-58
Stage Modification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-58
Beam Deceleration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-59
Detection Principles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-59
Beam Deceleration Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-60
Beam Deceleration Mode Imaging Procedure . . . . . . . . . . . . . . 7-61
Quick Loader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-62
General description. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-62
Loading rod . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-63
Gate valve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-63
Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-64
Sample Carrier, Sample Gate and Stage Adapter. . . . . . . . . . . 7-64
Installation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-65
Loading position. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-65
Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-66
Loading a sample. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-66
Rod Loading Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-66
Unloading a sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-67
CryoCleanerEC. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-68
Parts and Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-68
Flanges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-69
CryoCleaner Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-69
Dewar Vessel Refilling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-69
Removing Nitrogen Vessel . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-70
Baking Nitrogen Vessel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-71
Replacing Nitrogen Vessel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-71
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-71
Spare Vessel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-71
Specimen Holder Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-72
Older Interface Adapter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-72
Location positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-73
Interface pillar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-73
Multi-Holders. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-74
16 Position Stub Holder (1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-74
Angled Stub Holder (2) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-74
Analytical Holder (3). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-74
Polished Mount Holders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-75
Clamp Stubs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-75
Torx Drivers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-75

C-viii C O N F I D E N T I A L – FEI Limited Rights Data

1 SYSTEM OVERVIEW

User Manuals

FEI MICROSCOPE SYSTEMS SAFETY MANUAL

It provides important information required during operation and
maintenance for a product and personal safety. Be sure to read at least
this manual!

USER OPERATION MANUAL

The User Manual is delivered in the electronic PDF file only. However, it
is possible to print parts of the manual if this is desired.
It is recommended to read the appropriate User Manual section before
operating any of the microscope function. Most importantly, you should
locate the topics necessary to operate the microscope in the proper way
to safely achieve the best results.
The manual is divided into the following chapters:
1. System Overview (this chapter) 
gives overview of the user manuals and system capabilities.
2. System Control 
describes the system hardware (interface elements, vacuum system,
system states, Equipment).
3. Software Control 
describes the interface that sets and controls system operation,
giving the function of each tool, menu item and control page.
4. Alignments 
explains how to align the equipment to achieve the optimal
performance.
5. Operating Procedures 
gives procedures for how to use the system features.
6. Maintenance 
gives allowed step by step cleaning and maintenance procedures.
7. System Options 
explains relevant options that are integrated into or accessory to the
system.
In the PDF file, you can take advantage of the searching and navigation
possibilities. The following conventions are observed:
• Some software functions use shortcuts, which are given beside the
heading in the brackets (for instance: Save (Ctrl + S)) and in the Help
menu / Keyboard Shortcuts… (see Chapter 3).
• A reference to the specific software element is highlighted in bold. For
instance: “Clear the Stage module / Coordinates tab / Z coordinate
check box.”

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System Overview: System Capabilities

System Capabilities

The Quanta Scanning Electron Microscope (SEM) produces enlarged

images of a variety of specimens, achieving magnifications of over
100 000× providing high resolution imaging in a digital format. This
important and widely used analytical tool provides exceptional depth of
view, minimal specimen preparation, and the ability to combine the
technique with X-ray microanalysis.

SYSTEM PERFORMANCE
The main instrument components used for imaging of the samples are:
• Electron source 
The electron beam is emitted within a small spatial volume with a
small angular spread and selectable energy.
• Lens system 
The beam enters the lens system consisting of several
electromagnetic or electrostatic lenses and exits to hit the specimen
surface.
• Scan unit 
The scan generator signal, fed to the deflection systems, moves the
beam in a raster pattern over the specimen area. The electrical
voltage changes as it rasters. This signal, modulated by the detection
system signal produces the onscreen imaging of the specimen
surface.
• Detection unit 
Electrons striking the specimen react with its surface producing three
basic types of signal: backscatter electrons, secondary electrons and
X-rays. The detection system picks up these signals, converts them
into a digital signal which is then sent to the control PC and displayed
on the monitor.

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 System Overview: System Capabilities

FIGURE 1-1 SEM SCHEMATIC OVERVIEW

FILAMENT PINS

ELECTRON GUN
SUPPRESSOR

EMITTER

CONDENSER LENS SYSTEM

LENS(ES)
SCAN UNIT

DEFLECTION
SCAN GENERATOR M
SYSTEM

FINAL LENS

R
TO
T EC DETECTION UNIT
DE

SPECIMEN

Computer Control
The xT microscope Server and xT microscope Control (User Interface)
software integrate SEM functionality within a Windows 7™ operating
environment.
These software consist of programs defining specific instrument settings
for particular applications, ensuring reproducibility of complex
procedures (for instance imaging, management of image capture,
storage, and data output devices etc.). They also control instrument
hardware (the column, detector(s), stage, EDX, vacuum functions etc.).

Vacuum System
The entire electron path from gun to specimen must be under vacuum so
that the particles do not collide with air molecules. Various levels of
vacuum are necessary, so a Turbo Molecular Pump (TMP) backed by a
pre-vacuum pump (PVP), obtains the necessary specimen chamber
pressure. The Quanta has the following operating vacuum modes to deal
with different sample types.
High Vacuum (HiVac)
This is the conventional operating mode associated with all scanning
electron microscopes.
Low Vacuum (LoVac) / ESEM™
In the gaseous modes (LoVac, ESEM) the electron column is under
lower pressure than the specimen chamber. Either mode can use water
vapours from a built-in water reservoir, or an auxiliary gas which is
supplied by the user and connected to the gas inlet provided for this
purpose. Observation of outgassing or highly charging materials can be
made using one of these modes without the need to metal coat the
sample, which would be necessary for conventional HiVac mode.

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System Overview: System Capabilities

Stage
The Quanta has a computer-controlled high-accuracy five-axis stage. It
offers precision specimen computer controlled manipulation and
automation of all axes for overall spatial orientation on highly repetitive or
extremely irregular samples.
Specimen exchanges take place through a chamber door which exposes
the specimen stage when opened. The exchange takes a few minutes.
Software and interlocks protect the system against a damage and users
against an injury.
The Quanta chamber, stage, and wafer holder accommodate wafers up
to 6", or other devices, in a high-vacuum environment.

Image Viewing and Capture

Because the amplified detector signal is displayed synchronously with
the beam scanning, there is a correspondence between brightness of an
image point on the monitor screen and the signal detected at the
corresponding point on the specimen.
Magnification is the ratio of the size of the viewing monitor screen to the
size of the area scanned on the specimen. Higher magnification is
achieved by reducing the size of the area scanned on the specimen.

Analysis Capability
Convergence of the SEM and X-ray detection system (e.g. EDX –
Energy Dispersive X-ray) (option) at short working distance allows
precision chemical analysis at high resolution of surface.
Various vendor options are compatible with the instrument.

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2 SYSTEM CONTROL

System Layout

The standard layout of the Quanta 250 / 450 / 650 system is based
around a dedicated microscope controller along with an electrical
console to power the microscope console (vacuum, gun, column, stage
etc.).

FIGURE 2-1 QUANTA STANDARD LAYOUT SCHEME

Interface Elements

SOFTWARE
The software control contains graphic applications within Windows 7™
operating environment. xT microscope Server starts and stops basic
microscope functions. It allows to open and close the xT microscope
Control software (UI – user interface or sometimes xTUI within dialogue
boxes) which controls all system functions including detection and
analysis, scanning, image gathering, manipulation and output,
magnification, etc.
All user account levels created via FEI User Management software
ensure for the particular users admission to both the operating system
Windows 7™ and the xT microscope Control software. The hierarchy of
user account levels consists of the following:
• FEI Account Administrator
• FEI Supervisor Users
• FEI Microscope Users
• FEI Non-active Users
For information on Logging on and Logging off, the start-up of the system
and all the features of the UI elements see Chapters 3 and 5.

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System Control: Interface Elements

HARDWARE
The system is computer controlled and as such has a Microscope
Controller which must be turned on (use the power button on the PC) to
operate the microscope by means of the software. The Electrical
Console powers components of the Microscope Console (vacuum,
gun, column, stage...). The support computer can hold some other
software utilities. The switch box switches the keyboard and the mouse
to either of the two computers. The control software facilities and data
are displayed graphically on the LCD monitor and are superimposed
around and on the image. The other LCD monitor is used either as an
extended desktop of the Microscope controller or as the support
computer monitor. To control software utilities one can use a keyboard,
mouse, joystick (option) or the Manual User Interface (option).

Power Button
The console / system power is activated by pressing the green power
button located on the microscope console front panel. This switches the
sub-systems on and allows the interface and communication with the
microscope controller. Most of the functions are activated via the
software control.

FIGURE 2-2 CONSOLE POWER BUTTON ON / OFF

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 System Control: Vacuum System

Vacuum System

There are two main vacuum sections:

• Electron source / Column
• Specimen chamber.
Both sections are vented for a sample exchange. In operation the Gun /
Column section is always under the high vacuum. The Specimen
chamber is at the pressure required for the given mode (HiVac / LoVac /
ESEM).
All valve and pump operations are fully automatic, except the manual
environmental backing valve (EBV).

FIGURE 2-3 THE QUANTA VACUUM SYSTEM

Legend: 

ABV . . . . Auxiliary Bypass Valve

AGV . . . . Auxiliary Gas Valve
BG . . . . . Buffer Gauge
BV . . . . . Buffer Valve
EBV . . . . Environmental Backing Valve
EG . . . . . Chamber Gauge
HVG . . . . High Vacuum Gauge
ChEV . . . Chamber Evacuation Valve
ChIV . . . . Chamber Isolation Valve
NVC . . . . Needle Valve Control
PVP . . . . Pre Vacuum Pump
SIV . . . . . Servo Isolation Valve
TMP . . . . Turbo molecular Pump
TVV . . . . Turbo Venting Valve
VV . . . . . Venting Valve
WBV . . . . Water Bottle Valve

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System Control: Vacuum System

VACUUM STATUS
The vacuum status controls are in the Vacuum module. The Pump
button starts pumping for the operating pressure and the Vent button
starts venting for a sample or detector exchange (see Chapter 3).
In the Status module at the bottom of any page the actual vacuum status
is represented by the colored icon, which may have three possible colors
with the following meaning:
• Green: PUMPED to the desired vacuum mode
• Yellow: TRANSITION between two vacuum modes 
(pumping / venting / purging)
• Gray: VENTED for sample or detector exchange

Pump button
When the Pump button is clicked and the status is Vented, or when
changing vacuum mode, the target pressure that the system pumps to
depends on the selected vacuum mode. The Pump button is highlighted
in and not accessible.
For the High Vacuum the system achieves the lowest pressure possible.
For the Low Vacuum / ESEM it achieves the pressure specified in the
Vacuum module / Chamber Pressure adjuster. The purge function can
be defined in the Preferences… dialogue / ESEM tab (see Chapter 3).
When the Pump button is clicked and the status is Transition (venting),
the venting procedure stops and the system immediately starts to pump
to the currently selected vacuum mode.

Vent button
When the Vent button is clicked and the status is Pumped, the
confirmation dialogue appears. After confirmation, the system switches
off the detector voltages, high voltage supplies, vacuum pumps and uses
the appropriate valves to vent the system with the use of air or dry
Nitrogen brought to the Nitrogen Inlet. Nitrogen is recommended to
obtain the better vacuum for high resolution imaging in HiVac mode.
The Vent button is highlighted and not accessible. After a specified
venting time the venting valve closes and the vacuum status should
indicate Vented. The chamber door could be opened and the button is
enabled again.
When the Vent button is clicked and the status is Transition (pumping),
the dialogue appears. After confirmation, the pumping procedure stops
and the venting procedure starts.
When the Vent button is clicked and the status is Vented, the dialogue
appears. After confirmation, the venting valves re-open for the specified
venting time and then the valves close.
Note: 
If you vent the system in order to change a detector, wait until the icon
with a grayed specimen chamber appears in the Status module.
Otherwise there is a risk of a detector assessment malfunction, and as a
result the PLA (see below) will not be known by the system.

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 System Control: Vacuum System

VACUUM MODES
The Vacuum module / High Vacuum / Low Vacuum / ESEM radio
buttons are used to select the instrument target operating mode when a
Pump sequence is initiated.

Environmental Backing Valve (EBV)

The behaviour of the system in each of these modes depends on the
state of the manual EBV. The following describes the operation of the
manual (EB) valve relative to the states and cycles of the vacuum
system:

TABLE 2-1 EBV STATE WITH APPROPRIATE ACTIONS

State Action
Open The vacuum state changes to Low Vacuum or ESEM. 
The High Vacuum detector high voltage switches off. The
available ESEM detector is selected and switched on. 
The Purge cycle settings applies, using the selected gas. 
The Pressure is adjusted to the selected value, using the
selected gas.

Close The vacuum state changes to High Vacuum. 

The Low Vacuum / ESEM detector is disabled and
switched off. The last used High Vacuum detector is
selected. When the pressure is sufficiently low the
detector high voltage is enabled (when applicable). 
The admission of the gas stops. The pressure lowers to
the lowest level.

The system automatically recognizes the EBV Opening / Closing and

continues in operation.
Caution: 
If the user closes the valve without being prompted to do so by the UI
dialogue a pressure burst near the filament could occur, lowering its
lifetime. A warning is shown in this case.

High Vacuum (HiVac) Mode

The high vacuum condition is common throughout the column and
specimen chamber. The typical pressure value is within the order from
10-2 to 10-4 Pa.

Low Vacuum (LoVac) / ESEM Mode

In these gaseous modes, the column section is under the lower pressure
than the specimen chamber where the pressure ranges from 10 to
200 Pa (LoVac) or from 10 to 4000 Pa (ESEM). These modes uses water
vapour from a built-in water reservoir or a gas from an auxiliary gas inlet
(the drop down list).
The system automatically detects the gaseous detector installed and
offers a relevant vacuum mode in the Vacuum module.
When Low Vacuum / ESEM mode is entered from ESEM / Low
Vacuum mode by selecting an appropriate mode radio button, nothing
happens unless there is a different gas type being used for the two
modes. In this case, the appropriate gas type is selected.
When Low Vacuum / ESEM mode is entered from HiVac or from the

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System Control: Vacuum System

Vented status, the system prompts a user with the PLA Configuration
dialogue (see below). This happens only for the first time after a Vent
procedure.
Pressure
The Chamber Pressure adjuster is used to set and display the target
chamber pressure. Pascal, Torr or Millibar units are available and can be
selected in the Preferences… dialogue / Units tab (see Chapter 3).
When the system is in a LoVac / ESEM mode and the Chamber
Pressure value is changed, the pressure automatically changes to a
new value. When the system is in any other status and the chamber
pressure value is changed, the new value is used as the target pressure
when the system starts pumping to a Low Vacuum / ESEM mode again.
The actual specimen chamber pressure is displayed in the Status
module / Chamber Pressure: field.

Pressure Limiting Aperture (PLA)

The maximum allowed specimen chamber pressure in a LoVac / ESEM
mode is determined by the size of the PLA and a gas type.
The PLA Configuration dialogue prompts to inform the system about
the PLA size (in case it is not a part of a dedicated gaseous detector)
according to the figure and the application when pumping or switching to
a LoVac / ESEM mode. Along with a gas type, this information sets
pressure limits and rates for pressure changes.
Clicking the OK button after selecting an appropriate pole piece radio
button (cone or a detector with an integrated PLA) informs the system
that it is mounted on the lens insert. The system starts pumping to the
LoVac / ESEM mode. From that point on, this information is automatically
used until the system is vented again, when the PLA is set to “unknown”.
Clicking the Cancel button leaves the system in its actual status mode
(Pumped or Vented).
PLA Cones
In some cases it is possible to install a cone on the actual gaseous
detector to achieve some special characteristic:
• The Standard Insert is installed at all times. Gaseous detector and /
or the PLA cone are pressed onto the insert to form a gas seal.
Chamber gas (flowing through the detector / PLA aperture) is pumped
out through the holes in the sides of the insert. A gas-restricting
aperture is found at the top of the insert.
Note: 
This aperture also acts as a final or objective aperture. The pressure
above this aperture is considered to be very low. Any pollution that
accumulates on this aperture greatly affects the image. If astigmatism
is not possible to correct, it is usually a sign that this aperture needs
to be cleaned or replaced.
• The X-ray PLA cone (option - 500 µm aperture) is used for EDX
analysis (see Chapter 7) at a longer working distance (profile extends
down to 8.5 mm). Samples are imaged at 10 mm working distance,
which is the stage eucentric position and the collection point of the
EDX detector. It is used in conjunction with the LFD.
The longer profile of this cone minimizes the low voltage beam
dispersion and skirting of the primary beam in the gaseous
environment of the chamber, allowing more electrons to interact with
the specimen when focused and increasing the signal to noise ratio.
To fit the X-ray PLA cone, remove any existing detector or PLA cone

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 System Control: Vacuum System

from the standard insert, then press the X-ray PLA cone into place.
• The Low kV PLA cone (500 µm aperture) is installed onto the
standard insert in case the LFD is used for low vacuum and low
voltage imaging (i.e. below 5 kV) to reduce beam loss in the gas. It is
used when imaging at shorter working distances (< 9 mm) and
restricts the lower magnification limit.
• The Hot Stage cone (option - 1000 µm aperture) is used with the
heating stage in combination with the hook wire or LFD. It can be
used without the hot stage when beam protection is desired with a
larger field of view.
Note: 
When the PLA Configuration dialogue appears, select the appropriate
cone according to the figure and the name.

Using Gas
The Low Vacuum / ESEM mode allows a user to image samples in a
gaseous atmosphere, which can be selected in the drop down list box:
• the Water vapour from a built-in water reservoir located in the back
part of the microscope console,
Note: 
On occasion the water reservoir needs to be filled (see Chapter 6).
• the gaseous environment supplied by a user via the Auxiliary inlet
placed on the back of the console.

Caution! 
Maximum overpressure for the Auxiliary gas and Nitrogen inlets is 
10 kPa (0.1 bar). The Nitrogen inlet is used only for venting the
chamber with air or the nitrogen preferably.

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System Control: Vacuum System

When using a particular pressure limiting aperture, there are pressure

limits for different gasses.
TABLE 2-2 MAXIMAL CHAMBER PRESSURE [PA (TORR)] 
UNDER DIFFERENT GASEOUS ENVIRONMENT

Working Gas 500 µm Aperture 1000 µm Aperture

Water - H2O 2 700 (20) 750 (5.5)
Nitrogen - N2 4 000 (30) 750 (5.5)
Air
Carbon Dioxide - CO2
Nitrogen Dioxide - NO2
Argon - Ar 1 000 (7) 200 (1.5)
*)
C xH y 4 000 (30) 750 (5.5)

Caution! 
The system doesn’t watch the limits and higher overpressure
(especially for gasses not listed) set by a user! It could switch off the
emitter! In such cases the system could need to be started up by a
service engineer.
Note: 
*) Combustible gases (acetylene for instance) must always be used with
respect to safety issues.
Purging
During this procedure the specimen chamber is automatically pumped
down to a lower pressure to remove the old gas, then it is flooded with
the new one (selected in the Vacuum module) to a higher pressure. This
takes place several times, until the old gas is removed and the chamber
is mostly filled with the new gas. This is applied when the system is:
• pumping to the LoVac / ESEM mode from the vented status.
• in the LoVac / ESEM mode and the gas type is changed.
• in the LoVac / ESEM mode and the Purge button is pressed.
The purging can be set up, started and terminated in the Preferences…
dialogue / Low Vacuum tab (see Chapter 3).
Note: 
This procedure can take several minutes, according to Preferences
setting. Wait until Vacuum status indicates Pumped, because detectors
do not start operation till desired pressure is reached.

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 System Control: System States

System States

There are several system states:

• Complete shutdown – service and emergency reasons
• Shutdown – emergency reasons
• Overnight – when not using the system overnight
• Full operation – when working
Both Shutdown system states could be set only by a supervisor. 
See detailed description of all following processes and elements within
the chapters 2, 3 and 4.

SYSTEM STARTUP
In the Complete shutdown state the system is disconnected from all
sources used for an operation. To bring the system to the Shutdown
state, connect following sources:
• electrical – power cord
• operating gas – nitrogen inlet (option)
To bring the system to the Full operation state follow the procedure:
1. Push the Power button on the Microscope console panel (it starts to
shine).
2. Switch on the Microscope controller. The operating system
(a) Windows 7™ loads and displays the appropriate icons on the
monitor desktop.
3. Double-click the xT microscope Server icon to start the software (all
seeming LED’s should be green – Initialized).
4. Click the Start button to start the server. Wait until all elements are
fully functional (green – Initialized).
5. Click the Start UI button to start the xT microscope Control
software. The main window appears behind the XTUI Log On
dialogue.
Note: 
This step could take place automatically, if Advanced / Autorun UI
check box is ticked. 

6. Enter your Username and a Password (a). 




7. Click the Stop button to stop the server. Wait until all elements turn
grey – Stopped.
8. Repeat steps No. 4, 5 and 6.
9. Select the desired Vacuum module / Vacuum mode radio button and 
click the Vacuum module / Pump Button. Wait for the Pumped
status.

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System Control: System States

10.Click the Column module / Beam On button. A Column module /

Source progress bar indicates the actual status and the button turns
yellow when finished.
See Chapter 5 to set desired imaging conditions.

Note:
a)
Once you have your FEI Microscope user
(or Supervisor) account set up via FEI User
management software by FEI Account Administrator
(see Chapter 3), you can use your name and password to access both
Windows 7™ system and the xT microscope Control software. Take
note of the Password policy (see below), which helps to protect individual
settings and results.

Overnight
In the Full operation state all microscope equipment and accessories
are in use or ready to use. When leaving the system, it is advisable to
bring it to the Overnight state by following the procedure:
1. Click the yellow Column module / Beam On button to switch off the
beam.
2. If one needs to remove the sample, click the Vacuum module / Vent
button. Wait for the Vented status and remove your sample.
3. Click the Vacuum module / Pump button to pump to the High
Vacuum. (b)
4. Select (c) the File menu / Log Off (active user name) to log off the
present user and to provide the Log On dialogue for entering another
one. Switch off the monitor.

Caution!
Do not stop the xT Microscope Server services (clicking the xT
microscope Server software / Stop button or switching off the
Microscope computer) when the system is under vacuum – always
vent the microscope before stopping the xT Microscope Server!

Note:
b)
It is strongly recommended to always leave the chamber in HiVac
mode when not being used. When the sample chamber is left in the
LoVac mode, water vapour is likely to accumulate in it, PVP lifetime
decreases and the water reservoir or gas cylinder empties prematurely.
c)Waiting for a new user leaves the status of the xT microscope
Control software non-operational and only the xT microscope Server
software is active. Therefore changing a user does not require Logging
off / Logging on at Windows 7™ level.

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 System Control: System States

SYSTEM SHUTDOWN
In case of emergency bring the system to the Shutdown state by
following the procedure:
1. Click the Column module / Beam On button to stop the accelerating
voltage. A Column module / Source progress bar indicates the
actual status and the button turns grey when finished.
2. Click the Vacuum module / Vent button to vent the chamber.
3. Click the xT microscope Server software / Stop button.
This stops the UI, the xT microscope Server application services and
switches off the console (The power button on the microscope front
control panel stops shining).
4. Shutdown the Windows 7™ and switch Off the monitor. (d)
If there is a demand to bring the system to the Complete shutdown (e)
state, disconnect the power cord and any other input / output if used.
Note:
d) The power plug should not be disconnected. The system can be left in
this state if electrical power is supplied to the instrument because the
pumps are running and pumping the column.
e)
The Complete shutdown procedure should only be carried out by a FEI
service engineer. It brings the system to the non-powered state, where the
vacuum in the column area is no longer supported by running pumps. All
valves are closed, and the electron column and specimen chamber areas
are vented. Normally it is used for a system transportation or for service
actions, like repair to essential systems (electrical and air supplies).

PASSWORD POLICY
After the FEI software installation there are two initial users / passwords
common for the OS Windows and the xT microscope Control software
(xT UI):
• supervisor / supervisor
• user / user
At the first time log in the operating system Windows 7 a user is
automatically forced to change their password. After that the xT UI
accepts it and enables to log in from that point on.
Each password (either for any new user or after the 90 day period
expiration) has to meet the following conditions:
• at least 7 characters long,
• the stem must be significantly different from a previous password and
shouldn't contain complete dictionary word and user name,
• must contain at least one character of each of these character
groups:
– Uppercase letter
– Lowercase letter
– Number
– Symbol (/, *, -,+ etc.)

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System Control: System States

POWER FAILURE
Take sufficient measures to avoid power failures. If it occurs while the
instrument is completely operational, the microscope comes down to a
safe state and the following happens:
• The accelerating voltage is switched off abruptly.
• The electron emission is switched off.
• The specimen chamber vents gently, automatically.
• The vacuum in the instrument is no longer supported by running
pumps. All valves are closed, so the vacuum in the column and
chamber is not lost at the moment.
• The microscope controller and the support computer are switched off,
the momentary adjustments of all system parameters (accelerating
voltage, magnification, stage positions etc.) are lost if they were not
saved.

Emergency Off
To switch off the electrical power completely in case of emergency, follow
this quick and safe procedure:
1. Push the red EMERGENCY (EMO) button 
(option - see the Safety Manual).
If the button is not installed proceed as follows:
2. Switch off the breaker switch labeled MAINS S1 at the cabinet back,
which is placed at the very right side in the row.

FIGURE 2-4 MAINS SWITCH BOARD

If this is not easily accessible:

3. Turn off the mains wall switch (if present), and / or disconnect the
mains plug from the mains socket.

WAR N I N G ! 
The temperature stage water chiller (options – separate device in
the microscope vicinity) are powered separately via the individual
power cords. The hazardous voltages may be present on this
equipment even when the microscope power plug is disconnected!

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 System Control: Equipment

Equipment

DETECTOR TYPES AND USAGE

The Detectors menu shows all installed detectors, the selected one has
a tick mark next to its label. Availability of detectors (full color label)
depends on the actual vacuum mode. The system remembers the last
detector used for a particular vacuum mode in the quad and its Contrast
& Brightness settings.
For settings and handling of particular detectors see Chapters 5 and 7.
TABLE 2-3 ALL DETECTORS TYPES

Detector Name UI Tag Vacuum Mode Detected Signal Max. Pressure [Pa] Note
Everhart-Thornley ETD HiVac SE (tunable energy)  3× 10-2 S
BSE
Large Field LFD LoVac, ESEM SE + BSE 200 S
Gaseous Secondary GSED LoVac, ESEM SE 1000 µm aperture: 750 S / LM
Electron 500 µm aperture: 2600
CCD camera CCD any light, infra-red light any S
External EXT detector- detector-dependent detector-dependent
dependent
Gaseous Secondary GAD HiVac, LoVac, SE 1000 µm aperture: 750 O / LM
Electron ESEM 500 µm aperture: 2600
Gaseous Backscattered GBSD LoVac, ESEM SE, BSE 10 (500 optimal) - 2600 O / LM
Electron
Concentric Backscattered CBS HiVac, LoVac BSE 200 O, LM
/R
Scanning Transmitted STEM I HiVac, LoVac, TE any O,
Electron Microscopy ESEM
Wet STEM STEM I HiVac, LoVac, TE any O, R
ESEM
Annular STEM STEM II HiVac, LoVac, TE any O/R
ESEM
low voltage, high contrast vCD HiVac, LoVac BSE 200 - retractable O / LM
2600 - lens mounted /R
ESEM & Gaseous GSED  HiVac, LoVac, SE, BSE 2600 O / LM
Analytical / ESEM (simultaneously in
GAD individual quads)

Note: 
SE = secondary electrons, BSE = back scattered electrons, 
TE = transmitted electron, S = standard, O = optional, 
LM = lens mounted R = retractable, boldface - preferred SEM modes

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System Control: Equipment

STAGES AND ACCESSORIES

Quanta 250 (50 × 50 mm) Stage

The stage has X, Y, Z and Rotation movements motorised, all with a
manual override and the manual Tilt movement. Motorised movements
are software controlled (an integrated part of the xT microscope
Control software – see Chapters 3 and 5), stage positions are displayed
on the screen.

FIGURE 2-5 QUANTA 250 STAGE (4 AXES MOTORISED)

Legend: A = Negative end stop

1 = Tilt lever B = 30° stop
2 = Tilt monitor C = 45° stop
3 = X axis D = 75° stop
4 = Rotation E = Tilt scale
5 = Z axis F = Stage lock
6 = Y axis G = Stage ground

Sample holder
There are single stub and the multiple holders provided. 
The single holder has a spring clip fitting and a secure-fitting screw. The
multiple holder is a 7-stub holding disc with a spring clip fitting only.
Both holders have the same threaded shaft which screws into the stage
rotation head center and can be securely attached to the stage by means
of the conical locking piece.

FIGURE 2-6 QUANTA 250 SAMPLE HOLDERS

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 System Control: Equipment

Quanta 450 / 650 (100 × 100 / 150 × 100 mm) Stage

The stage has X, Y, Z, Rotation and Tilt movements motorised, all with
a manual override. Motorised movements are software controlled (an
integrated part of the xT microscope Control software – see Chapters 3
and 5), stage positions are displayed on the screen.

FIGURE 2-7 QUANTA 450 / 650 STAGE CONTROLS

Tilt

Z axis

Rotation

Y axis

X axis

Stage ground
and Interface
connector

Sample Holder
There is the single stub holder provided.
Both holders have the same threaded shaft which screws into the stage
rotation head center. The specimen should not be thicker than 2 mm, or
it is impossible to bring it to the eucentric position.

FIGURE 2-8 QUANTA 450 / 650 SAMPLE HOLDERS

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System Control: Equipment

Stage movement Limits

The motorised movements of the stage can be operated under software
control for more advanced location mapping. This includes Shift, Get,
Track and the Stage module functionality. A live image can be
repositioned either by the stage movement (manual or software) or by
the Beam Shift. The tilting mechanism can be locked for more stability at
high magnifications using the software Clamp feature.
Note: 
When moving the stage or tilting the specimen, the magnification may
need to be reduced not to lose the feature of interest off the screen.

FIGURE 2-9 STAGE MOVEMENT SCHEMA

TABLE 2-4 STAGE FEATURES AND LIMITS

Item 50 × 50 mm 100 × 100 mm 150 × 150 mm Note

X [mm] -25 to +25 -50 to +50 -75 to +75
Y [mm] -25 to +25 -50 to +50 -75 to +75
Z [mm] 25 + 25 0 + 60 0 + 60 holder + stage*
R 360° 360° 360° continuous
T -15° to +75° -5° to +70° -5° to +70°
*)
Eucentric Position WD = 10 11.6 29.2 *) *)
distance between a sample
[mm] top surface and the stage base
Clamp No Yes Yes
Maximum sample 250 2 000 5 000 for all tilt angles
weight [g]

Note: 
* holder Z movement means possibility to manually screw the sample
holder in or out, stage movement means motorised stage movement.

Caution! 
The positive Z value direction depends on the Link Z to FWD status 
(see Chapter 5).

Caution! 
If the maximum sample size is near to the limit, stage tilt could be
limited. Beware of hitting the objective pole piece!

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3 SOFTWARE CONTROL

This chapter describes the functionality of each part of the user interface.

SOFTWARE INTERFACE
The software control contains graphic applications within Windows 7™
operating environment. xT microscope Server starts and stops the
basic microscope functions.
It makes possible to open and close the xT microscope Control
software (UI – user interface or sometimes xTUI in the dialogue boxes)
which controls system functions including imaging, image and movie
gathering / manipulation / output, detection and analysis, scanning,
magnification, stage navigation, chamber and column pressure, etc.
All user account levels are created via FEI User Management software,
ensuring for the particular users admission to both the operating system
Windows 7™ and the xT microscope Control software.

OTHER SOFTWARE AND HARDWARE

Call Customer Service for advice before installing software or hardware
that is not required for system operation. Other software, such as screen
savers or hardware network cards, may corrupt the xT microscope
Server / Control software under some circumstances and may invalidate
warranty.
For more detailed information about Windows 7™, refer to the
Microsoft® Windows™ User’s Guide shipped with your system.

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Software Control: Software Interface Elements

Software Interface Elements

ICONS
Icons are small symbols indicating a specific software application.
Double-click the icon to activate the program.
There are also functional icons in the toolbar for selecting some
software functions quickly. Clicking any causes it to be highlighted and
activated, clicking it again or clicking another one (depending on a
particular case) causes it to become normal and deactivated.
Some functional icons have additional down-arrow next to the right side.
Clicking the arrow displays a pull-down menu with choices, while clicking
the icon performs a particular function (cyclic changeover of choices,
setting the default parameters etc.).
There are also some informational icons in the status field, for
instance, that indicate some particular system status.

TOOL-TIPS
This functionality activates when the cursor is left over a user interface
item for more than two seconds. A short explanation of the item appears
until the cursor is moved away from the item.

PULL-DOWN MENUS
The microscope uses menu-oriented software; you perform functions by
choosing items from the Menu bar. The Menu bar selections contain
pull-down menus that display grouped listings of available commands or
settings. Some menu items are shown in gray and cannot be selected
because of the system immediate condition.
Pull-down menu selections followed by the ellipsis (…) indicate, that a
dialogue box will display (the same behaviour occurs when the selection
is a command). Selections with a right arrow indicate that an additional
submenu of choices will display. If a selection is a parameter value, the
new value is updated immediately and a check mark appears in the pull-
down menu.

Using the Mouse

The click / right-click / wheel-click represents click with the left / right /
wheel mouse button on the item throughout this manual. The click & drag
/ right-click & drag / wheel-click & drag means holding the mouse button
during the action.
Click & drag the cursor down the menu to a desired item and then
release the mouse button.

Using the Keyboard

Press ALT + the underlined letter (for example, ALT + F for the File menu),
and then select from the choices by clicking it or by hitting the Enter button
after its location with the up / down (left / right for submenus) arrow keys.
Some often-used commands can be quickly activated with the use of
shortcut keys (a combination of simultaneously pressed keys) at any time.
This possibility is given by a particular button combination on the right
side of the pull-down menu adjacent to the appropriate command.

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 Software Control: Software Interface Elements

COMMAND BUTTONS
carry out or cancel functions. They activate when clicked and some are
highlighted (changed color) to show the corresponding function activity.
Command buttons have labels that describe the actions performed by
clicking them. The most common ones, which are typically used in
dialogues are:
• The OK button applies all changes made in the dialogue and closes it.
• The Finish button saves new settings, ends the procedure and closes
the dialogue.
• The Save button saves new settings at that point without closing the
dialogue.
• The Apply button saves and applies new settings at that point without
closing the dialogue.
• The Cancel button discards all changes (made from the last save) and
closes the dialogue. It has the same effect as closing the dialogue with
the cross (Alt + F4).
• The Next button moves a user to the following dialogue after
necessary settings have been done.
• The Previous button moves a user to the previous page when
settings need to be changed.

LIST BOXES
contain available choices, such as screen resolution, magnification
settings, etc. Click the List box to roll down a list of available values, then
click the desired one. The drop down list automatically closes and
displays the new value as the actual one. The change of the setting is
immediate.

PROPERTY EDITORS
group list of related parameters and their values. The editable
parameters have a white background, the fixed parameters are shaded.
A user should click in the Value side of the relevant property Name and
then select its value from the drop down list or enter it using a keyboard.

EDIT BOXES
let you input text information (such as passwords, labels or precise
numbers) using the keyboard. Some edit boxes, which are not part of a
dialogue, require to confirm the input by pressing Enter. If you press Esc
before leaving the edit box, its previous value is restored.

RADIO BUTTONS / CHECK BOXES

Within a group of related round Radio buttons, only one selection can
be made active at any time by clicking in the individual box.
A single one or a group of square Check boxes can be ticked / cleared
by clicking inside the individual one.

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Software Control: Software Interface Elements

ADJUSTERS
allow to change parameters, such as contrast, brightness, gamma etc. in
a continuous way by clicking & dragging the middle adjuster or clicking in
the grey bar. They always have a label in the upper left and right corners
for readout information. Double-click the value in the upper right corner
enables to enter a precise value (and the unit in particular cases) using
the keyboard.

Exponential Adjuster
This is an exponential response adjuster – the further from the center is
the large adjuster button pulled, the larger is the relative change. The
adjuster button always snaps back to the center of the slider.
The middle adjuster button is for coarse adjustments, while the end
arrows are for fine adjustments (single step increments).

Linear Adjuster
Some adjusters have linear response (like the small adjuster placed
below the exponential one). Its button position always corresponds to the
actual parameter value within an available range.

Preset Adjuster
This kind of adjuster is used for values that have both a continuous
range, a list of presets and direct value editing to achieve total control.
The button on the left side of the adjuster toggles between modes:
• Drop down list: 
clicking the -/+ buttons on the right of the drop down menu steps
through the pre-set values Up / Down in the list, but only shows one
value in the text area. Clicking the down-arrow rolls down the whole
list of values. If the list extends further than is visible, a scroll bar
appears. Clicking a value in the list enters it as an actual value in the
text area displayed at the top. 
Double-clicking a value in the text area enables to edit it.
• Adjuster mechanism: 
The adjuster has a fine control (see above).

Spinners
allow to change a parameter in an incremental way from a list of pre-
defined values by clicking on an arrow.

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 Software Control: Software Interface Elements

2D CONTROLS
are represented by an X-Y box. The position of the crosshair
corresponds to the actual parameter value with respect to its full range
being represented by the perimeter of the box.
Clicking & dragging anywhere inside the box changes the active quad
cursor to the four-ended arrow and positions it to the screen point
corresponding to the actual control value (minimum in the middle of the
screen and maximum at the edges). It can be dragged in four directions.
Clicking & dragging directly on the X / Y axis changes the active quad
cursor to the two-ended arrow, which can be dragged in the
corresponding direction only. To fix the values, release the mouse button.
The right-clicking over the 2D box opens a dialogue with choices:
• The Coarse / Fine sets the mouse sensitivity – long / short mouse
path necessary for the full range.
• The Adaptive Sensitivity adjusts the mouse control response to be
the same at any magnification.
• The Zero brings the control value to zero and the cursor to the center
of the box.
• The Back brings the control value one step back (only one step is
remembered).
• The Clear Memory clears condition values, which have been
remembered automatically during the considered 2D control use.
These remembered values are used to estimate new values, which
have not been remembered yet.
The menu may contain less or some other functions that are actually
available for the particular parameter. Selecting the corresponding menu
item activates the function.

MODULES
visually combine various software elements, which are related into a
labelled group. Complex software elements like UI pages or dialogues
are typically composed of modules.

DIALOGUES
appear when the system needs more information from you before it can
carry out a command, or want to give you some important actual
information. Some dialogues do not let you access other functions until
you close them, other ones let you perform other tasks while they remain
onscreen and active (for example, the Preferences dialogue can remain
opened while performing other tasks).

TABS
In modules or dialogues containing more interface elements than would
fit into the limited area the Tabs are used. These related elements are
split into the groups (sections) and each one is supplemented with the
labelled Tab. Clicking the Tab brings it to the foreground displaying the
corresponding group of interface elements.

PROGRESS BARS
indicate progress of a long ongoing procedure over time. It is often
displayed in a dedicated dialogue.

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Software Control: xT microscope Server Software

xT microscope Server Software

The xT microscope Server application starts and stops the software

service controlling basic microscope functions and also the user
interface (UI) software xT microscope Control.
Run the xT microscope Server (from the Windows Start
menu or double-click the icon) – the application window
appears. The title bar right-clicking opens a dialogue that
offers the option to minimize the server to the UI top bar.

FIGURE 3-1 xT MICROSCOPE SERVER WINDOW

• The Server State / UI State modules display the RUNNING or

STOPPED state of the xT microscope Server / xT microscope Control
software services. During a transition between these states
STARTING or STOPPING is displayed.
• Some Microscope module buttons change its label and behaviour
depending on the actual state.
The Start / Stop buttons start / stops xT microscope Server services.
If the xT microscope Control (UI) is running, Stop button closes it at
first. The microscope console must be ON (green power button is lit)
before the Start button is enabled!

Caution!
Do not stop the xT Microscope Server services when the system is
under vacuum – always vent the microscope before stopping the xT
Microscope Server!
The Start UI / Stop UI button opens / closes xT microscope Control
software.
The Show UI / Hide UI button calls / hides the UI main window.
The Advanced button displays the Administration module
containing information helpful when calling the service (specifying the
software operation / hardware function state).
– The Autorun UI check box: when ticked (default), the Start button
automatically starts xT microscope Control after starting the Server.

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 Software Control: xT microscope Control Software

xT microscope Control Software

xT microscope Control software – simply User Interface (UI) – is made

up of several elements which compose the main window, displaying
status and control features within the Windows 7 operating system.
Note: 
To ensure correct displaying of all UI entries (dialog and edit boxes, info
fields etc.) within the Windows 7 environment choose the FEI 01 theme
display appearance.
Note: 
Today the UI supports wide screen display which leads to a slightly
different appearance of some UI elements in comparison to this manual.

FIGURE 3-2 THE MAIN WINDOW

1
2
3 5

4 - Quad 1 4 - Quad 2

4 - Quad 3 4 - Quad 4

1. The Title Bar – labels the application

2. The Menu Bar – contains all operation menus and submenus
3. The Toolbar – contains functional icons for the most frequently used
microscope controls and for the fast access to the Pages
4. Image Windows – image windows with adjustable Databar
5. Pages and Modules – microscope and image control elements
organized into modules making up the pages
6. The Preferences dialogue – presetting of operating conditions

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Software Control: xT microscope Control Software

TITLE BAR
displays the application icon and name plus the standard Windows
buttons: Minimize and Close, which are enabled.

FIGURE 3-3 THE TITLE BAR

The Close button quits the xT microscope Control software (accelerating

and detectors voltages are switched off for the security reasons).

MENU BAR
displays pull-down menus across the screen below the Title Bar.

FIGURE 3-4 THE MENU BAR

Select pull-down menus from the menu bar by:

• clicking on the Menu title
• ALT + underscored keyboard letters
• ALT + keyboard arrows + Enter button
Note: 
Some menu functions have their equivalents in the toolbar. In such
cases, the corresponding toolbar icon is shown next to the function title
in the following text.

File Menu (Alt + F)

opens File menu administrative functions:
Open…
displays a standard dialogue for opening images previously stored to a
media. Supported file formats are TIF8/16/24, JPG and BMP (see
Chapter 5). The dialogue displays, by default, the location (path) last
used to open or save files from the UI.
Save (Ctrl + S)
saves the image using the format, location and base of name set by the
last used Save As function in that quad. An incremental suffix with a
selectable number of digits ensures that every image is saved as a new
file, e.g. Name_001.tif, Name_002.tif, etc.
Save As…
opens a dialogue for saving images, which provides an opportunity to
change the file name and location. An image can be saved in TIF8/16/
24, JPG or BMP file format.
The dialogue displays, by default, the location and the name last used to
save / open a file in the selected quad. A user can change a location,
name base or suffix, select different image format (Save as type), and
also choose whether to Save the image with / without Databar and with
/ without overlaid graphics by ticking / clearing an appropriate check
box. The settings is remembered per quad and used for the subsequent
Save actions.

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FIGURE 3-5 SAVE AS… DIALOGUE

Save All… (Ctrl + Shift + S)

opens common dialogue for saving images from each quad, providing an
opportunity to change the file names and locations.

FIGURE 3-6 SAVE ALL… DIALOGUE

Image Properties (Shift + F1)

allows a user to view multiple parameters at which an image was
captured.
Record Movie
allows a user to make digital video files (AVI) for dynamic experiments.
The tick next to this menu item and the change of the corresponding
toolbar icon indicates the movie recording (see Chapter 5).
Import / Export
opens a sub-menu with selection of importable / exportable items
Selecting an item opens standard Open / Save As dialog for choosing
location and file name. Following items can be both imported (i.e. loaded
and used) / exported:

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Software Control: xT microscope Control Software

• The Stage Positions… stored also with the use of the Stage module 
(.stg files)
• The Patterns used in the patterning module (option) (.ptf files)
• The Scanning Presets… parameters (.scp files)
• The Quad Presets… parameters (.qps file: Beam type / Detector type
/ Detector Mode / Detector contrast & brightness / Digital Contrast /
Digital Brightness)
• The System Parameters… saves wide range of actual microscope
settings, including above mentioned ones (.par files). When importing
them back likewise only selected ones are loaded.
Print (Ctrl + P)
opens the print dialogue enabling a choice of printer and settings suitable
to print an image.
Log Off User
logs off a present User and provides the Log On dialogue for the next
microscope user. When a user logs off the system goes to a safe state:
the accelerating and detector voltages are switched off automatically.

Caution! 
Logging off an actual user does not close all microscope operations! 
(see Chapter 2)
Exit
closes the xT microscope Control software (the actual user is
automatically logged off first) and leaves a user in the operating system
environment. xT microscope Server is still running and controls the
microscope in operation.

The Edit Menu (Alt + E)

opens some helpful functions:
Copy (Ctrl + Ins) / Cut (Ctrl + x) / Paste (Ctrl + v) / Delete (Del)
These functions represent commonly used operating system functionality.
Select All (Ctrl + A)
selects all items within a selected quad.

The Detectors Menu (Alt + D)

opens the selection of all installed Detectors (see Chapters 5 and 7).
Detector list
contains various detectors for the microscope operation. Detectors not
mounted or not serviceable under an actual microscope conditions are
disabled (greyed out). The selected detector for the selected quad shows
a tick next to its label.
• An 3rd party video signal can be selected, which is indicated as
“External” in the databar. Contact a FEI service person about a
connection details.
• The CCD camera reflects the inner space of the specimen chamber.
• The Mix sets a possibility to interfuse signals from 2 or 3 detectors.

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The Scan Menu (Alt + S)

opens the scanning control functions:
Pause (F6)
pauses the imaging. This function is used automatically 
with Snapshot and Photo functions.
Select the Scan menu / Pause or press the F6 button or click / double-
click the toolbar pause icon to stop scanning at the end of the actual
frame / immediately.
When the quad is going to be paused at the end of the frame 
the toolbar pause icon is pressed-in and has an orange 
background. When the quad is paused the icon remains 
pressed-in and its background colour reverts to normal and 
a large pause icon appears in the corresponding quad.
Select Scan menu \ Pause item or press F6 button or click the toolbar or
quad pause icon to release the pause function (the icon button pops out)
and to return the scanning to the previous state.
Shift + clicking the toolbar pause icon pauses / activates all quads with
an electron imaging at once.
Snapshot (F4) / Photo (F2)
activates a preset scan (see the Preferences… / Scanning tab) 
to acquire an image. The icon could be selected by clicking the small
black arrow next to the toolbar icon.
Active Preset Snapshot (Ctrl + F2)
If any of six presets is activated by clicking the numbered button
(becomes yellow), image acquiring starts with corresponding
parameters. Use the toolbar expand / hide arrow to change preset
parameters. These presets could be Exported / Imported with the use of
appropriate buttons / menu items. The functionality is available only if
activated in the Preferences… / General tab / ).
Note: 
Shift + clicking the Photo icon / active Preset Snapshot button or when
pressing Shift + F2 / Ctrl + Shift + F2 key takes Photo / active Preset
Snapshot from all quads at once. In this case when in addition a large
screen resolution is selected (4096 x 3536) and the Drift Correction
functionality (see Preferences… / General tab) is used an imaging is
delayed, but the result will be correct.
Videoscope (F3)
This function shows the video intensity along the currently scanned
horizontal line for correcting contrast and brightness.
Reduced area (F7)
This mode is useful when focusing and correcting an astigmatism as the
scan speed is faster in the smaller area. When Reduced area is chosen,
the small green frame appears at the last used place onscreen, which
could be adjusted by clicking & dragging. It is also possible to adjust
scan parameters independently on the full-frame setting.
• Moving: Place the mouse cursor over the selected area. The arrow
changes to a 4-ended arrow. Click & drag the selected area to the
desired position and release the mouse button.
• Changing the size: Place the mouse cursor over the edge of the
selected area. The cursor changes to a 2-ended arrow, either
horizontal or vertical. A corner can also be used to move two sides.
Click & drag the side out or in to obtain the desired size and release
the mouse button.

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When the Reduced area frame is being manipulated, it turns yellow until
released, then it reverts to green.
Full Frame (Ctrl + M)
is the default scanning mode, typical for navigation and imaging.
Spot (Ctrl + K)
When starting this mode, the beam is blanked and the scanning is
switched off. Actual beam position is represented by a green cross in all
electron quads. You can click & drag it or click anywhere around the
screen to change its position.
Line
In this mode, the green horizontal line is displayed in all quads. The
beam scans along this line. You can click & drag it or click anywhere
around the screen to change its position.
External
switches to activate an external control of the scanning system, such as
EDX system beam control. The external scanning mode is indicated by
the External label displayed in the upper right corner of all imaging
quads.
Beam Blank (Ctrl + B)
deflects the beam off axis high in the column and protects the specimen
from unnecessary exposure. When the beam is blanked the toolbar icon
is highlighted. Clicking it releases the blanker and returns the beam to
scan the specimen.
Slow / Fast Scan (Ctrl + Shift + , / .)
brings the scanning condition to the preset 
Slow (left icon) / Fast (right icon) scan value (see the Preferences… /
Scanning tab). When either of the two presets is selected the respective
icon is highlighted.
Slower / Faster Scan (Ctrl + , / .)
sets the scanning condition to the next preset Slower (left arrow) / Faster
(right arrow) value (see the Preferences… / Scanning tab). The spinner
box shows the actual dwell time, but does not enable to change or select
directly its value - the values are changed one step up or down.
Mains Lock
When ticked, the scanning (line or frame sawtooth signal) is
synchronized with the mains AC oscillation. This greatly diminishes
blurring and jittering of the electron imaging resulting in smooth image
edges at higher magnifications and slow scan conditions.
Line Integration
With this function each line scan is repeated several times (from 2 to
255) before proceeding to the next line. Signal data collected from these
passes are integrated and displayed as an actual image line.
This imaging method reduces sample charging (in comparison with
single pass with longer dwell time) and improves overall image quality.
Scan Interlacing
This function splits an imaging area into blocks defined by the number of
lines (from 2 to 8). In the first instance the first line of each block is
scanned, then the second one etc. This imaging method significantly
reduces sample charging.

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Note: 
When any of the two above mentioned functions is 
active, it is represented in the toolbar scan speed 
spinner with the letters LI / SI. 
Only one of them can be active at a time.
Live
is the default mode, leaving the imaging unfiltered for
collecting raw direct images - one frame follows another.
Average
continuously averages a specified number (2 or more) 
of frames, resulting in a better signal-to-noise ratio. This process
continues until stopped by changing the scanning condition or by
pausing the quad.
This is used mostly for fast scanning to reduce imaging noise. During
averaging, the image is updated continuously and actions such as
focusing, moving the stage, etc. can still be performed.
Note: 
The Average is set independently also for the optical window (option),
but using averaging with more than 4 frames is not recommended,
especially when moving the stage.
Integrate
allows accumulative noise reduction by true integration over a specified
number (1 or more) of frames. This process continues until the selected
number of frames is reached and then pauses the quad automatically.
During and after image accumulation, you cannot change the focus or
perform other actions influencing the imaging.
This can be used as an alternative to slow scanning to obtain high quality
images of slightly charging specimens.
Note: 
Clicking the down-arrow next to the toolbar icon displays menu items
Live / Average (# frames) / Integrate (# frames) / Number of Frames
enabling to select number of averaged or integrated images (depending
on the actually active Filter Mode indicated by the icon for the selected
quad). Clicking the toolbar icon itself changes the Live / Average /
Integrate mode in cycle.
The Number of Frames is set and remembered independently for the
Average and Integrate filters. Both the Filter mode and Number of
Frames is set and remembered per quad, so live and filtered imaging
can run at the same time. Settings are particular for the Reduced Area
and for the Full Frame also. The Photo function uses the Filter Mode and
Number of Frames pre-set (see the Preferences… / Scanning tab).
As the scanning could take a significantly long time period, one can
restart it from the beginning with the use of Ctrl + R keys (Restart Scan).
Scan Rotation (Shift + F12)
activates the on-screen tool to rotate the scan field. It has no effect on
the stage movements and is solely a scan coil function used to orient the
imaging relative to a specimen feature and/or detector direction.
A non-zero scan rotation is indicated by an icon in the Status module,
and its value can be also displayed in optical quads (see Chapter 5).

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The Beam Menu (Alt + B)

opens the Beam menu functions:
Electron Beam / CCD Camera
makes the quad or single screen active to the Electron Beam / CCD
Camera (the displayed icon sequence) with respect to the source,
column, scanning, and detector settings. Only one is active at any time,
but can be operated independently for each quad.
Another possibility to change the beam for the particular quad is right or
left clicking the toolbar or image databar beam icon.

The Stage Menu (Alt + S)

opens the stage and sample navigation functions:
xT Align Feature
opens the procedure that helps to navigate along a feature that extends
off the screen at the desired magnification. The procedure uses the
stage rotation (see Chapter 5).
Scan Rotation Align Feature…
opens the procedure that helps to navigate along two sample points. The
procedure uses the scan rotation (see Chapter 5).
Compucentric Rotation (F12)
places a green circle in the selected quad. By rotating the circle a
different viewing orientation of the sample area can be achieved by a
physical stage rotation and adjustment of X and Y axes. Stage rotation
keeps the observed feature in the center of the field of view. If this does
not occur, the alignment should be performed to locate the stage center
and calibrate the stage (see Chapter 4).
Define User Units…
activates a procedure guiding a user to determine User Units for X and Y
stage axes. These are used for relative stage movements associated
with the regular features mapping (in particular integrated circuit
applications) (see Chapter 5).
User Units
organises the stage software to recognise the defined user units rather
than the default metric measurements. The X and Y coordinates now
operate in User Units which are indicated in the Stage module /
Coordinates tab by the UU symbol (see Chapter 5).
Clamp
toggles on / off a mechanical stage clamp in order to prevent stage
vibrations during high resolution imaging and at high magnifications. This
menu item is greyed out on systems without a securing Clamp.
While the stage is clamped, any Z and Tilt movement requirement
automatically releases it from that point on.
This feature is dedicated to all stages except the 50 mm stage which has
no Clamp, but has a Tilt lock instead.
Beam Shift Reset
zeroes the beam shift. A feature observed with a non-zero Beam Shift is
automatically moved back to the imaging center using the stage.

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Zero Beam Shift

zeroes the beam shift without moving the stage. A feature observed
before selecting this function is moved from its position by the measure
of the applied beam shift.
Auto Beam Shift Zero
automatically resets the beam shift each time it reaches the maximal
value during the Get function (the point-to-point stage movement) and
corrects the imaging position with a stage movement.
Home Stage (Shift + F3)
starts procedure which moves all motorized axes to their hardware limits
and ensures that the physical stage position agrees with the coordinates
readout. During the home stage procedure the xTm: Stage Information
dialogue displays its progress. The stage axes are moved to their end-
switches in the following order:
1. Z (lowest position), 2. T (tilt), 3. X, Y and R (rotation) at the same time.
When the stage is homed correctly it ends up in the following position:
X / Y = 0 / 0
R = 0° 
T = 0° 
Z = preset position, depends on the stage type

Caution! 
Do not run the Home Stage procedure, when a large sample is
inserted (6” wafer for instance) because of possible collision.
Home Stage Without Rotation
executes Home Stage function (see above) without rotation. When the
stage is homed without rotation the stage Rotation reference is greyed
out. This is useful when a large specimen is inserted and stage rotation
could cause a collision with equipment inside the chamber.
By default the function is enabled and automatically reverts back to the
enabled status after every venting / pumping cycle.
Center Position (Ctrl + 0 - digit)
moves the stage to coordinates X = 0, Y = 0.
Touch Alarm Enabled
activates the Touch Alarm for the stage. This function automatically stops
the stage movement and displays Touch Alarm warning dialogue
whenever the stage or a conductive specimen touches the objective lens
or any other equipment conductively connected to the chamber. This
functionality is used also when the stage engines start to rise the power
over the determined level.
Unlink Z to FWD
This feature functions in an opposite way as the following one. 
The Z coordinate value represents then the distance from the Z-axis
home position (stage base). The dialogue warns you about the stage 
Z-axis positive move direction.

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Link Z to FWD (Shift + F9)

sets the Z coordinate value to the actual Free Working Distance (FWD)
value. This allows accurate movement between the sample top surface
and the end of the objective lens. The related toolbar icon changes
according to the Z-coordinate status:
• Greyed icon: the function is disabled – the high voltage is switched off
(so there could be no electron imaging) or all quads are paused.
• Red question mark: the function is enabled – Z is not linked to FWD.
Use this function as soon as possible, after a proper focus.
• Red circle: the function is enabled – Z is roughly linked to FWD, but it
needs correction. It happens e.g. after: changing the specimen, focusing
and linking Z to FWD at a long WD and then moving the stage to a short
WD. Focus carefully at a WD around 10 mm and use this function again.
• Green double-ended arrow: the function is enabled – Z is properly
linked to FWD. Now it should be safe to change the working distance
by setting a Z coordinate in the Stage module.
Enable Z-Tilt map
Some movements of the tilted stage are not safe because of a possible
collision with the final lens. The table (not user editable) with a pairs of
values indicates the maximum safe Tilt angle for a certain Z value when
coupled. It can be used to guarantee safe usage of the stage (tilt
restriction) for a flat samples only and when a proper Link Z to FWD is
established.
Note:
This functionality is not available for the Quanta 250 model.
Enable Safe Stage Moves
When ticked the software takes into account all accessories installed
inside the chamber. That’s why the stage doesn’t move to the target
position following the straight path. When the magnification is large and
stage movements are expected to be tiny, it is not necessary to switch on
this functionality.
Tilt 0° (Ctrl + E)
tilts the stage to 0°.
Sample Navigation (Ctrl + N)
toggles on / off function that enables to navigate electron imaging (scan
field) towards desired places on a specimen using either paused or
loaded sample image (usually captured at much lower magnification).
The Sample Navigation can be selected independently for any quad,
regardless of its actual content and status. A tick next to the menu item
indicates that the function is selected for the active quad. As soon as this
quad is paused, the Sample Navigation indicator appears in the upper
right corner of the quad.
Navigation Montage...
This procedure enables to capture the sample Navigation image to be
used in the Sample Navigation (see Chapter 5).
Navigation Alignment...
This procedure aligns the Navigation image according to the live
reference image (see Chapter 5).

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The Tools Menu (Alt + T)

opens the Tools menu functions:
Auto Contrast Brightness (ACB) (F9)
activates the automatic contrast and brightness routine. 
The system attempts to set the Contrast and Brightness of the selected
detector in the selected quad to suit the actual sample and conditions so
that the majority of grey levels is displayed.
User Auto Contrast Brightness
examines grey levels of the selected quad imaging and stores their
minimum and maximum. Next time the ACB function is used, it attempts to
set the Contrast and Brightness so that the resulting imaging grey levels
lies between this minimum and maximum instead of full black and white.
A tick next to this menu item indicates the user grey level limits active.
Clearing the tick reverts the ACB to its default setting.
Auto Focus (F11)
activates the automatic focus routine. The system attempts to correct the
focus independently of the working distance or Z-coordinate set.
Auto Stigmator (Ctrl + F11)
activates the automatic procedure to correct an astigmatism.
Note: 
When ACB / Auto Focus is activated the dialogue appears to show the
progress. The function can be interrupted by clicking the Stop Now
button, which leaves the imaging / the focus (WD) at the actual stage of
progress. Clicking the Cancel button before the function ends returns the
imaging back to its original status / the original WD value.
Set Default Parameters (Ctrl + F11)
loads default settings for the actual Vacuum Mode. The function switches
UI to Quad image mode and selects the default detector for display 1 and
the CCD camera for display 4. The microscope and image parameters
are selected so that there is a big chance to get an usable image
immediately.
Set HFW… (Ctrl + H)
enables to set the desired Horizontal Field Width, i.e. the width of the
scanned area. This is an alternative to the setting of magnification.
Display Saturation (Shift + F11)
displays signal clipping in the selected quad by means of replacing the full
black / white with dark blue / yellow color. The function can be used for
electron imaging, but cannot be applied to the optical imaging.
The saturation display is selected independently for each quad. A tick
next to the menu item indicates whether the function is active for the
selected quad.
Image Post Processing (Ctrl + F7) / 
Undo Image Post Processing (Ctrl + Shift + F7)
Starting this function corrects image properties according to the Image
Enhancement module / Process tab setting (see below).
Lab Notes…
opens the Windows Notepad application over the UI for a user to make
immediate notes and remarks. The Lab Notes can be used to open, edit
and save any text file without the necessity to hide the xT UI.

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FEI Movie Creator…

provides a dialogue over the UI for setting up a collection of sequenced
TIF images, and lining them up into an AVI movie (see Chapter 5).
Application status…
The dialogue is displayed over Quad 4 showing continuously updated
system Messages. The System status tab offers informations about the
system hardware, which are used for service engineers.
• Pop-up on Message Severity: None / Error / Warning / All 
specifies which kind of messages is going to be shown automatically
on screen. Three icons in the lower right corner enable to separately
switch on / off displaying of Error / Warning / Information messages.
• Clear button clears all actual messages from the window.
• Hide button hides Application Status window.

FIGURE 3-7 APPLICATION STATUS

The Window Menu (Alt + W)

opens the Window menu functions:
Center Cross (Shift + F5)
places a cross in the center of all imaging quads. This function is
automatically used in Alignment procedures to aid the centring of
features and can be used to align a sample against a stored image in
another quad.
Alignment rectangle (Shift + F6)
places a dashed rectangle in the center of all electron image quads. This
function is used for some Alignment procedures automatically.
CCD 10 mm Marker
places a short horizontal line with 10 mm label in all optical quads to help
user with a sample positioning to a correct working distance and with the
first focusing. Only Supervisor is allowed to change the marker position
by double-clicking a new position and by confirming this action in the
popped up dialogue.
CCD Axis Marker
places axes indicator in all optical quads to help user with 3D orientation.
Crosshair Cursor
shows the cursor as a rectangular cross through the entire quad.

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Undo / Redo Digital Zoom #x

When using the digital zoom (see below), it is possible to undo / redo the
last magnification / reduction step.
Large Image Window (Ctrl + F5)
This function activates / deactivates the full screen quad imaging on the
secondary monitor.

FIGURE 3-8 LARGE IMAGE WINDOW

Large Image Window Configuration

Here one can select, whether to show an Active quad, or any selected
one. Activating the Use Single Image Size option sets the imaging
window size corresponding to Single Image mode size. These options
are also available in the bottom right corner of the large image window.
Remote Display Mode
When using the Remote Imaging (option) this feature enables correct UI
imaging at the remote site. It is also used for a remote service.
Use of this function decelerates slightly a UI performance and it is
displayed in the bottom left quad corner.
Single / Quad Image Mode (F5)
toggles the image display area between two possibilities:
• Single Image Mode displays one quad over the whole UI imaging
area – useful for observing details.
• Quad Image mode is useful for comparing imaging of the same
sample area taken with different detectors or scan properties.

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The Help Menu (Alt + H)

opens the Help menu and system information functions:
Documentation… (F1)
The Help window shows complete User Manual in PDF format using an
embedded Acrobat Reader with its useful navigation, search and
selection tools. The window remembers its position and size for the next
showing up.
Clicking the Question mark at the right side of the module header (see
Preferences… dialogue / General tab / Show context help per
module item) opens the relevant part of the User Operational Manual.

FIGURE 3-9 ONLINE DOCUMENTATION

Keyboard Shortcuts…
The shortcuts list in tables is displayed in the same way as the on-line
documentation (see above) and with the same behaviour.
Phase Diagram…
Opens the PDF file with the Water phase diagram and the ESEM
vapour pressure table for a quick reference.
About xTUI…
displays a window containing information about the product version. The
window automatically disappears after the first click.

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TOOLBAR
displayed below the Menu bar is made up of functional icons linked to the
most frequently used system controls. It also contains group of icons for
quick switching between UI Pages. The toolbar can be a bit different in
content or style (see the Preferences… / General tab).

Rest the cursor over the icon for two seconds without clicking it to its
explanatory tool-tip.
Whenever a function is selected the corresponding icon is highlighted
(blue frame) to indicate the function is active (except of auto-functions,
which display a progress bar).
Note: 
If any icon represents a menu function, refer to the corresponding menu
for its description.

Magnification (HFW) / High Voltage / 

Spot Size (Beam current) List Boxes
Click on the list box to expand a list of pre-set and actually allowed
values. Choose one by clicking on it and it is applied immediately (see
the Preferences… / Presets tab).
• The Magnification is possible to display as the Horizontal Field
Width (HFW) alternatively (see the Preferences… / General tab /
Image dimension control item).
The Spot size is defined as the actual electron beam diameter on the
specimen surface and it is expressed by a relative number (see
Chapter 5). The optional way to the Spot size number is the electron
Beam Current value (see the Preferences… / General tab / Spot
size / Beam current control item). Both physical quantities are
related. The electron beam current value is approximate and valid
only if the microscope is well aligned.


Degauss (F8)
starts the procedure which puts all actually used electron lenses to a
normalized state by removing their hysteresis effects. For a few seconds
while the procedure is running all live imaging disappear or turn fuzzy,
and then return back.
Use this function with (almost) focused imaging to obtain the most
accurate Magnification, Horizontal Field Width (HFW) and Working
Distance (WD) readouts.

Imaging Pixel Resolution List Box

This list contains available imaging pixel resolutions (also effective for
captured images). Selecting a new resolution results in an immediate
change of the scanning raster and since the present dwell time remains
unchanged, the actual scanning frequency (both Line and Frame time)
changes.

Direct Measurement
This button enables to quickly access the measurement tool without
necessity to change a page. Clicking the icon deactivates (grey color) /
activates (yellow color) the functionality (see Chapter 5).

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IMAGE WINDOWS
The xT microscope Control software (UI) uses 4 independent image
windows – quads for imaging samples. Each quad can contain imaging
from any detector (including External and CCD), paused imaging or
images loaded from a file. Additionally, quad 3 can display a mix of
imaging from quads 1 and 2, and quad 4 can display a mix of imaging
from quad 1, 2 and 3.
It can be displayed either 4 quads at the same time – Quad Image mode
or one quad over the UI imaging area – Single Image mode.
Each quad consists of its imaging area, adjustable Databar containing the
imaging parameters, selectable overlay (user-defined coloring, annotations,
measurement) and some status symbols (Pause, Sample Navigation, etc.).
At any time, just one quad is selected (has focus), and all functions
(related to a single quad – Pause, Sample Navigation, image
processing) applies only to imaging in this quad. The selected quad is
marked by the highlighted (blue) Databar and optionally also by the blue
frame (see Preferences… / General).
Depending on the quad content and the status, some mouse functions
are available over its area:
• Electron imaging (incl. External and Mix): focus, astigmatism
correction, Beam Shift, magnification change (coarse, fine), zoom (in
/ out), Contrast & Brightness, lens alignment, Scan / Compucentric
Rotation, XY-move (get or track mode)
• Optical imaging: 10 mm Marker placement, Compucentric Rotation,
Z-move (track), Tilt
Note: 
Due to a hardware limitations, some detectors cannot be used
simultaneously. They can still be selected for different quads at the same
time, but if one of them is started, the other quads with incompatible
detectors are automatically paused. 
The optical imaging is automatically activated (if it is paused), when the
venting procedure starts. 
When it is paused and any stage movement takes place, the pause icon
turns red and a list of changed axes is displayed.
The Databar
displays optional instrument, imaging and labelling information. They can
be placed in any order and expand or contract to fit the quad width as
long as there is enough room (see the Preferences… / Databar tab).
Clicking some of the image databar fields induces an active menu
related to it with appropriate choices. Clicking the label field induces the
label editing menu and double-clicking the micron bar induces the image
properties window (see above).

FIGURE 3-10 DATA BAR EXAMPLES

Active electron quad

Inactive electron quad

Active optical quad

Note: 
The Databar information are always related to the actual imaging. If the
imaging is paused or an image is loaded from a file, they could differ from
the actual system conditions.

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PAGES AND MODULES

The software controls on the right side of the screen are organized into
Pages, which are divided into Modules holding specific functions. The
required page can be selected either by clicking the corresponding icon
button or with the use of short-cuts (see below).

TABLE 3-1 PAGES AND MODULES LIST

Pages Modules (Tabs)

Beam Control 1. Vacuum, 2. Column, 3. Magnification, 4. Beam, 
5. Tuning, 6. Detectors, 7. Status

Navigation 8. Stage (Map / Coordinates / Tilt / Navigation) 

9. Stage Z, 10. Scan Rotation, 6. Detectors, 7. Status

Processing 11. Measurement / Annotation, 12. Digital Zoom, 

13. Enhanced Image (LUT / Mix 3 / Mix 4 / Color / Process), 
6. Detectors, 7. Status (reduced)

Beam Deceleration 2. Column, 4. Beam, 5. Tuning, 14. Beam Deceleration 

(option see Chapter 7), 6. Detectors, 7. Status

Detectors 15. Detector Settings, 16. Quad Presets, 

14. Beam Deceleration, 6. Detectors, 7. Status

Alignments 17. Alignments (Instructions / Individual steps), 8. Status

Note: 
The number in front of the module name represents an order in which the
modules are introduced in the following text. 
For Software Interface Elements control see above.

1. The Vacuum module

is used to control the pressure and the gas type in the specimen
chamber. The Pump button starts pumping the specimen chamber and
the column down. The system allows the accelerating voltage to be
switched on only when the column is sufficiently evacuated. The Vent
button starts venting for a sample or detector exchange after the user
confirmation (see Chapters 2 and 5). The Mode radio buttons bring the
system to:
• the High Vacuum mode, which is the conventional operating mode
(associated with all scanning electron microscopes), used for
observing conductive specimens which can withstand low pressure
conditions and does not outgas.
In this mode the system pumps continuously to achieve the lowest
possible pressure.
• the Low Vacuum mode for observing non-coated and non-
conductive or partially conductive specimens.
• the ESEM Mode for observing natural status of samples.
In the last two modes, the chamber pressure is controlled using the
Chamber Pressure adjuster, while the column is at a much lower
pressure. The gas environment can be selected from the list box.
The system automatically switches to one of the modes when the chamber
is Vented and a dedicated detector is installed. If no dedicated detector is
installed, user is asked to determine a detector mounted.

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2. The Column Module

contains controls for setting the electron beam conditions:
The Beam On Button
switches the accelerating voltage on (yellow button) / off (grey button). If
the source is not started (empty progress bar), this button starts it first
(green progress bar).
The Spot Preset / Continuous Adjuster
enables to adjust the electron beam Spot size in the selectable accuracy
steps (see the Preferences… / General tab). The actual spot size
number from the factory preset list is displayed in the text area of the
adjuster, toolbar (default) and in the Databar (if selected). Only values
usable for actual imaging conditions are displayed.
Beam Spot size number could be set in the range from 1 to 10 and it
influences both the focused electron beam area and the Beam Current.
The lower is the Spot number, the lower is the Beam Current.
The High Voltage Preset / Continuous Adjuster
enables to adjust the overall electron beam acceleration voltage (from
200 V to 30 kV in 100 V steps) either continuously or using the pre-set
values (see the Preferences… / Presets tab). The actual High Voltage
value is displayed in the text area of the adjuster, toolbar and in the
Databar (if selected).

3. Magnification / HFW Module

The continuous adjuster offers a variety of ways to control the imaging
magnification (see above). The magnification range changes
dynamically according to the working distance and can also be controlled
with the use of other tools (see Chapter 5).
The Magnification is possible to display as the Horizontal Field Width
(HFW) alternatively (see the Preferences… / General tab).
Magnification Control
• Clicking the end arrow increases / decreases magnification by 5%.
• Clicking between the end arrow and the button increases /
decreases magnification by 20%.

4. Beam Module
Stigmator 2D Control
enables to correct image astigmatism. The crosshair indicates the actual
setting of the stigmator.
Shift + right-clicking over an imaging quad triggers the astigmatism
correction. Unlike the 2D box control, this is magnification sensitive and
therefore it suits for fine corrections at high magnifications, or employ the
Adaptive Sensitivity functionality (see above).
Beam Shift 2D Control
indicates and controls the beam shift with respect to the objective lens
axis. It is useful for fine image shifts without stage movement.
Shift + clicking over an imaging quad triggers the Beam Shift function.
The mouse cursor changes to a hand one that "holds" the image and
drags it over the screen. Because of a limited Beam Shift range, this
works well only for high magnifications, or employ the Adaptive
Sensitivity functionality (see above).

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 Software Control: xT microscope Control Software

Note: 
Right-clicking over the 2D box opens the menu with following particular
choices:
• The Reset sets the Beam Shift value to zero and moves the stage to
compensate the resulting imaging shift (same as the Stage menu /
Beam Shift Reset function).


5. The Tuning Module

The Source Tilt 2D Control corrects an image illumination drop by
changing an efficient angle of the beam coming from the gun area into
the electron column. In the Crossover mode activated with the button
the onscreen image shows the electron source tip instead of the sample
surface. Bring it to the screen center (green cross).
Note: 
Right-clicking over the 2D box opens a menu with following particular
features:
• The Auto Alignment finds optimal conditions automatically.
Note: 
The Source Tilt / Auto Alignment is available only for spot sizes 5 or
higher.

6. Detectors Module
contains continuous adjusters to control the active 
detector Contrast (electronic gain) and Brightness (voltage offset). The
values are remembered for each detector and quad. The adjusters are
disabled if the detector is not available or cannot be controlled (e.g. CCD
camera or an External detector).
Contrast / Brightness / Enhance Continuous Adjusters
Regardless of the detector actual gain range, the Contrast & Brightness
range is always 0 - 100 (%) and the small / large step size is 0.1 / 1 (the
Brightness step size may differ for some detectors in order to achieve a
sufficient sensitivity). A direct value can be entered by double-clicking
the Contrast / Brightness value.
The Ctrl + Clicking & left-right / up-down dragging controls Contrast /
brightness.
Note: 
Some of the Low Vacuum detectors could have the special Detectors
module with specific controls.

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Software Control: xT microscope Control Software

7. Status Module
can be found at the base of most 
pages, displaying the following information in a full or constricted form,
some of them as a tooltip (said values are approximate only):
• The Chamber Pressure: shows the specimen chamber pressure.
• The Emission Current: shows the electron current emitted from the
source.
• The tool-tip Chamber: 
shows pressure in the corresponding vacuum system section.
The system conditions are displayed by means of the icons:

TABLE 3-2 STATUS ICON MEANING

Icon Status
Column / Chamber Pumping or Venting 

Column / Chamber Vacuum 

(Vacuum ready for microscope operation)

Column Vented / Chamber Vented 

Stage axes – Lock (any one) / Unlock (all) 

Displays when Dynamic Focus is On 

Displays when Scan Rotation is not zero 

Displays when External scanning mode is On 

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 Software Control: xT microscope Control Software

8. Stage Module
consists of the tabbed sections (see Chapter 5).
• The Map tab displays the stage positions location in a visual map
form and as a list for selection.
• The Coordinates tab displays numerical values of a particular
position. Stage movements along selected axes could be locked.
• The Tilt tab contains correction features for the tilted imaging.
• The Navigation tab helps to navigate across the sample surface.
Note: 
The stage movement can be aborted by hitting the keyboard Esc key.
Don't hesitate to do so if you are not sure that the initiated movement is
safe!

FIGURE 3-11 THE STAGE MODULE

9. Stage Z Module
This module enables to softly move the stage in the Z-axis 
direction. The more the slider is pushed to the each side, the faster is the
stage motion. Clicking the slider bar moves the stage by a small step.

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Software Control: xT microscope Control Software

10. Scan Rotation Module

controls and displays the Scan Rotation value (see Chapter 5).


11. Measurement / Annotation Module

combines tools for measuring and making annotations in an imaging
quad. A measurement tool, an annotation shape or a text label can be
selected from the first three icons at the top of the module, and then
drawn in an imaging quad. All objects are sequentially indexed and
displayed in the list box below icons. The properties of the objects is
possible to change in the property editor (see Chapter 5).


12. Digital Zoom Module

The procedure takes place in the computer memory only and helps to
navigate across the enlarged view. Click the + / - magnifying glass
button to enlarge / reduce the view in the selected quad. Click the Undo
button at the top right side of the module (visible only when applicable) to
turn over between a digital magnification last used and a normal view.
Click & drag the green bordered area inside the Digital Zoom image or
click inside the green rectangle and move it by Ctrl + keyboard arrows to
change an observed area in the selected quad. Change the observed
area by dragging the green borders. Press the Ctrl + + / - keyboard
button to enlarge / reduce imaging in the selected quad. When the digital
zoom is applied, the icon appears in the appropriate quad.

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 Software Control: xT microscope Control Software

13. Enhanced Image Module

consists of tabbed sections offering various digital image enhancements.
In contrary to Detector module / Contrast and Brightness functions,
these enhancements are applied only to the active quad independently.
In case a user changes the default settings of LUT / Color / Process
tab, its background color changes to green. The digital processing can
be applied to any live, paused or loaded image, including an optical one
(see Chapter 5).

FIGURE 3-12 THE ENHANCED IMAGE MODULE

14. Beam Deceleration Module

In the Beam Deceleration mode a negative potential (Stage Bias) is
applied on the stage, which influences both primary and signal electrons.
It allows to decelerate the primary beam up to 50 V landing energy 
(option – see Chapter 7).

15. Detector Settings Module

enables to choose the selected quad detector 
and adjust its parameters.
The Detector list box contains list of detectors actually available for the
selected quad (the same as enabled items in the Detectors menu). The
list box always displays the detector actually selected in the selected
quad.
The rest of the module dynamically changes according to the selected
detector and its parameters, which may change from quad to quad (see
Chapters 5 and 7).

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Software Control: xT microscope Control Software

16. Quad Presets Module

The Import / Export button functionality is the same 
as the File menu \ Import / Export items (see above). 

17. Alignments Module

contains alignments which enable to optimize the system performance
(see Chapter 4).
• The Alignments list box contains list of Alignment procedures
available for the actual user level (User, Supervisor or Service).
• The Instructions info box displays the selected alignment procedure
instructions.
• The Steps module shows an actual alignment page with all
necessary components.

Caution! 
A user must understand the procedures at the appropriate level
before proceeding with any adjustment. Improper alignments can
make the system difficult to use.
Note: 
Some alignment modules may have some features distributed differently
than others, but functionality is the same, if it is not mentioned.

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 Software Control: Preferences… Dialogue

Preferences… Dialogue

This dialogue can be opened by selecting Preferences… 

(Ctrl + O - letter) from the pull-down menus: Scan and Tools. The menu
from which it is chosen dictates the tab opened on entry. Once the
Preferences dialogue is opened, any of the tabs can be chosen.
The Preferences dialogue consists of tabbed sections. Clicking the
required tab opens a section that allows changing and presetting
conditions for a group of the related functions. Only one tab can be
opened at any time.
The items changed remain valid (for a specific user) until changed for the
next time.
Some of the preference controls are beam dependent. In this case, an
active beam type is indicated by the corresponding icon and items
change accordingly.

The Units Tab

allows a user to change the Units of Measure and Pressure. The
choices affect the Stage module input boxes, the databar display, the
status module and so on.

FIGURE 3-13 UNITS PREFERENCES

Selection possibilities are:

• Units of Measure: Millimeter [mm] / Micrometer [µm]
• Pressure: Pascal [Pa] / Torr [Torr] / millibar [mbar]

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Software Control: Preferences… Dialogue

The DataBar Tab

specifies content of the databar displayed at the base of all quads. The
configuration and available items differ for the beam selected (Electron /
Optical) for the selected quad. The Label can be set independently for
each quad.

FIGURE 3-14 DATABAR PREFERENCES

There are two lists in the dialogue, one labelled Available and the other
Selected. Items in the Available list can be added / removed individually
(> / <) or as a whole (>> / <<) to / from the Selected list. The Selected list
contains items that are displayed in the Databar. The items in the
Selected list can be Moved Up, Moved Down, Top or Bottom according
to priority or preference. This in turn changes the order of the displayed
items in the databar.
The Label and Micronbar can be chosen by ticking an appropriate
check box. Their area expands or contracts as other items are added to
or removed from the databar. The Micronbar scales to the magnification.
Clicking the Label… button brings up a dialogue to edit the label of any
quad(s). The same dialogue can be opened by double-clicking the actual
label in any quad.
Clicking the Browse Bitmap… button opens a dialogue to load a bitmap
into the databar.
Note: 
The limit for entries is displayed in the dialogue as it is updated. It is
possible to select more items than can be displayed. The databar
preview should be used to check available space.

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 Software Control: Preferences… Dialogue

The Presets Tab

allows a user to change the pre-set values in the High Voltage,
Magnification and Pressure drop down lists. The configuration and
available items differ for the beam selected (Electron / Optical) for the
selected quad. A value can be changed by selecting it in the list and
entering a new one in the edit box just below the respective title. The
new value replaces the selected one and is immediately sorted into the
list. The number of entries in the list remains fixed.

FIGURE 3-15 PRESETS PREFERENCES

The High Voltage list can be changed to span any values from 200 V to
30 kV. The values must be entered in kilovolts (0.2 means 200 V).
The Magnification list can be changed to hold frequently used
magnifications. Values that are in the pre-set list but cannot be applied to
the actual SEM conditions are not shown in the toolbar / Magnification
list box. Magnification range is from 20× to 1 000 000×.
Note: 
Alternatively the Magnification could be displayed as the Horizontal Field
Width (see the Preferences… / General tab).
The Pressure list can be changed to hold specific values frequently used
in the Low Vacuum / ESEM mode in the range from 10 to 4 000 Pa (from
0.075 to 30 Torr) depending on selected gas type and pressure limiting
aperture.

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Software Control: Preferences… Dialogue

The Scanning Tab

allows a user to change the dwell-times (scanning speeds) table and to
set-up the Slow scan / Fast scan / Snapshot / Photo function. The
configuration and available items differ for the beam selected (Electron /
Optical) for the selected quad.

FIGURE 3-16 SCANNING PREFERENCES

On the left side of the module there is a dwell-time preset list with the
fixed number of entries. Selected Preset values can be changed in the
Property Editor on the right side of the module. Following properties are
editable (depending on the kind of the preset):
• Dwell Time: one point beam duration time
• Line Integrate: no. of line scanning repetition
• Resolution: no. of points, Width × Height (image resolution)
• Integrate (1, 2, 4, 8, 16, 32, 64, 128, 256): no. of integrated frames
• Acquisition (8 bits / 16 bits): sets the captured image bit depth
• Drift Correction (Yes / No): corrects imaging drifting when integration
filter is active. When activated, the text below the blinking quad pause
icon notifies a user.
• Continuous Scan (Yes / No): when starting up a Snapshot / Photo
function, scan in progress is finished before image grabbing starts.
This functionality is convenient for charging samples but it requires
same scanning conditions for scan in progress and Snapshot / Photo
function preset.
• Action activated at the end of Photo / Snapshot function:
Save saves the image using an automatic file name and format,
Save As… opens the Save As dialogue to save the image,
None just pauses imaging.

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 Software Control: Preferences… Dialogue

Following properties are informative only:

• Line Time: line scan duration time,
• Frame Time: image-scan duration time,
• Refresh Rate: imaging refresh frequency.
Slow (large green sector) / Fast (small green sector) preset icon
indicates the matching dwell-time value. To change it move an icon up or
down just by pressing and dragging it.
Snapshot (F4) / Photo (F2) (different cameras) preset icon indicates the
matching dwell-time value. Set all possible properties in the Property
editor.
The Default button restores the default dwell-time list and preset
settings.

The Movie Tab

provides two groups of controls: Timer to set-up the movie frame-rate
and File to set-up the path name and format of the resulting movie (see
Chapter 5).

Sensitivity Tab
The preset sliders control the sensitivity of the Manual User Interface
(MUI – option).

FIGURE 3-17 SENSITIVITY PREFERENCES

All MUI controls are represented except the Magnification. The Default
button sets the original settings.

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Software Control: Preferences… Dialogue

The ESEM™ Tab

enables to customize the specimen chamber purging, which is
automatically initiated when the system pumps the vented chamber
directly to the Low Vacuum mode (see Chapters 2 and 5).

FIGURE 3-18 LOW VACUUM PREFERENCES

Purge Mode module radio buttons:

• No Purge – The purging is switched off and the chamber pressure
goes directly to the set Low Vacuum mode value. The gas mixture in
the chamber slowly changes to the new gas type.
• Automatic – All purging parameters are set automatically, according
to the mounted Low Vacuum detector (Cone).
• Custom – The Custom parameters (Minimum Pressure, Maximum
Pressure, Number of cycles) defined in the Purge Settings module
edit boxes are used. The default values are the same as in Automatic
mode.
The Purge button enables to start the purging (using the actual Purge
Mode and Settings) manually when the system is already pumped to the
Low Vacuum; otherwise, the button is disabled. When the purging is
running, the Purge button becomes highlighted. Clicking on the
highlighted button stops the actual purging procedure and returns the
system to operation in Low Vacuum.
Notes: 
– The new Purge Mode or Settings is applied immediately after clicking the
OK or Apply button, even if the purging cycle is already running. 
– During the purging procedure, the chamber pressure is not ready for
SEM operation (the vacuum status is Pumping). Therefore, clicking the
Purge button automatically switches off the accelerating voltage. 
– The Purge Settings is not remembered separately for each user. If it is
of any importance, please check these Preferences before starting the
Low Vacuum operation.

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Magnification Tab
controls the imaging and stored / printed image databar magnification
display. The constant imaging pixel size is set at the toolbar. When
storing / printing an image (while in a Single or Quad imaging mode) the
databar magnification display may not be correct.

FIGURE 3-19 MAGNIFICATION PREFERENCES

The Screen preferences area sets the imaging databar magnification

display behaviour while the File / Print preferences area sets the
storage / printing databar magnification display behaviour. Selecting the
radio button activates its functionality:
• The Real screen size: the imaging pixel width is handled.
– The Active view: the databar magnification value depends on
whether the Single or Quad UI imaging mode is selected. It is
displayed in the databar and stored / printed with an image with an
icon representing the Single / Quad UI imaging mode.
– The Single image: Single image mode magnification value is
displayed in the databar and stored / printed with an image.
– The 4-quad image: Quad image mode magnification value is
displayed in the databar and stored / printed with an image.
• The Polaroid 5” film width is handled. A recalculated magnification
value is displayed in the databar and stored / printed with an image.
• The User device width (set by a user via the edit box) is handled.
A recalculated magnification value is displayed in the databar and
stored / printed with an image.
The Keep Screen and File / Print settings synchronized check box
keeps both settings identical.

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Software Control: Preferences… Dialogue

General Tab
contains variety of user settings of both UI behaviour and microscope
operation, which are of less importance and/or does not logically belong
to other Preferences section.

FIGURE 3-20 GENERAL PREFERENCES

Each item of the General Preferences is represented by single line

displayed in the property editor. Clicking on the corresponding Value
displays a drop down list with the settings available for that item.
Note: 
Some changes become visible after the next UI start. 
Some of the items are model dependent and some of them are intended
for options.
Categories
To make navigation among the number of preferences easier, they are
divided into three groups. Selecting appropriate group from the
Category drop down list will display in the below property editor only the
items belonging to this group. Selecting Category All will display all items
at once.
UI Appearance
• Spot size / Beam current control (Spot / Current) 
Selects a way of the toolbar parameter presentation.
• Image dimensions control (Magnification / HFW) 
Selects a way of the magnification representation and control.
• Frame active Quad (Yes / No) 
Switches on / off additional highlighting of the active Quad
• Enable zooming on mouse click-and-drag (Yes / No) 
Enables / disables the (un-)zoom function linked to the left mouse
button
• Switch sample tracking on mouse wheel click (Yes / No) 
switches the tracking movement control linked to the mouse wheel
between click-and-move and click-and-drag modes

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 Software Control: Preferences… Dialogue

• Spot Size Step (0.1 / 0.01 / 0.001) 

enables to set the accuracy of the spot size setting.
• Show context help per module (Yes / No) 
Toggles question mark display in the module header on / off.
• Pause stops immediately (Yes / No) 
The Pause function acts instantly / waits for the complete scan.
• Display Scanning Presets toolbar (Yes / No) 
Enables to display 6 preset scanning parameters at the toolbar.
Image and graphics
• Restart Average Filter when magnification change (Yes / No)
• Restart Average Filter when scan rotation change (Yes / No)
• Restart Average Filter when beam shift change (Yes / No)
• Restart Average Filter when stage moves (Yes / No)
The above four items enable to choose whether the image averaging
should be restarted when the indicated parameter changes.
Restarting the Average Filter causes the image to blink and get
noisier; on the other hand, the averaging slows down the imaging
response to the changed parameter.
• Display beam icon in databar (Yes / No) 
Adds an "atom" picture to the first position in the Databar. This is likely
to disappear in the future.
• Blinking pause icon during image integration (Yes / No) 
If Yes is selected, the blinking Pause symbol is displayed in Quads
which are being stopped. Otherwise, the Pause symbol appears only
after the image acquisition has actually stopped.
• Display Recording Movie message 
(No / 1 second / 2 seconds / 5 seconds / 30 seconds) 
During the Movie Recording, some information may be displayed in
the recorded Quads. This selection controls if and how long such
information shows up.
• Hide Rotation controls when not used 
(No / 10 seconds / 30 seconds / 60 seconds) 
Specifies if and when the on-image Scan / Compucentric Rotation
control should be automatically switched off
• Display Scan Rotation in CCD quads (Yes / No)
• Display Tilt Corrections in CCD quads (Yes / No) 
The above two items specify if the Scan Rotation / Dynamic Focus
and Tilt Correction indicator and value should be permanently
displayed in the CCD image(s); only non-zero values are displayed.
• Display Stage Map in Navigation quads (Yes / No) 
shows saved positions in any navigation image, which is available
(Nav-Cam, Navigation Montage, Navigation Alignment).
• Reset Enhanced Image parameters on file open (Yes / No) 
specifies, whether set Enhanced Image module parameters should
be employed or not when opening saved image.
• Save digitally zoomed images as (Entire image / Zoomed area) 
When saving an image, this option enables to save only the zoomed
area or the entire scanned area..
• Show legacy scanning resoplution (Yes / No) 
This item enables to display old format screen resolutions in the
toolbar drop-down list (see Chapter 3)..

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Software Control: Preferences… Dialogue

Microscope Operation
• Interactive databar (On / Off) 
Turns image databar fields to be active (directly editable when
possible) / inactive.
• Lower stage when venting the chamber 
(No / By 5 mm / By 10 mm / Full down) 
Specifies if the stage should automatically move to a lower Z-axis
values when user Vents the chamber. This is recommended settings,
because it greatly diminishes the chance of hitting the final lense pole
when closing the chamber doors after mounting a higher specimen.
• Change magnification when pumping 
(No / Set to 100× / Set to 200×) 
Specifies if the magnification should be automatically set to a low
value when the chamber is being pumped (presumably after
replacing the specimen)
• Switch off CCD automatically 
(No / 1 minute / 10 minutes / 30 minutes / 1 hour / 2 hours / 6 hours) 
Specifies if and when the CCD should be automatically switched off.
The countdown starts when un-pausing the CCD image and
continues regardless of the operator activity
• Pause beam quads when switching off HV (Yes / No) 
Specifies if the SEM image Quads should be automatically paused
when switching off the High Voltage
• Allow Beam Shift in Get mode (Yes / No) 
Enables / disables automatic using of BeamShift when a user
requires very small point-to-point movements (double-click in the
image at high magnifications). When enabled, the Stage menu item
Auto Beam Shift Zero allows selecting if the BeamShift should be
automatically reset each time the point-to-point stage movement is
required.
• Blank beam during long stage moves (Yes / No) 
If Yes is selected, the electron beam is automatically blanked during
long software controlled stage movements. This may protect
extremely sensitive samples from exposure to the beam in undesired
areas.
• Reverse Joystick movement (Yes / No) 
Normally the joystick movement direction corresponds to the stage
movement, so the imaging moves in the opposite direction. This
setting changes the stage response to the joystick movement
direction.
• Venting valve opening time (value) 
This item enables to prolong the venting time (default value is 180 s)
to eliminate residual vacuum which makes impossible to open the
chamber door or shortens the venting time.
• Automatic move to Nav-Cam position (Yes / No) 
When moving the navigation camera, the stage moves to the position,
at which the Nav-Cam image could be acquired.
• Move to zero tilt for Nav-Cam image (Yes / No) 
Sets the stage tilt to 0° automatically when grabbing the Nav-Cam
navigation photo. The stage returns to the original tilt when finished.
• Default quad for Nav-Cam image (quad 1 / quad 2 / quad 3 / quad 4) 
Sets the quad at which the navigation image will be placed.
• Unpause CCD quads when venting the chamber (Yes / No) 
When yes, the CCD display is automatically released.

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 Software Control: FEI User Management Software

FEI User Management Software

The FEI User management software allows to FEI Account

Administrators, FEI Supervisors and FEI Microscope Users to organise
user accounts that can possibly be used to run the xT microscope
Control software. It allows the creation and removal of user accounts, the
setting of user passwords and group membership, as well as the copying
and removal of user data.
You can start the software from the system Start menu. This brings up
the Log On dialogue box, containing Username and Password text
fields, for entering the User Management software.

CONTROL POSSIBILITIES
• Context menu – You can reach some context options by right-
clicking (see below).
• Drag and Drop actions – Instead of using menu options, you can
sometimes simply click & drag items from one icon to another (set
user group).

FEI ACCOUNT ADMINISTRATORS

As the highest account level, FEI Account Administrators have rights that
allow them to create and delete users and change their properties over
the following user groups (in order of significance):
• FEI Account Administrator
• FEI Supervisor Users
• FEI Microscope Users
• FEI Non-active Users
Each of these accounts has its own opportunity to operate the
xT microscope Server and Control software. The first FEI Account
Administrator is created during the system installation.

FIGURE 3-21 FEI ACCOUNT ADMINISTRATORS CONTROL OVERVIEW

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Software Control: FEI User Management Software

File Menu
contains the following items:
• Log On: click to log on (active when user is logged out).
• Log Out: click to log off (active when user is logged on).
• Refresh (F5): click to refresh the user tree.
• Exit: click to exit the FEI User management program.

Account Menu
contains the following items, which are accessible only for FEI Account
Administrators (with the exception of set password function). 

• Create (Ins): click to add a new user or supervisor. 















• Remove (Del): click to remove an existing user. A user must be

highlighted first.
If an FEI Microscope User has user data, the account administrator is
warned that user data will be removed also. If any additional user is to be
removed, that additional user’s data is removed without warnings. 



• Set password: click to make a password for a user who must first be
highlighted in the tree. 
An FEI Account Administrator can change the password for any user
from a lower level account.




• Set user group: click to set the group for a user who must first be
highlighted in the tree. When confirmed, a user is moved to selected
group. When moving a user from the FEI Microscope Users group to
the FEI Non-active Users group, his user data will be removed. A
warning is displayed in this case.

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 Software Control: FEI User Management Software

• Properties (Alt + Enter): click to see and change the properties for
that user who must first be highlighted in the tree. 








Userdata menu
contains the following items.
• Copy (Ctrl + C): click to copy user data from a user of the same or a
lower level group.
• Paste (Ctrl + V): click to paste user data into your own account or into
the accounts of a lower group level. It is not possible to copy user
data inside the FEI Supervisors User group.
• Remove: click to delete user data from a selected account of equal or
lower group level.

Help Menu
contains the following items: 

• Legend: clicking provides an explanation of icons used in the tree. 









• About: displays the FEI User Management software version and

copyright.

ACCOUNT LOGGING
This accounting utility monitors user, log on / off actions, session time,
filament lifetime and the UI status. It works with two log files located in
c:\Program Files\FEI\data\accounting\:
• accounting.tmp is a temporary running file during use of the
equipment at each user session, updated every 15 seconds so that
any power down or operating system crash situation can be time
logged.
• accounting.log is permanent file to which the previous data are sent
when a new session is started. This file is only readable by the FEI
Supervisor User or higher level.
These files can only be deleted at factory or service level. Each one is a
text – CSV file so it can be loaded into Microsoft Excel for processing. 
It can also be viewed by the particular FEI utility:
c:\Program Files\FEI\Exe\feiaccountinglogviewer.exe

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Software Control: Entering Commands in Summary

Entering Commands in Summary

USING MOUSE

Keyboard + Mouse button Function

(Shift +) Click selects a control element:
single-arrow cursor toolbar pause icon: pauses / activates (all) quad(s)
(Ctrl +) Click selects a graphical item within an imaging area
single-arrow cursor (adds another one to the selection)

Click & drag (+ Shift) selects an area to zoom in (out)

single-arrow cursor
Shift + Click & drag activates the Beam Shift
hand-cursor
Double-click Electron Imaging: 
Get mode: moves a point to the quad center
Optical Imaging: 
places 10 mm marker
Right-click & drag focuses by dragging the mouse left-right
double-arrow cursor
Shift + Right-click & drag corrects an imaging astigmatism by dragging the
four-arrow cursor mouse left-right – X stigmator or up-down – Y
stigmator
Ctrl + Click & drag controls the detector contrast / brightness 
by dragging the mouse left-right / up-down
Ctrl + Wheel-scroll Up / Down increases / decreases the magnification coarsely
(Ctrl+) Wheel-click & drag Electron Imaging: 
Track mode: moves the stage (joystick-like control)
Optical imaging: 
moves the stage in Z-axis direction (tilts the stage)
by dragging the mouse up / down (left / right)

Note: 
The given sequence of the key press and mouse button click is important for some
functions.

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 Software Control: Entering Commands in Summary

USING KEYBOARD
TABLE 3-3 WINDOWS SYSTEM KEYS 

Key (+ Key) Function

Enter equivalent to the OK button in dialogues
Esc 1. equivalent to the Cancel button
2. stops the stage motion at that point 
Note: 
During particular procedures, Home Stage for instance, 
use the software Cancel or Stop button!
Tab switches between entry fields within dialogue boxes
(Shift +) Arrows 1. selects an item within list boxes
2. moves the stage approximately by (40%) 80% 
of the field of view in corresponding direction
Alt (F10) underlines menu bar item characters – 
by hitting it a corresponding menu list is expanded
Alt + Tab Switches between running applications: each time the Tab key
is hit while holding the ALT key pressed a pointer jumps to
another application icon. Releasing the Alt key at any time
makes application just listed active.
Alt + F4 closes active application or Windows operating system
Del(ete) deletes a selection, texts or graphics
Ctrl + A selects all items, texts or graphics within an active window
Ctrl + C copies a selection to the clipboard – temporary memory
Ctrl + V pastes content of the clipboard 
at the pointer position – text / to a window – graphics
Ctrl + X cuts a selection to the clipboard – copies and deletes it

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Software Control: Entering Commands in Summary

TABLE 3-4 FUNCTION AND SPECIFIC KEY SHORT-CUTS 

Key (+ Key) Function

F1 Displays On-Line Documentation

Shift + F1 Opens Image Properties window

(Shift +) F2 Starts Photo with the active beam 

(in all quads with the same beam at once)

(Ctrl + ) F3 Toggles Videoscope On / Off (in all quads)

Shift + F3 Starts Home Stage procedure

F4 Starts / Stops Snapshot

F5 Toggles Single / Quad Image mode

Ctrl + F5 Toggles Large Image Window mode

Shift + F5 Toggles Center Cross display

F6 Pauses / Activates scanning

Shift + F6 Toggles Alignment rectangle display

F7 Toggles Reduced area / Full Frame Mode

Ctrl + F7 starts Image Post Processing

F8 Degauss

F9 Starts Auto Contrast and Brightness procedure

Shift + F9 Link Z to FWD

F11 Starts Auto Focus procedure

Ctrl + F11 Starts automatic Astigmatism correction function

Shift + F11 Toggles Display Saturation function

(Shift +) F12 Toggles Compucentric (Scan) Rotation tool

Ctrl + 0 - number Moves stage to X=0, Y=0

Ctrl + B Toggles Beam Blank function

Ctrl + E Tilt stage to 0°

Ctrl + F Sets FWD to 10 mm

Ctrl + H Sets Horizontal Field Width (HFW)

Ctrl + K Sets Spot mode conditions

Ctrl + M Sets Full Frame scanning conditions

Ctrl + Shift + M Starts movie recording dialogue

Ctrl + N Toggles Sample Navigation

Ctrl + O - letter Opens Preferences dialogue

Ctrl + P Opens Print dialogue

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 Software Control: Entering Commands in Summary

TABLE 3-4 FUNCTION AND SPECIFIC KEY SHORT-CUTS 

Key (+ Key) Function

Shift + P Next pattern

Ctrl + R Restarts scan

Ctrl + (Shift +) S Saves images (from all quads)

Ctrl + Z Moves stage to the Last position

Ctrl + Shift + Z starts Take Nav-Cam Photo procedure

Ctrl + (Shift +) , Sets one step slower (slowest) scanning

Ctrl + (Shift +) . Sets one step faster (fastest) scanning

Ctrl + (Shift+) Tab (Backward) Steps between quads

Ctrl + Page Up / Down Left / Right Steps between pages

Ctrl + 1 / 2 / 3 …  Selection of the particular page (the number corresponds to

- letter keypad the toolbar page icon sequence)

(Ctrl +) + / - Increases / Decrease magnification 2x (Digital Zoom)

* Rounds off magnification to the nearest round value

Ctrl + arrow Moves the digital zoom area by one screen pixel in the
respective area

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Software Control: Entering Commands in Summary

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4 ALIGNMENTS

At the Alignments page select an alignment procedure available from

the list box. Always follow the instructions given in the Instructions
module. The Step displays the present control step number and the total
number of steps. You can find some additional explanation in this
chapter.

COMMON RULES
Alignments should be performed in the quad 1. In other case it is not
possible to ensure the correct functionality of the Contrast, Brightness
and Auto functions used at the Alignments pages.
Before one aligns the Electron column, be sure that the final lens
aperture is clean and properly centred.
During adjustment procedures it is allowed to change the magnification,
the scanning speed, to use reduced area and to optimize image contrast
/ brightness. It is also possible to correct astigmatism and to focus an
image (for a particular alignment this is forbidden).
During adjustment procedures it is not allowed to change a Vacuum
Mode, a Spot size and a High Voltage. Do not use the Beam Shift at any
time during the adjustment procedures, as this is set to the zero value at
each alignment section. All specimen movements can be made using the
stage, either mechanical or motor driven, where appropriate.

BUTTONS AND CONTROL ELEMENTS

The following particular buttons and control elements (see Chapter 3)
have the same behaviours for all alignment procedures, when available:
• The Start button starts the procedure and proceeds with following
dialogues.
• The Contrast / Brightness adjusters enable to optimize the image
quality during alignment.
• The Auto button executes the appropriate alignment action
automatically for a particular voltage / spot / direction (whatever
suitable) with the use of the Image Recognition software. If this utility
does not recognize image features well, the procedure is aborted and
Warning message appears onscreen. In this case change the
imaging conditions (better focus, slower scanning, or lower
magnification) and try again.
• The Crossover button activates the Crossover mode, where the
onscreen image shows the electron source tip instead of the sample.

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Alignments:

ALIGNMENT LIST
The list of alignments accessible for a Supervisor is represented, 
the User alignments list is reduced and is represented by (U) sign.
• 1 - Source Control
Filament setting for a particular accelerating voltages, emission
current setting.
• 3 - Gun Alignment
Centres the electron beam at various high voltages and spot sizes.
• 4 - Condenser Alignment
Minimizes the image shift at various HV and Spot sizes.
• 5 - Final Lens Alignment (U)
Minimizes the image shift during focusing.
• 6 - Stigmator Alignment
Eliminates image shift during normal stigmator correction.
• 7 - Stage Rotation Center (U)
Sets the stage rotation centre for the compucentric rotation.
• 8 - PLA Centering (U)
Centers the PLA.
• 9 - Filament Exchange
Filament saturation and parameters settings after the filament
exchange.
• 94 - CCD Camera Alignment
Optimizes the CCD camera imaging performance.
• 154 - Water Bottle Venting
Enables to vent the water bottle in case of refilling.

Recommendation
The system alignment should be made whenever necessary. Some
procedures may influence the others, therefore care should be taken to
monitor an influence of actions taken.
Alignment procedures should be carried out:
• Preventive maintenance once per month: 1
• Whenever needed: 6 / 7
To improve the accuracy, repeat alignment 7 after each Stage menu /
Home Stage or Home Stage Without Rotation procedure.

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 Alignments: 1 - Source Control

1 - Source Control

This procedure enables the fine filament saturation after its replacement
or after the system long period shut down to bring the microscope to the
perfect working condition.

FILAMENT SETTINGS
The Gun Tilt setting is saved for the particular accelerating voltage,
contrary to the Filament Exchange procedure (see below).

Particular Control Elements

• The Filament Voltage adjuster controls the filament voltage.
• The Limit Voltage check box inhibits (when ticked) the Filament
Voltage to exceed the set value. Tick it after the saturation procedure
is completed.
• The Autobias On check box maintains (when ticked) the Emission
Current in the set range.
• The Bias adjuster (available when the Autobias On check box is not
ticked) controls the voltage between the filament and the Wehnelt
cap, which influences the emission current.
• The Emission Current adjuster sets the Emission Current value.
Note: 
The higher is the current, the shorter is the filament lifetime. Typical
operation value is about 100 µA.
• The Filament Current shows the actual filament current value. The
OK check box indicates the filament to be in order.
• The Filament Lifetime shows the time the present filament is heated.
• The Gun Tilt 2D control corrects the image illumination drop or the
filament mechanical misalignment.

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Alignments: 3 - Gun Alignment

3 - Gun Alignment

After finishing the procedure there should be no image shift, no out of

focus and no brightness change during microscope operation.
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continue…

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 Alignments: 4 - Condenser Alignment

4 - Condenser Alignment

The values between the ones adjusted by this alignment are

interpolated.
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Alignments: 5 - Final Lens Alignment

5 - Final Lens Alignment

Particular Control Elements

• The Modulator button starts automatic objective lens current
oscillation to facilitate the process.

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 Alignments: 6 - Stigmator Alignment

6 - Stigmator Alignment

Particular Control Elements

• The Modulator button starts automatic stigmator oscillation to
facilitate the process.

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Alignments: 7 - Stage Rotation Centre

7 - Stage Rotation Centre

The stage rotation has a mechanical center and it can be controlled by

changing the Stage module / Coordinates tab / R value. The stage
moves around its mechanical center. In some circumstances this is not
desired because a rotation around the field of view center would be more
useful.
The magnification should be from 500× to 2 000×, and the sample
should have a recognisable feature close to the center of the stub, which
is mounted in the stage center. Make sure the tilt is zero.

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 Alignments: 8 - PLA Centering

8 - PLA Centering

The device holding a PLA can either be a detector or a cone. This

alignment brings the image area to the screen center.

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Alignments: 9 - Filament Exchange

9 - Filament Exchange

Note: 
It is important to be aware of the following procedure - one should be
practised to be familiar with it.

Particular Control Elements

• The Emission Current shows the Emission Current value.
• The HV button switches the high voltage on.
Other elements not described here see above: 1 - Source Control
alignment.
The Filament Saturation Procedure
The Gun Tilt setting is saved at the 20 kV. The value is used for all
voltages for the beginning, until changed in 1 - Source Control. Inserting
a specimen is not absolutely necessary, although it can help during the
questing the reason of a poor image.
1. Select ETD, release quad 1. Switch the HV on (wait a few seconds
until the target HV value is reached). Switch to the Crossover mode.
2. Increase the Filament Voltage gradually. When you reach about 1.50
V value and still do not get any signal, try to increase the Contrast.
3. In the Crossover mode, as you increase the filament voltage (see
details below), try to avoid both black and white areas in the filament
image by adjusting contrast and/or brightness.
4. Slowly increase the filament voltage as long as the signal level
increases (the filament is properly saturated at the point the signal
increases with increasing the filament voltage no more). You can find
the saturation point by step slightly over it and then back.
5. Tick the Limit Voltage check box to prevent an unwanted filament
over saturation.

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 Alignments: 9 - Filament Exchange

Filament Exchange (continued)

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Alignments: 94 - CCD Camera Alignment

94 - CCD Camera Alignment

This procedure optimizes the CCD camera imaging performance. 

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 Alignments: 154 - Water Bottle Venting

154 - Water Bottle Venting

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Alignments: 154 - Water Bottle Venting

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5 OPERATING PROCEDURES

This chapter describes how to use the Microscope system from an

application point of view. The following subjects are covered:
• Specimen Preparation and Handling
• Obtaining an Image
• Optimising an Image
• Detector types and usages
• Capturing and Handling a Single Image
• Saving Multiple Images (Recording Movies)
• Measurement and Annotation Functions

Caution! 
These procedures assume you are familiar with the xT microscope
server and xT microscope Control software (see Chapter 3), which
are necessary to start and operate the microscope.

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Operating Procedures: Specimen Preparation and Handling

Specimen Preparation and Handling

The specimen material for high vacuum must be able to withstand a low
pressure environment (without outgassing) and the bombardment by
electrons. It must be clean and conductive. Oil and dust may
contaminate the chamber environment, which could hinder or even
prevent evacuation to the level needed for standard SEM operation.
Note: 
Always wear lint- / powder-free clean room gloves when reaching into
the specimen chamber to minimise oils, dust, or other contaminants left
inside the chamber.

NEEDED ITEMS
• Class 100 clean-room gloves
• Specimen stubs and conductive adhesive material
• Tools: tweezers, 1.5 mm hex wrench
• Prepared or natural specimen

NATURAL SPECIMEN
If no coating is desired the Low Vacuum mode can be used to stabilise
the specimen for observation. This mode is useful if there is a suspicion
that a coating might alter the specimen.
If the specimen contains any volatile components, such as water or oil,
and therefore will not withstand coating, then the ESEM mode can be
utilised with the correct environment gas and pressure to allow
observation of the specimen in its natural state.

COATED SPECIMEN
If the specimen is nonconductive (plastic, fibre, polymer or other
substance with an electrical resistance greater than 1010 ohms) the
specimen can be coated with a thin conductive layer. This conductive layer
reduces beam stir due to sample charging and improves imaging quality.
For successful imaging, rough surfaced specimens must be evenly
coated from every direction. Biological, cloth and powder specimens may
require carbon or other conductive painting on portions of the specimen
that are hard to coat.
Coating reduces beam penetration and makes the imaging sharper. It
may mask elements of interest for X-ray analysis (thus the use of carbon
for geological and biological specimens).
For more information on specific preparation techniques, see Scanning
Electron Microscopy and X-Ray Microanalysis, 2nd ed. by Joseph
Goldstein et al., Plenum Press, New York, 1992.

MOUNTING SPECIMEN TO HOLDER

Wafers and PGA devices have individual sample-mounting procedures.
If you are using a wafer piece or other sample, attach the specimen to
the specimen holder using any suitable SEM vacuum-quality adhesive,
preferably carbon or silver paint. The specimen must be electrically
grounded to the sample holder to minimize specimen charging, make
sure the specimen is conductively attached to the holder.

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 Operating Procedures: Microscope Control

Note: 
The sample holder is not directly grounded to the chamber ground because
it is connected to the BNC feed allowing to measure the specimen current.

Caution! 
Store samples and sample holders in a dry and dust free
environment. Dust on samples can get drawn into the electron
column, degrading imaging and requiring service response.

Microscope Control

OPERATION PRE-CHECK
It is assumed, that the microscope is in the Full operation state 
(see Chapter 2).
To ensure correct operation in any Vacuum mode, check the following list
before continuing. After obtaining a preliminary image, you can then
experiment with your settings.
TABLE 5-1 QUANTA SETUP CONDITIONS

Adjustment E-Beam Setting

Vacuum mode HiVac: conductive samples 
LoVac: nonconductive, mixed or contaminating samples 
ESEM: wet samples (use H2O gas medium)
Accelerating Select voltage relative to specimen type: 
Voltage - low voltage for surface imaging, beam-sensitive samples and slightly charging
samples 
- high voltage for conductors, high resolution, compound info (BSE, X-ray)
For example: 
- biological sample High Voltage = (1–10) kV 
- metal sample High Voltage = (10–30) kV
Spot size HiVac and LoVac: 3 or 4 
ESEM: 4
Pressure HiVac: the lowest 
LoVac: 60 Pa (0.5 Torr) 
ESEM: 600 Pa (3.7 Torr)
Scan rate HiVac: fast (dwell time about 0.1 - 0.3 µs) 
LoVac and ESEM: slow (dwell time about 1 - 3 µs)
Free Working Set the highest specimen point to approximately 10 mm (yellow mark in an optical
Distance (FWD) quad) and press Ctrl + F to set WD to 10 mm.
Magnification Set to lowest – from 50× to 200×
Standard  HiVac: ETD (SE) 
Detector LoVac: LFD 
ESEM: GSED
Filtering HiVac: Average (4 frames for fast scans) 
LoVac and ESEM: Live
Contrast  With contrast at minimum value adjust brightness to just show a change in intensity to
& Brightness the screen. Increase the contrast to produce a reasonable image on screen. Increases
in brightness and decreases in contrast produce softer images and vice versa.

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Operating Procedures: Microscope Control

INSERTING / EXCHANGING SPECIMEN 

AND / OR DETECTOR
1. Click the Vacuum module / Vent button. The confirmation dialogue
appears.
After an automatic accelerating voltage switch off (or manually the
Column module / HV button), the vacuum system switches off the
pumps and opens the appropriate valves to vent the system. After a
specified venting time the venting valve will close.
Note: 
If the venting valve closes before the chamber is at the atmospheric
pressure (the door is not possible to open), click the Vent button once
more to open it again.
If you vent the chamber in order to change a detector, wait until the
Status module vacuum icon (chamber part) is grey. Otherwise there
is a risk of a incorrect detector determination, and as a result the PLA
(see Chapter 2) is not recognised by the system.
2. When vented, open the specimen chamber and, using lint-free gloves
or tweezers, place a specimen into the specimen holder. Secure the
specimen stub with an appropriate hex-wrench unless a spring-clip
holder has been used.
3. Install any additional detector if it is not already done (see below).
4. Adjust the Eucentric Position (see below).
5. Close the specimen chamber door.

SELECTING VACUUM MODE

When a specimen and appropriate detector(s) are installed correctly,
continue the procedure (see above):
6. Check the Vacuum module / High Vacuum / Low Vacuum / ESEM
mode radio button. Dialogues appear to promote closing / opening of
the manual EBV if it is not already done (see above).
For the Low Vacuum mode select the appropriate gas from the drop
down list and the target Chamber Pressure that the system pumps to.
7. Click the Vacuum module / Pump button. While pumping, choose the
highest specimen point and bring it to the 10 mm Working Distance
(yellow line in CCD Quad).
Under normal operation, the system will know the PLA size for the
detector installed. This will allow the system to set automatic pressure
range limits for the aperture installed, thus avoiding vacuum errors
when setting chamber pressure. In some cases a user will be
prompted for PLA Configuration.

WAR N I N G ! 
The system can be damaged by using the Low Vacuum / ESEM
mode without an appropriate PLA. Do not select a PLA Cone which is
not actually mounted onto the objective pole piece (see Chapter 2).
8. Wait for the vacuum status Pumped (Status module / green icon).

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 Operating Procedures: Imaging Optimising

OBTAINING IMAGING ON SCREEN

Continue the procedure (see above):
9. Select an appropriate detector (see below) and resume the chosen
quad.
10.Click the Column module / Beam On button to ramp up the
accelerating voltage. An imaging appears in the active quad.
11.Focus the imaging and Link Z to FWD (see Chapter 3).
12.Adjust to a suitable magnification, optimize the imaging using the
Contrast & Brightness, Focusing, Astigmatism Correction etc.
(see below).
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Imaging Optimising

PRINCIPLES OF SEM IMAGING

All scanning beam microscopes screen with the same fundamental
technique. The primary beam is scanned across the specimen surface in
a regular pattern called a raster. Normally, this raster consists of a series
of lines in the horizontal (X) axis, shifted slightly from one another in the
vertical (Y) axis. The lines are made up of many dwell points and the
time of each dwell point can be shortened or prolonged (dwell time). The
number of points per line can be increased or decreased as well as the
number of effective lines (resolution). The result is a picture point (pixel)
array. Low or high resolution imaging can be obtained by changing these
factors. The larger the pixel array, the higher the imaging resolution. The
imaging is created pixel-by-pixel in the computer memory and displayed
on a monitor screen.
The signal emitted by the specimen surface as it is illuminated with the
primary beam is collected by the detector, amplified and used to adjust
the intensity of the corresponding pixel. Because of this direct
correspondence, the pixels displayed on the monitor are directly related
to the specimen surface properties.
The raster consists of many (typically one million) individual locations
(pixels) that the beam visits. As the beam is scanned, the signal emitted
by the sample at each beam position is measured and stored in the
appropriate digital memory location. At any time after the beam scan, the
computer can access the data and process it to change its properties, or
use it to generate a display.

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Operating Procedures: Imaging Optimising

MAGNIFICATION
Magnification is calculated as the displayed dimension (L) divided by
the sample scanned dimension (l).
If the observed sample point size is made smaller while the monitor size
remains constant, the magnification increases. At low magnification, one
gets a large field of view. At high magnification, you point only a tiny
sample area.
It is possible to set a corresponding data bar magnification readout in the
Quad Image and Single Image modes and in the saved image 
(see the Preferences… / Magnification tab).

FIGURE 5-1 MONITOR IMAGING AND SCANNED SAMPLE

Changing Magnification
• The Toolbar list box is used to select from a predefined values.
• The Keyboard control (+ / - / *): the numeric pad plus key (+) / the
minus key (-) increases / decreases the magnification 2× and rounds
the value. The star (*) key rounds the magnification value 
(e.g. 10 063× becomes 10 000×).
• The Mouse wheel control: Coarse / fine control can be operated by
the Ctrl / Shift key and scrolling the mouse wheel up / down to
increase / decrease the magnification.
• The Selected Area Zooming In / Out is a quick way of zooming in /
out on an area of interest. Click inside the imaging area & drag to
make a dotted box over the area of interest (the cursor changes to a
magnifying glass with a + sign). Release the mouse button and the
selected area increases to fill the whole quad (window) with respect to
the sides ratio. Clicking & dragging + Shift consecutively reverses the
above described technique (the cursor changes to a magnifying glass
with a - sign). The escape button cancels the operation at any time.
• The Magnification module (see Chapter 3)
• The Digital Zoom module (see Chapter 3)

SCAN SPEED AND FILTERING

To make a good imaging it is necessary to find a balance between scan
speed, charge, sample damage and signal to noise ratio.
A noisy imaging can be improved by decreasing the scan speed. If
charge or sample damage are the limiting factors it is better to use a
faster scan speed in combination with an Average or Integrate filter 
(see Chapter 3).

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 Operating Procedures: Imaging Optimising

CONTRAST AND BRIGHTNESS

The contrast and brightness can be set manually either by adjusting the
Detectors module controls (see Chapter 3) or using the MUI (option).
1. Select a medium speed scan in an active quad.
2. Reduce the contrast to zero and adjust the brightness to a level so that
the last gray level can be seen, by eye, before the screen goes black.
3. Increase the contrast so that the imaging appears.
4. If necessary, adjust the brightness level to improve the imaging.

Using Videoscope (F3)

This mode could facilitate contrast and brightness optimization to obtain
full gray scale imaging level range.
Three yellow horizontal lines (placed over the quad) indicate white (top
line), gray (middle line) and black (bottom line) levels. The oscillogram
signal amplitude / central position reflects a contrast / brightness of the
just scanned line. If the oscillogram is cut by the bottom / top line, the
signal level is clipped in black / white. This should be avoided because
the imaging details are lost in the clipped areas.
Tuning the oscillogram exactly between the top and bottom lines for a
feature of interest (with the use of the reduced area) results in the full
detailed imaging. The signal clipping may be used to obtain harder
contrast conditions when more black and white is needed. The signal
amplitude lowering decreases the contrast, i.e. the imaging looks softer.
1. Select a slow scan in an active quad.
2. Activate the Videoscope (F3 / Scan menu).
3. Reduce the contrast to zero and adjust the brightness level to the
lower dashed line (black).
4. Increase the contrast so that the signal level just touches the upper
dashed line (white).
5. If necessary, adjust the brightness level once more so that the
average signal level is roughly in the middle.
6. The high and low peaks should just touch the dashed lines.
Note: 
Use also the following functions to optimize 
the Contrast / Brightness (see Chapter 3): Auto Contrast Brightness
(F9), User Auto Contrast Brightness, Display Saturation (Shift + F11).

FOCUSING
Find a feature of interest with distinct edges on a specimen. Use a
combination of contrast, brightness and magnification adjustments to
maximize the imaging quality.
1. When the mouse cursor is over an imaging area, right-click & drag
(the mouse cursor changes to a double-ended arrow). Move the
mouse from side to side until the selected quad imaging is sharp, then
release the mouse button.
2. The focus function (cursor) is active over the whole screen without
any interference with other controls. If the full mouse motion is not
sufficient to get the focus: release the mouse button at one side of the
screen, move the mouse cursor to the opposite one and right-click &
drag again (over an imaging area) to continue focusing.
3. If this is a new specimen first time focusing, run the Link Z to FWD
function (see Chapter 3).

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Operating Procedures: Imaging Optimising

Focusing at a higher magnification makes the result more precise. For

example, for an output at the 2000× magnification focus at 4000× –
8000× magnification.
To avoid scanning too long and contaminating or even damaging the
sample before you take the final image, move away from the feature of
interest with the X and Y stage controls, and focus until the image is
sharp on an adjacent area.

Focusing with MUI (option)

Use coarse and fine focus knobs. The imaging immediately responds to
the MUI.
Note: 
Use also the following functions to focus 
(see Chapter 3): Reduced area (F7), Auto Focus (F11).

CORRECTING ASTIGMATISM
This optical aberration is caused by different focal lengths for rays of
various orientation, resulting in a directional imaging blur (X and Y rays
are not focused to the same plane on the edges).
There are special coils serving to correct this imperfection, which is
usually better visible at higher magnifications (3000× or more). You need
to correct astigmatism when you change the imaging conditions.
1. Focus an image.
2. Bring the imaging just slightly out of focus. The imaging appears to
become sharper in one direction whereas in perpendicular direction
blur increases (blurring or stretching).
3. Bring the imaging just slightly out of focus in the other direction to
observe the opposite directional blur.
4. Focus to the midpoint between the two directions, where the blur is
visible.
5. Use the Beam module / Stigmator 2D control.
The Mouse: shift + right-click & drag while in the selected quad. This
results in a 4 arrowed cross appearing on the screen with the cursor
position at its center. Move the cursor around the screen to achieve
maximum sharpness. When you are satisfied, release the mouse
button.
The MUI (optional): adjust imaging sharpness with the stigmator X
and Y knobs until the best result is achieved. The computer beeps
when the stigmator limits are reached.
6. Repeat steps 1–5 as necessary.
If astigmatism is severe and the cross is close to the edge of the screen
when nearing correction, release the mouse and reposition the cross in
the center of the screen. Then repeat the procedure above to perform
further astigmatism correction. You can use reduced area
advantageously (see Chapter 3).
If astigmatism cannot be corrected, there may be some other reason,
usually the final lens aperture is dirty (see Chapters 4 and 6), the
magnification may be too high for the beam spot size (see below) or the
sample is charging (apply conductive layer or use the Low Vacuum /
ESEM mode).
Note:
For normal astigmatism correction use the automatic Tools menu / Auto
Stigmator procedure (Ctrl + F11).

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 Operating Procedures: Imaging Optimising

DIGITAL IMAGING ENHANCEMENT / 

IMAGING MIXING / COLORING
The Enhanced Image module offers various digital imaging
enhancements.
Note: 
When saving the image with the digital enhancements applied, be sure
to choose the correct file format (see below).
LUT (Look-Up-Table) Tab
enables to monitor and modify a grey level distribution (histogram).
• The Presets list box enables to select the Digital Contrast, Digital
Brightness and Gamma values using pre-defined or custom presets.
• The D. Contrast continuous adjuster sets a digital contrast in the
range from -10 to +10 (negative values lead to an inverse imaging).
• The D. Brightness continuous adjuster sets a digital brightness in the
range from -2.0 to 2.0.
• The Gamma continuous adjuster corrects image brightness non-
linearly in the range from -10 to +10.
• The Auto Levels button sets the three above mentioned parameters
automatically according to the imaging / image quality.
• The Graph window graphically displays (blue line) the applied
modification. Original / modified values are on the horizontal / vertical
axis.
• The Histogram button switches on / off the grey level distribution
(corresponding to the active quad image) display. The left / right side
corresponds to black / white original image pixels. The height of the
red line is proportional to the number of pixels with the corresponding
grey value.
• The Save button saves the actual setting as the custom preset.
• The Default button restores the default values.
• The Undo / Redo button cancels / applies again the last changes.
Mix 3 / Mix 4 Tab
The Mix feature operates in quad 3 / quad 4 and is enabled only if the
Detector menu / Mix is selected for a quad 3 / 4. It uses the processed
images (Average / Integrate, Digital Contrast, Digital Brightness, Digital
Zoom), not the raw detector signals. Any combination of live and paused
images can be mixed together, providing all mixed images have the
same pixel resolution. However, there are some logical limitations and
behaviours:
• The Average and Integrate filters are disabled.
• Pause / Activate influences the mixed imaging only, not its sources.
The Mix quad is always paused immediately regardless of the actual
scanning status.
• The CCD image is not mixed.
Note: 
In the Mix 3 tab the Source 3 controls and the Select 1+2+3 button are
disabled.
• The Presets list box enables to select the mixing ratios and colors
using pre-defined or custom presets.
• The Source 1 / 2 / 3 linear continuous adjuster tunes the mixing ratio
of quad 1 / 2 / 3 imaging. The adjuster % values influences
correspondingly the resulting image and the other ones change
automatically to reach the 100% sum.

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Operating Procedures: Imaging Optimising

• Clicking the Color control areas (below each Source adjuster)

enables to select a color, replacing the source image black (left) /
white (right) one. The image grey scale is linearly transformed to a
new color spectrum before it is mixed with other image(s).
Note: 
Color imaging (see below – the Color tab) is converted to greyscale
one before mixing.
• The Invert check boxes inverts the corresponding source spectrum. It
has the same effect as exchanging the left and right colors selection.
• The Select 1+2 / 1+2+3 button selects between quads 1+2 or quads
1+2+3 mixing modes.
• The Save button saves the actual setting as the custom preset.
Color Tab
enables to colorize a grey scale imaging. An imaging already colored
with the use of the Mix 3 / Mix 4 tab cannot be colored again, the Color
tab is disabled.
• The Presets list box enables to select the color profile using pre-
defined or custom presets.
• The Coloring Control area displays the selected quad histogram
and enables to create a color profile.
Right-clicking into the histogram area adds the vertical borderline with
a divided triangle at the top (right-clicking onto an existing one
removes it). Clicking & dragging a borderline changes its position
along the histogram. Clicking onto the left / right part of the triangle
selects the left / right border color. The imaging grey scale between
two borderlines is linearly transformed to a new color spectrum.
• The Hand button enables to select and color a particular image grey
level. Clicking it opens the color selection dialogue: select a color and
click the OK button. The mouse cursor changes to the hand image.
Click the feature image you want to highlight. New borderline is
added into the histogram with a rectangle at the top. The selected
grey level is marked with the chosen color. You can move this
borderline and change its color the same way as a borderline with a
triangle at the top. By dragging the rectangle left / right side the
highlighted grey level range could be changed.
• The Enable check box switches on / off actual color settings for the
active quad image.
• The Save button saves the actual setting as the custom preset.
The Process Tab
Here a user can set parameters, which adapt image when clicking the
Apply button, or when selecting the Tools menu / Image Post
Processing (Ctrl + F7). The Undo button, or the Tools menu /Undo
Image Post Processing (Ctrl + Shift + F7) reverts the corrections back.
• The Denoising strength (0 / 1 / 2 / 3 / 4) removes dust and scratches
from the image.
• The Sharpening strength (0 / 1 / 2 / 3 / 4) influences the image
sharpness.
• The Undo / Redo button cancels / applies again the last changes.
The Custom settings could be saved.
Note: 
This functionality works only with greyscale images (not colored via
Color tab), images which are paused or with loaded saved ones.

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 Operating Procedures: Imaging Optimising

ACCELERATING VOLTAGE
The choice of accelerating voltages – in the UI named High Voltage (HV)
– and Beam Currents for the active display is possible via the toolbar
dropdown list boxes. The HV and beam current are independent, so any
change of the voltage will not influence the current.
Besides a normal list box behaviour an intermediate value can be
entered into the toolbar editable HV text box or set by the Column
module / High Voltage adjuster on the Beam control page. This provides
a calculated range of beam current / spot values. Default values in the
list box are set in the Preferences… dialog / Presets tab.

BEAM SPOT SIZE / BEAM CURRENT

This is one of the basic operating parameters. In other way it is
represented as the function of the electron beam diameter (usually
presented as the Spot size, expressed by a relative number), the final
lens aperture diameter and its opening angle set by the condenser.
Both the focused beam area and the beam current increases with the
increasing spot number. There are 10 pre-set spot size numbers
selectable from the Column module / Spot list box and from the
corresponding toolbar list box (see the Preferences… dialog / Presets
tab). An intermediate value can be set by the Column module / Beam
current / Spot size adjuster on the Beam Control page.
Either electron Beam Current or Spot Size can be displayed within the
User Interface. This can be set in the Preferences… dialog / General
tab / Spot size / Beam current control item.

Adjusting Spotsize for Imaging

Spotsize is considered to be close to ideal when the edges of the beam
just touch when adjacent lines are scanned. If the spotsize is too large,
overlaps occur and the imaging appears out of focus. If the diameter is
too small, electronic noise appears.
Deciding which spotsize is correct for a particular magnification can be
determined when you achieve good focus and astigmatism correction
easily at the chosen magnification.

TABLE 5-2 SPOTSIZE USE RECOMMENDATION

Spotsize Best Use

1, 2 Very high resolution (mag >50 000×)

3, 4, 5 Standard imaging, SE, BSED, LFD, GSED

5, 6, 7 BSED, CL, X-ray analysis, EBSP

When you change spotsize, adjustment of the Detector module /

Contrast and/or Brightness may be necessary to optimize the imaging.
An alternate approach is to click the toolbar Auto Contrast &
Brightness icon.

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Operating Procedures: Standard Detectors

Standard Detectors

DETECTOR SETTINGS MODULE

Detector exchange and modification of its conditions via Detectors page
/ Detector Settings module are immediate.

GASEOUS DETECTORS IMAGE PROCEDURE

1. After the pumping and purge process click the Beam On button.
2. The Bias (detector voltage) adjuster in the Detector module is
automatically adjusted to 70% of maximum value. Adjust it if
necessary to increase a signal or to stop possible discharges. The
Contrast adjuster (electronic gain) is set to the value last used.
3. At the lowest possible magnification, adjust the Contrast / Brightness
if necessary, until the bright circle of the used cone can be seen in the
centre of the image.
4. Increase magnification and adjust Contrast / Contrast / Brightness
more precisely.
Note: 
The Auto Contrast Brightness does not change the bias setting (because
of discharges). If the functionality is unsatisfactory, change Bias and try
again.

Discharges between Gaseous Detectors and Sample

Excessive voltage may cause a “breakdown” between the detector and
the sample, chamber, pole-piece etc. This could damage the sample (at
ground) but does not damage the detector. This condition is indicated by
white flashes or streaks across the imaging, and on some systems a
large discharge could make the system unstable or cause the chamber
to vent and switch off the HV. There are several factors that could cause
detector voltage breakdown:
• The Bias is set too high.
• A sample is too close to the detector.
• Gas pressure is low (depending on the detector and the environment).
• Air in the chamber (water vapour purge cycle not complete)
• A sample is not grounded to the stage, or the stage is not fully
grounded (BNC plug not connected).

INFRARED CCD CAMERA

Imaging obtained with this camera assists in overall sample and stage
orientation by enabling to view the inner space of the specimen chamber
(an optical quad). It protects the objective pole piece and retractable
detectors against collision when moving (especially in the Z-direction) or
tilting the stage. IR LED’s are used to light the specimen chamber interior.

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 Operating Procedures: Standard Detectors

EVERHART THORNLEY DETECTOR (ETD)

It is a scintillator photo-multiplier type detector collecting electrons
generated by the primary beam interaction with the specimen surface. It
is permanently mounted in the chamber over and to one side of the
sample. It works in Modes:
• Secondary Electrons (SE)
• Backscattered Electrons (BSE)
• The Deceleration Mode is available, when it is on 
(option, see Chapter 7)
• Custom

ETD Settings
The Detector Settings / Mode list box enables to choose a SE / BSE
mode (the Grid Voltage is set to +250 V / -150 V) or a Custom mode, for
which the Grid Voltage could be set by the adjuster in a range from -240
to + 260 V. When the voltage is negative (use a range of -25 to - 240 V),
SE are repelled from the ETD detector and only BSE are detected.

LARGE FIELD DETECTOR (LFD)

This detector is used with the standard insert. The field of view is
unrestricted and the magnification range is identical to that of HiVac
mode (assuming no other pole-piece accessory is mounted).
The signal from the LFD contains more BSE information than the GSED
signal. The detector is ideal for general imaging; it is also the only
gaseous SE detector that can be used simultaneously with a BSED
Detector.

FIGURE 5-2 LFD AND ITS CONFIGURATION

Installing and Setting the LFD

The LFD plugs into the signal connector behind the conical lens. In some
cases the user is prompted for the PLA size. Select No Accessory in the
PLA Configuration dialogue or appropriate Cone if installed.
Note: 
After inserting the LFD, Preferences… / ESEM tab / Purge mode
changes to Automatic despite any previous selection. This ensures that
the proper chamber environment is achieved (see Chapter 3).

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Operating Procedures: Standard Detectors

GASEOUS SECONDARY ELECTRON

DETECTOR (GSED)
The GSED is integrated into a flexible printed circuit board and plugs into
the signal connector behind the conical lens. It is used for general wet
imaging and for high pressure imaging with auxiliary gases.
The overall image consists of a very pure SE signal with very little BSE
signal component, due to the detector design and chamber geometry.
This pure SE signal makes this detector best suited for resolution
imaging. The field of view is less than the LFD at the lowest
magnification. The lower magnification range is about 240× at 7 mm WD.

FIGURE 5-3 GSED AND ITS CONFIGURATION

Installing and setting the GSED

1. With your gloved hand, grasp the detector by the rigid connector end.
Hold it with the detector head facing towards you, and the yellow
Torlon ring facing up.
2. Insert the detector (gold fingers facing forward) into the connector
located at the back of the chamber, behind the conical lens. This is
made easier by inserting the right side of the detector in to the visible
portion of the connector, then rotating the detector into position.
A keyed connector position prevents the user from inserting the
detector upside-down.
3. Place the yellow Torlon ring of the detector head under the lens insert
and press the detector head up onto the insert. This requires little
force and can be done with one finger. The yellow Torlon seal should
be fully in contact with the lens.

FIGURE 5-4 THE GSED INSTALLED

Signal
Connector

Flexible
printed
circuit
board

Mounting
collar

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 Operating Procedures: Standard Detectors

Removing the GSED

Caution! 
DO NOT change the order of the following procedure! Otherwise
you can damage the detector.
1. Remove the detector head from the lens insert first. Do this by
catching a fingernail or thumbnail (of the gloved hand) on the FRONT
of the yellow Torlon ring and pull down (there is a shoulder machined
into the Torlon ring which is specifically designed for this purpose).
2. Pull the other end of the detector out from the connector.

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Operating Procedures: Capturing and Handling Single Image

Capturing and Handling Single Image

After obtaining a good image quality, the image could be paused and
saved. It is possible to save an image using the File menu or using the
Scandium database software (option) image saving function.
Setup the file name label and harddrive destination for the image to be
saved using the next available label / number prior to the capture
session. Set the databar information important for the archiving 
(see the Preferences… / Databar tab).
The conditions for a good image quality are:
• Slow scan speed (longer dwell time) of the beam.
• Select a pixel resolution from the drop down list box to suit the detail
in the image, i.e. no tearing pixelated edges.
• Increase the magnification at least 2× above the desired value, focus
and correct the astigmatism (using the reduced area), then return the
magnification back.
• Use the Videoscope to set the Contrast and Brightness accurately,
otherwise use the Auto Contrast Brightness procedure.
• Use Pause / Snapshot / Photo / Active Preset Snapshot / filtering
functions (see Chapter 3).

IMAGE TYPES
A computer perceives an image as a two-dimensional array of numbers
– bitmap. Each array element is called a pixel and is represented as an
integer value. Frequently, the pixel is represented as an unsigned 8-bit
integer in the range [0, 255], with 0 / 255 corresponding to black / white
and shades of gray distributed over the middle values. A 16-bit
representation produces up to 65 536 different shades of gray (it is not
possible to distinguish onscreen), which may be crucial for obtaining
accurate data in analysis.
The raw scanned image is always a greyscale bitmap. The colors are
possible to add digitally as a result of particular features. The UI is able to
display and save images with a various bit depth:
• The Greyscale 8 / 16 bit image offers 256 / 65 536 levels of grey.
Live / Averaged and Integrated images are scanned as 8 / 16 bit
ones. For the Mix quad images a selection between the 8 or 16 bit
mode is possible.
• The Color 24 bit image offers 256 levels of each primary color (red /
green / blue).
Digital colors coming from the Display Saturation feature, from the
Image Enhancement module / Color tab, from the Mix quad with color
mode set changes an image bit depth so there is no way to save it
without them. When user wants to obtain the image without these
color enhancements, it is necessary to turn off the respective UI
functions.
An image is possible to be saved with / without colored digital overlaid
graphics (Measurement and Annotation) (see the respective
checkbox in the Save As dialogue). Other types of overlaid graphics
over an image are never saved (icons, controls, etc.).

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 Operating Procedures: Capturing and Handling Single Image

Digital File Formats

The image captured can be saved in various digital formats, depending
on the resulting color and bit depth needed. Generally there is no reason
to save an image with a higher bit and color depth than available in an
original one. Over against saving an image with a lower bit and color
depth than available leads to the loss of information. The message is
displayed in this case onscreen.
• The TIF 8 / 16 – greyscale image type
• The TIF 24 file – color image type
TIF file contains active processing information, which could be utilized
for a databar setting (see the Preferences… / Databar tab).
• The JPG file is a compressed file format employing a lossy
compression algorithm resulting in the small file size with a little loss of
information, depending on the particular image appearance and the
compression level (factory preset to 80%). The 8 / 24 bit depth is
automatically selected when saving the greyscale / color image file.
• The BMP file is an un-compressed file format. The 8 / 24 bit depth is
automatically selected when saving the greyscale / color image file.

SAVING / OPENING / PRINTING

The following universal file handling functions could be used:

Image Capturing
1. Select the area of interest and set the Magnification, the Scan
condition, the image pixel Resolution and the Databar information
that are required in the saved image (see above).
2. Make the best image using any suitable method you are familiar with.
3. Use the Pause (F6) / Snapshot (F4) / Photo (F2) / Active Preset
Snapshot (Ctrl + F2) function. The scan makes one screen / quad
pass (or several passes when the number of integrated frames is
larger) and pauses.

Image Saving
• Save (Ctrl + S) stores the image to the predetermined location with
the last used filename including an incremental number.
• Save As… opens a dialogue for saving images (this provides an
opportunity to change the file name, its location, and the possibility to
save also Databar and overlaid graphics). Both functions can be linked to
the Snapshot / Photo function (see the Preferences… / Scanning tab).
• Save All... behaves the same way as Save As functionality, but
enables to save images from all four quads at once.
• Open… opens a single image file into the selected quad. The
dialogue displays, by default, the location used in the last Save As…
utilization.

Image Printing
1. Capture the image (see above) or open a saved one.
2. Click the File menu / Print… (Ctrl + P), the printer setup dialogue
appears so that the choice of printer and settings can be established
to print the selected quad.
3. Complete the print setup and click the OK button to activate the
printer and print an image.

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Operating Procedures: Recording Movies (Saving Multiple Images)

Recording Movies (Saving Multiple Images)

This function captures dynamic experiments performed with the

microscope and creates the digital video files (AVI). Up to 4 imaging quads
(not the optical one) can be recorded simultaneously with a synchronized
start. It is possible to switch between single and quad image window while
the video is recording. The movie has the following embedded features:
• Resolution 768 × 512 or 1536 × 1024
• Databar image optionally included in the video
• Average or Integration changeable during recording
• Scan speed changeable during recording
• Reduced area pauses recording of all quads
• Remaining time indicator
• Single frame TIF images recordable during video sequence
• Compressed AVI (*.avi) formats
• Start, Stop and Pause onscreen indicators
• Preferences set-up dialogue
Note: 
For the quad(s) with the Enhanced Image module / Color tab / Enable
check box ticked, the Movie recording is paused, the colored TIF files
are stored anyway if selected (see below).

MOVIE TAB PREFERENCES DIALOGUE

The Preferences… (Ctrl + O) / Movie tab provides two modules, one to
set-up conditions for timing (labelled Timer), the other to set-up save
conditions for the resultant movie (labelled File).

FIGURE 5-5 MOVIE PREFERENCES

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 Operating Procedures: Recording Movies (Saving Multiple Images)

Timer module
The parameters in this section can be changed when the digital video is
inactive, but are disabled during recording. The digital video is recorded
asynchronously to the scanning.
• The Movie check box – AVI (Digital Video) timer: 
After the Delay time, the image of each active quad is stored
immediately (even in the middle of the frame) as a new frame in the
video stream.
• The TIF check box: 
After the Delay time, images series of each active quad are stored at
the end of the running scan (the system waits) in TIF format.
• In the read only area additional information are given about the
number of stills (frames) per time unit (seconds, minutes).
If both TIF and Movie check boxes are ticked, AVI and also TIF files are
stored. In this case the AVI file is not reconstructed from TIF files, which
means the directly recorded movie can be different from the movie
reconstructed from TIF files.
Note: 
TIF files are better to save in many cases as they can be built into a
faster AVI and the databar display can be customized when building an
AVI file (see below). 
If both AVI and TIF are recorded, the AVI may be jerky due to delays
when writing TIF files to a disk. TIF delay must always be longer than or
equal to the Movie delay.

File module
Names of Movie [TIF] files are composed as follows: 
File name, (quad name), Numeric seed, [- series number].avi [tif]
For example: MovieName (Quad1) 015 [- 00023]. avi [tif] 
[The series number always has five digits form with leading zeros.]
• The File Name – a generic file name must be entered here, otherwise
the Movie tab cannot be closed. Do not use punctuation, dashes or
other non-alpha-numeric characters, otherwise the movie maker is
not able to build an AVI.
• The Save in – a path to an existing directory must be entered here,
otherwise the Movie tab cannot be closed. Use the Browse button to
find the location.
• The Numeric Seed – enter any number from 1 to 999 which is
converted to the three digit form with leading zeros. The numeric
seed is automatically incremented, after the recording has stopped,
or the video file size limit has been reached.
• The Video File Size – the maximum AVI video file size (lower than
2 000) in MB must be entered here, otherwise the Movie tab cannot
be closed. After reaching this size, the video file is closed and a new
one is automatically created, without interruption of the recording
process. A warning dialogue appears if the hard drive lacks sufficient
free space.
• The File Type – the list box with supported video compression format
types. Try to change the format if the resulting movie files are too big or
if the system is overloaded during the movie recording.
• The Record Databar check box allows the databar to be included in
the video (tif files).

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Operating Procedures: Recording Movies (Saving Multiple Images)

MOVIE PROCEDURE
The red dot button starts the recording of all active quads at the same
moment – no video / images are stored for paused quads. When a quad
is paused during the video recording, the storing of the video frames is
interrupted but the video streams keep synchronization for the next
recording.
When the red dot representing ‘Start’ is clicked, it turns to a red square,
representing ‘Stop’. Clicking the red square then stops the recording of
the video in all quads and closes all video files.
The red dot with the timer (displayed in the top right-hand corner)
indicates that recording is active in this quad. The Pause symbol
indicates that the record is running but the data from this quad are not
stored (the quad is paused).
The timer indicates the time estimation (in the hh:mm:ss format)
remaining to the end of the video. This is calculated from the average
disk space consumption and the disk free space.

Record Movie Procedure

1. Open the Preferences… / Movie tab. In the Timer module tick the
Movie or TIF check box and select the desired Delay time (the period
between stored frames).
2. In the File module fill in the File Name and give the Save in directory
path. Fill in the Numeric Seed value and the Video File Size. Select
the File Type and choose whether to record the databar with the
Record Databar check box.
3. Pause those quads which you don’t want to record. Set up the
imaging parameters in the live quad(s).
4. Select the File menu / Record Movie (a tick mark) or click the toolbar /
red dot button. When the scan resolution is higher than 1536 × 1024
the dialogue appears.

5. Choose either of the offered Resolution values at which the movie

starts to record.
6. Select the File menu / Record Movie again or click the toolbar / red
square button to stop the movie recording.

FEI MOVIE CREATOR

This is a separate program that creates a movie from a sequence of TIF
images. Click the Tools menu / FEI Movie Creator… to activate the
tabbed dialogues.
The following items are common for all tabs:
• The Databar Preview displays the databar created in the Databar tab.
• The Status displays the progress of movie creation process.
• The Create Movie button opens the File tab and starts the movie
creation process from the TIF files to a single AVI file.

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 Operating Procedures: Recording Movies (Saving Multiple Images)

• The Stop button stops the creation process.

• The Close button closes the FEI Movie Creator program.

File Tab

FIGURE 5-6 FEI MOVIE CREATOR TAB: FILE

• The Name Prefix – click the … button to browse the TIF files (with the
desired sequence prefix) directory. It is not necessary to choose the
first file in a row.

FIGURE 5-7 BROWSE DIALOGUE

• The Time Period – select the ms radio button to select a custom

timing for the movie playback. One may experiment (200 ms is good
for most movies to speed it up). Select the TIF Time radio button to
select a real timing for the movie playback.
• The Grey Movie button suppresses the colors in the resulting movie.
• From / To – enter the number of the starting / ending frame. This field
is filled automatically with the first / last frame available.
• Save in – enter the path where the AVI file should be saved. Click the
… button to browse it.
• File Name – enter the resulting AVI file name. This field is filled
automatically with the first image file name.

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Operating Procedures: Recording Movies (Saving Multiple Images)

Databar Tab
Settings made in this dialogue does not affect the databar or units
settings used in the UI.
Note: 
The Databar Preview does not show any item until you enter the File
tab / Name Prefix field.

FIGURE 5-8 FEI MOVIE CREATOR TAB: DATABAR

• The Available / Displayed items: lists – all items that can be entered
in the databar / are already present in the databar.
• > / >> (< / <<) buttons adds one / all item(s) from the Available list to
the Displayed list (removes one / all item(s) from the Displayed list
back to the Available list).
Since there is a finite amount of the databar space, the area expands
or contracts as other items are added to or removed from the
Databar. The item exceeding the allowable space is ignored.
• Move Up / Move Down / Top / Bottom buttons move a position up /
a position down / to the top / to the bottom in the Displayed list (a
position to the left / a position to the right / to the left / to the right in the
Databar Preview).
• The Label / Show Beam Icon / Micronbar check boxes set the
display of the appropriate items in the Databar. The Micronbar scales
to the magnification.
• The Units… button sets the Units of Measure / Pressure /
Temperature used in the movie Databar display.

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 Operating Procedures: Recording Movies (Saving Multiple Images)

Preview (tab)
Once the movie is set-up, opening the Preview tab automatically
displays the first image of the movie sequence.

FIGURE 5-9 FEI MOVIE CREATOR TAB: PREVIEW

• The Start / Pause / Stop button starts / pauses / stops the movie play
back. By dragging the adjuster one can run forward or backward
through the movie.

PLAYING A MOVIE
The AVI file movie can be played in the Windows Media Player or any
another more advanced movie editing program recognising the *.avi file
type.

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Operating Procedures: Stage Control

Stage Control

EUCENTRIC POSITION
Establishing the eucentric position is an important part of setting up a
sample for observation or modification.
At the eucentric position, the stage tilt and the beam axes intersect.
When the stage is tilted or rotated in any direction, this point remains
focused and almost does not shift. At the eucentric position, one can use
various system components in a safe and optimal way (e.g. GIS,
EDX…).
Eucentric position should be adjusted after loading any new sample, as
the sample loading clears all position information.
Note: 
For electron imaging of non-tilted sample the eucentric position
adjustment is not necessary. But it is still required to run the Link Z to
FWD procedure (see Chapter 3).

FIGURE 5-10 EUCENTRIC POSITION PRINCIPLE

Beam Beam

Eucentric position
Eucentric position
Point of interest
Point of interest

Stage
Stage Tilt

1) The point of interest is focused below the Eucentric 2) Tilting the stage moves the point of interest out of the
point (see 2). beam.

Beam Beam
Eucentric position 
Feature is at and Point of interest
eucentric position.

Stage
Stage Z adjustment

3) The point of interest is focused at the Eucentric point 4) Tilting the stage does not move the point of interest out
(see 4). of the beam.

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 Operating Procedures: Stage Control

Sample Top Surface Positioning

The distance between the observed sample and the stage rotation head
surfaces must be properly set to bring the stage to the eucentric position.
This procedure also prevents the specimen to touch the final lens when
moving the stage in the Z-axis direction.
With the standard specimen holder it is possible to move the sample (its
top surface) along the Z-axis up / down if required (holder movement).
This allows a flexibility to load large height specimens onto the stage.
50 x 50 mm Stages
1. Load a specimen onto the specimen holder.
2. Adjust the external Z coordinate as high as possible.
3. Put the Eucentric Position Adjuster on the stage base.
4. Bring the specimen top surface point to the 2 mm adjuster position by
turning the specimen holder internal screw. Lock the position with the
locking cone.
5. Close the chamber, and pump it.
6. Switch on the beam, focus the specimen top surface and run the Link
Z to FWD function (see Chapter 3). The WD is now recognised by the
system as the Stage module / Coordinates tab Z value.
150 x 150 mm Stages
1. Load a specimen onto the specimen holder.
2. Adjust the Z, so that the highest specimen point is approximately
10 mm below the lens.
3. Close the chamber, and pump it down.
4. Switch on the beam, focus the specimen top surface and run the Link
Z to FWD function (see Chapter 3). The FWD is now recognised by
the system as the Stage module / Coordinates tab Z value.
The Z coordinate can now be changed via the software Z control around
the eucentric position and further, but not less than 1 mm from the lens
for safety reasons.

Eucentric Position Setting Procedure

1. Apply the Stage menu / Auto Beam Shift Zero function.
2. Display the Window menu / Center Cross (Shift + F5).
3. Focus an image. Link Z to FWD and go to 10 mm WD.
4. Set stage tilt to 0°.
5. Using the Z-control, coarsely focus the image.
6. Set the magnification to 1000×, find a recognizable feature and center
it under the yellow cross by moving the stage.
7. Watching the feature, change the stage tilt to 10°. 
Using the Z-control, bring the feature back under the cross.
8. Change the stage tilt to -10°, and bring the same feature back under
the cross using the Z-control.
9. Change the tilt to 0°. The feature should not shift significantly. 
If the shift is > 5 µm, repeat steps from No. 6 to No. 9.

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Operating Procedures: Stage Control

SOFTWARE CONTROL
The Navigation page / Stage module controls the stage movements that
locate the position of the specimen by reference to coordinate points. It
consists of Map / Coordinates / Tilt Correction tabs.

Map tab
In the map area the stage schema is represented displaying all stored
locatable positions, which are listed in the Location list box for selecting.

FIGURE 5-11 MAP AREA ELEMENTS

2

7
9 6

3 5
4

TABLE 5-3 MAP AREA ELEMENTS

No. Function
1. Black +: mechanical stage center

2. Darker rim: the sample holder outline

3. Light grey dashed line: 

physical limit of the stage movement along X and Y axes

4. X / Y scroll bar: move the stage schema area in an X / Y

direction at different magnification factors

5. Magnification factor of the map area (1× – 100×)

6. Radar view: 
Black triangle: the moveable rotation angle controller 
Grey perpendicular lines: denote rotation position 
Grey +: stored positions as on the map

7. White × on a red background: a stored location with the

rotation noted by the black key position

8. Blue + in a red circle: actual stage position not stored

9. White + on a green background: indicates a stored position

highlighted in the location list.

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 Operating Procedures: Stage Control

Radar view
The small circle in the stage schema top right corner conveys the stage
rotation at any time by the black triangle and perpendicular lines position.
To rotate the stage, click the circle perimeter triangle &.drag it round and
release the mouse button at the desired position – the stage rotates
accordingly.
Location area
The Location list shows the Current Position and the Last Position
(the stage position before any movement) as default. When expanded, it
shows the positions list with a scrollbar.
Double-clicking anywhere in the circle area marks a new location (9) and
moves the stage to it.
The position selected becomes the actual active position and it is
highlighted in the list and also on the map (8).
Clicking a position name allows a user to edit it. Pressing the Enter key
or clicking a different item confirms the new name, pressing the Escape
key restores the old name.
• The Open button opens a stored Stage Map file (stg).
• The Save button saves a Stage Map file.
When closing the UI the system registry automatically keeps the
Stage Map file with the specific User name to be loaded after the log-
in procedure.
• The Clear button clears the existing Stage Map file including the
Location list.
It is possible to load / save stg file also with the use of File menu / Import
/ Export functions (see Chapter 3).
Map Menu
Right-clicking over the Map area, provides the drop down menu.

FIGURE 5-12 THE MAP DIALOGUE

• Clicking the Add current stage position item adds a new Location
list entry, using the actual active position. The new entry is named
Position X (X = 1, 2, 3…). If a name already exists (because a user
loaded a Map list from a Stage Map file), the value is heightened until
a unique name is obtained.
The Coordinates tab / Add button has the same functionality.
• Clicking the Update to current stage position item stores the
(edited) coordinate values under the selected name (an overwriting
confirmation dialogue appears).

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Operating Procedures: Stage Control

The Coordinates tab / Update button has the same functionality.

• Clicking the Remove selected position item deletes the selected
location(s) from the map and from the Location list.
The Coordinates tab / Remove button has the same functionality.
• Clicking the Magnification item provides menu allowing the Map
area magnification factor (5) to be selected. Scroll bars (4) appear if
necessary to move over the whole Map area.
• The Center view item brings the selected location to the center of view.
• When the Auto center on target item is ticked and the Magnification
factor is used, the active location remains in the center of view.
• The Show radar view item switches the radar view display in the
map area On / Off.
• The Zero radar view item resets the stage rotation to 0°, which is
represented by the black triangle 12 o’clock position.
• The Show notch item switches the blue triangle display in the map
area On / Off, giving a quick view about the stage rotation.
• The Stage location overlay item toggles the detector and chamber
door position display in relationship to a sample.
• The Display map in Navigation Quads item switches the stored
positions display in navigation images.

Coordinates tab
Three modes are possible via the list box:
• The Actual mode (default) displays actual position coordinates in the
edit boxes.
• The Target mode activates when clicking a stored position or when
editing a coordinate value.
• The Relative mode is used to move stage by a given value and to
repeat it several times if needed.
Clicking the Go To button drives the stage to a new location. This only
acts on just edited coordinates (with a tick mark). Hitting the Enter key
after editing of any coordinate value works as the Go To button short-cut.
Double-clicking a stored location moves the stage to the desired position
immediately.
During the stage motion the Go To button changes to the Stop button,
which stops the stage immediately.
Coordinates X, Y, Z, R, T
Edit boxes for X, Y, Z, R and T coordinates are filled with the selected or
actual position values. The value changed is automatically ticked.

Caution! 
Danger of hitting the pole piece! The Link Z to FWD procedure did
not pass (see Chapter 3). The red arrow next the Z axis alerts the
positive Z-axis stage moving direction is up. It means raising a
value in the Z axis edit box causes moving the stage up towards the
pole piece.
After running the Link Z to FWD procedure the symbol and the stage
moving direction changes. The black arrow next the Z axis indicates the
positive Z-axis stage moving direction is down.
The units of measure follow the Preferences… / Units setting, unless
the Stage menu / User Units function is active, in which case UU is
displayed for X and Y.
The software locks prevent inadvertent stage movement of selected
axes during particular applications. The edit boxes for locked axes are

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 Operating Procedures: Stage Control

disabled and the stage does not move in these directions. When any or
all axes are locked the Status module displays a closed lock instead of
an open one. By default all axes are unlocked.
When any axis is locked and the stage movement is required in that
direction (trying to move to the stored position), the warning dialogue
appears.
When the Compucentric Rotation check box is ticked, the R coordinate
operates as the Compucentric Rotation function.
Note: 
The R coordinate is permanently locked and its homing is disabled when
the heating or cooling stage is plugged in.

Tilt tab
When the appropriate check box is ticked, the function becomes active.
• The Dynamic Focus check box ticked – the focus automatically
changes as the beam scans from the image top to its bottom, trying to
follow the tilted specimen working distance change.
• The Tilt Correction check box ticked – the flat specimen
foreshortening compensation is on (in one direction, at a known tilt
angle, when the tilt axis is parallel to the stage XY plane).
Because the image is a two-dimensional representation of a three-
dimensional object, certain distortions occur. For instance, a square
grid image appears rectangular when you tilt the specimen. This
function corrects the aspect ratio and restores the square appearance.
• The Tilt Angle list box enables to choose between 2 modes.
In the Automatic mode the Tilt Angle is equal to the stage tilt plus
the Specimen Pre-tilt linear adjuster value (a Tilt Angle correction in
case the specimen is not parallel to the stage XY plane).
When in the Manual mode, the linear adjuster enables to manually
set the Tilt Angle from -90° to +90°. It is useful when the Dynamic
Focus with Automatic Tilt Angle does not give satisfactory results (or
cannot be used at all because the specimen is tilted in direction
different from the stage Tilt).
When switching from Automatic to Manual mode, the actual Tilt Angle is
not changed. When switching to Automatic mode, the Tilt Angle is set to
the actual stage tilt.
If the Dynamic Focus is on and the Tilt Angle is non-zero, an indicator is
displayed in the optical quad.
Notes: 
Both Dynamic Focus and Tilt Correction work properly only if the
specimen (scanned area) is tilted around the X-axis (in the same
direction as the stage Tilt). Therefore they cannot be used with Automatic
Tilt Angle in combination with a non-zero Scan Rotation. If the specimen
is tilted in a different direction, you have to align the tilt axis horizontally
using the Scan Rotation and then optimize the image focus by tuning the
Manual Tilt Angle.
Both functions are also disabled (check box cleared) in the Crossover
mode.
Due to the limited range of the dynamic focusing, the overall conditions
should be in certain limits. If the dynamic focus would be out of the
range, the checkbox becomes disabled. To enable it again, you can try
one or more of these actions: decreasing the Tilt Angle, increasing the
magnification or the working distance, decreasing accelerating voltage or
switching the Tilt Correction on (this helps especially at high tilt angles).

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Operating Procedures: Stage Control

Navigation Tab
Click the Get button to capture a selected quad imaging into the
Navigation tab. Drawing a green bordered box (by clicking & dragging)
inside it depicts an observed area from that point on.
By clicking & dragging the box inside the navigation image an observed
area could be changed (affecting the selected quad). By clicking &
dragging its boundary a box size could be changed, or it is also possible
to draw a new one.

STAGE RELATED FUNCTIONS

Stage Movements – Keyboard Shift

The stage can be moved by 80% / 40% of the field of view in
perpendicular direction by pressing / Shift + pressing the appropriate
keyboard arrow key.

Stage Movements – Track Mode

This function allows continuous directional stage movements at a
variable speed (see Preferencess… / General tab / Switch sample
tracking on mouse wheel click item):
• The Wheel-click & drag mode – the yellow dot appears onscreen in
a selected imaging quad at the mouse cursor point. Move the mouse
to the direction intended for an observation – a yellow arrow appears
onscreen denoting the direction opposite to the stage motion. The
motion speed raises with the distance between the arrow and the dot,
the direction can be changed by moving the mouse. When you come
to the place of interest, release the mouse wheel – the action stops.
• The Wheel-click & move mode – the mouse wheel does not need to
be held, just click the desired direction to start the Track motion and
click again to stop it.
In the optical quad clicking the mouse wheel activates the stage Z
movement, which can be seen live.
• Wheel-clicking & dragging the mouse up / down moves the stage
up / down (Z-coordinate).
• Ctrl + Wheel-clicking & dragging the mouse left / right tilts the stage
in positive / negative direction.
The direction is indicated by a yellow arrow, either pointing up / down
from the horizontal line or left / right from the vertical line.

Stage Movements – Get Mode

This function brings an image point of interest to the screen center.
Double-click an image point. The object is mechanically centered
onscreen by moving the stage, which is suitable for lower magnifications.
When working at higher magnifications, beam shift could be also
employed (see the Preferences… / General tab). In this case the object
is electronically centered onscreen by moving the electron beam. When
the beam shift comes to a limit in any direction, its value resets and the
necessary stage movement adapts the observed point position.

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 Operating Procedures: Stage Control

Beam Shift
When you want to employ the beam shift only (which is suitable for
higher magnifications), shift + click an image point. Drag the Hand cursor
to move the imaging area in any direction.
When the limit of the beam shift has been reached, either the Stage
menu / Auto Beam Shift Zero or the Beam Shift Reset function needs
to be applied (see Chapter 3). In this case the beam shift is reset and the
observed point position is adapted by the stage movement.
Releasing the mouse button stops the action.

xT Align Feature…
This utility is designed specifically for long features, extending off the
screen at the magnification required for an observation. It applies the
mapping process bringing the long feature either to the horizontal or
vertical axis to make the navigation easier. This can be performed at any
point within the stage field limits and takes into account the stage rotation
offset.
Note: 
xT Align Feature works best at the eucentric position (see above).
Longer distances result in a greater accuracy.

Caution! 
Watch the obstacles significantly extending from the sample plane,
as these may interfere with equipment under the lens.
1. Select a long feature of interest on the sample.
2. Click the Stage menu / xT Align Feature… Choose either Horizontal
or Vertical, which relates to the desired final sample orientation. Click
the first point along the feature, the P1 coordinates update.
3. Click the second point along the feature, the P2 coordinates update.
Right-clicking anywhere in the imaging area deletes points, enabling
to define them again.

4. Drag any point to change its position, if needed. Click the Finish
button to orientate the feature either Horizontal or Vertical, as
selected previously. Click the Cancel button any time to cancel the
function.

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Operating Procedures: Stage Control

Scan Rotation Align Feature

This procedure helps to navigate along a feature that is rotated
disadvantageously. Unlike the xT Align Feature… the rotation is
performed by scan coils instead of the stage.
1. Click the Stage menu / Scan Rotation Align Feature. Choose either
Horizontal or Vertical, which relates to the desired final sample
orientation. Click the first point along the feature, the P1 coordinates
update.

2. Click the second point along the feature, the P2 coordinates update.
Right-clicking anywhere in the imaging area deletes points, enabling
to define them again.
3. Drag any point to change its position, if needed. Click the Finish
button to orientate the feature or click the Cancel button any time to
cancel the function.

Compucentric Rotation (F12)

Clicking the Stage menu / Compucentric Rotation places a green circle
in the image window. The green triangle on its perimeter denotes, by its
position, the sample rotation relative to its original position when
mounted on the stage. Initially, this is in the 12 o’clock position. Click &
drag it around the circle to choose a new sample rotation.
The readouts displayed at the image window bottom provide information
about the Actual Rotation (original position) and the Target Rotation
(the selected position).
Releasing the mouse updates the stage position to bring the original field
of view (rotated to the Target Rotation position) onscreen. With the
sample at the eucentric position this can be performed at any sample
point irrespective of the mechanical stage center.
Clicking the written angles around the circle perimeter (0° / 90° / 180° /
270°) or the perimeter anywhere drives the stage to that rotation position
and the green triangle updates onscreen. Clicking the framed + / – sign
increases / decreases the rotation angle by an incremental value.

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 Operating Procedures: Stage Control

User Units
Clicking the Stage menu / User Units activates user defined units as the
basis of the stage coordination system. A tick mark appears next to the
label and UU in the Stage module / Coordinates tab next to the X and Y
value box. The stage coordinate system reverts to the last defined user
unit configuration.
Define User Units…
This procedure assigns user-defined points to stage points. The stage
coordination system can be anchored to either 1, 2 or 3 points,
depending on the sample management or application.
For example, if you choose a (0,0) position, you can drive the stage
relative to that origin using user defined units (0,1 / 1,0 points), which
may equal to some repeated sample structures etc.
Particular dialogue buttons
• Finish: ends the procedure at the point(s) 1 / 2 / 3 just defined.
• Details: displays the resulting coordinates with the possibility to
browse them (Go to button) and edit values.
1. Select a sample surface feature and view it at an appropriate
magnification to check its relation to other structures.
2. Click the Stage menu / Define User Units… A Start dialogue
appears. Click the Define New User Units radio button.

Redefine User Units – for changing or updating User Units.

Redefine User Units with Shift – as above with the Beam Shift.
Reset User Units so that they are equal to the Stage Units
Show how User Units are now defined – displays the actual
definition with the possibility to move the points step by step.
3. Click the sample user point (0,0), its coordinates appear in the
Details… module.
4. Repeat the step 3 for the sample user point (1,0).

5. Repeat the step 3 for the sample user point (0,1).

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Operating Procedures: Stage Control

6. Check the Finish if needed or Details the procedure.

Using 1-, 2- or 3- Point Alignments

TABLE 5-4 ALIGNMENT TYPE DIFFERENCES

Use 1-Point Alignment 2-Point Alignment 3-Point Alignment

Major Use Aligning to new point Aligning the stage axes with Transforming to nonstandard
directly offset from the specimen X-Y orientation units on dies or RAM arrays;
the existing location to correct for any distortion correcting for any distortion

Change in Scale None Scales the axes together X can be scaled differently from Y

Change in None Rotates both axes with a X and Y orientation can be

Orientation fixed 90° angle between axes different

Sample Navigation (Ctrl + N)

The Stage menu / Sample Navigation software feature enables to
navigate along the sample surface when the field of view is smaller than
desired (limited by an aperture for instance). For this purpose various
sample Navigation images can be dynamically and independently selected,
regardless of its actual content and status (paused, saved, loaded).
As soon as the selected quad is paused, the Sample Navigation icon
appears in the upper right quad corner to indicate the functionality.
A green rectangle showing the actually selected field of view (in the
selected quad) appears with the size corresponding to the magnification.
In quad(s) using Sample Navigation the Selected Area Zooming and the
Get features could be used.
To employ the Sample Navigation there are three possible techniques to
acquire (or to use) a Navigation image: Navigation Montage... / 
Navigation Alignment... / Nav-Cam (option – see Chapter 7).
Navigation Montage...
Set the Target HFW (Horizontal Field Width) range, which influences
information fields: the number of tiles – Map Size, the Estimated Time for
the procedure completion and the HFW of each tile – Single Image HFW.
The Use actual HFW check box ticked causes the system does not use
automatically the HFW according to the hardware configuration and sets
the user one. This is convenient when the image corners are rounded
and imaging does not cover an entire area.
The Switch of the beam when finished check box is convenient to use
in case a large Target HFW and long dwell times are used to capture the
Navigation image, because the process could take a significant time to
complete.
After a process completion the Sample Navigation is then automatically
set on.

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 Operating Procedures: Stage Control

Navigation Alignment...
This procedure in comparison to the Navigation montage or Nav-Cam
(option) enables to use any loaded or paused Navigation image, which is
calibrated according to the live Reference image.
Follow instructions given within the process and calibrate 4 image points.
If 2 points are sufficient for desired purposes, click the Compute 2pt
alignment button to finish the process after setting 2 align points.

FIGURE 5-13 NAVIGATION ALIGNMENT

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Operating Procedures: Stage Control

Scan Rotation (Shift + F12)

This function activates the onscreen tool to rotate the scan and align the
image. Because it is solely a scan coil function, it has no effect on the
stage movements. It is used to orient the image relative to mechanical
rotation and detector direction.
Clicking the Scan menu / Scan Rotation places a green circle in the
image window. The green triangle on its perimeter denotes, by its
position, the sample rotation relative to its original position when
mounted on the stage. Initially, this is in the 12 o’clock position. Click &
drag it around the circle perimeter to choose a new sample rotation.
The readouts displayed at the image window bottom provide information
about the Actual Rotation (original position) and the Target Rotation
(the selected position).
Clicking the written angles around the circle perimeter (0° / 90° / 180° /
270°) or the perimeter anywhere drives the stage to that rotation position
and the green triangle updates onscreen. Clicking the framed + / – sign
increases / decreases the rotation angel by an incremental value.

FIGURE 5-14 SCAN ROTATION

The smaller circle in the top right of an optical quad remains onscreen
when the Scan Rotation angle is different from 0°.

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 Operating Procedures: Measurement and Annotation Functions

Measurement and Annotation Functions

The Processing page / Measurement / Annotation functions give

a user many capabilities to measure distances, angles, diameters and
areas as well as locating and labelling items that are of significant
interest on the sample area.

TOOLS
Selected measurement or annotation tool is displayed as the tool icon.
Clicking the icon activates / deactivates the tool (the active one is
highlighted). Clicking the arrow next the icon symbol opens the list of
available tools to choose. The appropriate icon is shown from that time
on and the item can be drawn on screen. The drawn items are listed in
the list box.
• The Measurements enable to gain dimension information about a
specimen feature by overlaying it with a measurement graphic. By
changing the magnification these graphic elements resize
accordingly.




The Intensity Profile delineates the imaging profile across a freely

selected line.





• The Annotations enable to graphically label items of interest.

• The Text enables to add further information.
• The Trash can button deletes selected item(s).

Property Editor
enables to change a property of a selected Measurement / Annotation /
Text graphic by a selection from the drop down list or by a direct editing
of a text or a value.

Shape Creating
1. Choose the suitable Measurement / Annotation graphic tool.
2. Draw the graphic over the area of interest. This can be done by:
– clicking & dragging the cursor from the top left to the bottom right
corner of the rectangle shape.
– SHIFT + clicking & dragging: the shape starts to grow from the point
where you have clicked as from the center.
3. Choose the Text symbol and then just click where you require a text
in the image. Type the text into the Property editor text field. Click the
text or press the enter key to confirm it and the text appears
onscreen.

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Operating Procedures: Measurement and Annotation Functions

Shape Editing
Once a Measurement or Annotation symbol has been drawn, it can be
modified. Selected graphic is denoted by the addition of resizing
handles to the graphic outline (use pointer cursor).
Size and position the graphic correctly over the area of interest.
A number of other choices are available in the Property editor for each
graphics drawn.
• Move / Rotate graphic: click the cursor inside the boundary of the
pattern / in the vicinity of a corner & drag it (move / rotate cursor).
Pressing the Ctrl + Alt keys while hitting any arrow key moves the
pattern in an arrow direction for a fixed distance.
• Resize graphic: click & drag the resizing handle until the desired size
is reached (horizontal / vertical / diagonal resizing cursor). Pressing
the Ctrl key while dragging forces dimensions to be changed
proportionally. Precise dimensions could be also entered in the
Property editor.
• Selecting all Items (in a selected quad): press Ctrl + A.
• Delete selected Item(s): click the Trash can icon or press the
Delete key.

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6 MAINTENANCE

This section describes the procedures necessary for the maintenance of

the microscope that can be carried out by the Supervisor / User. For the
User maintenance is at a minimum due to Gun and Column design and
the long uptime expected from this class of instrumentation. Therefore
the more complicated maintenance is normally contained in a service
contract to be performed by a qualified service engineer.
At the user level items such as the following can be maintained:
• Cleaning Procedures Overview
• Standard Insert
• Wehnelt cap and the Filament
• Anode Assembly
• Column liner and Apertures
• Gaseous Detectors
• Stage Maintenance
• Refilling the Water Bottle
• Pre-Vacuum Pump Maintenance
• Troubleshooting

Caution! 
- read Chapter 1 (Safety and Handling) before proceeding with any
maintenance. 
- Parts that operate in vacuum should be handled carefully using
clean powder-free gloves. Parts not in use should be stored in
suitable containers or packed in aluminium foil. 
- the EDX window (if present) is very fragile and must be
protected from air burst or vacuum turbulence. It is
recommended to remove the detector before major cleaning
activities.
Note: 
Gas back fill (N2) should be maintained while the specimen chamber is
at ambient pressure. However, to avoid gas waste it is recommended
that the chamber should be left vented no longer than necessary.

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Maintenance: Cleaning Procedures Overview

Cleaning Procedures Overview

Frequency of cleaning is, in most cases, determined by necessity due to

poor image quality or gross astigmatism level. Recommended cleaning
procedures are given below for parts which operate in vacuum and which
are subject to possible contamination.

LIST OF APPLIED CLEANERS

• De-ionized or distilled water – H2O
• Ethanol – C2H5OH
• Ethanol p/a (Pro Analysis: 99.8% pure) – C2H5OH
• Isopropanol
• Neutral pH cleaning fluid (soap solution)
• CIF* or SOFT SCRUB (fine abrasive household cleaner) 
or 0.05 µm alumina powder

TABLE 6-1 HOUSEHOLD CLEANERS

Country Name

Austria CIF

Australia CIF

Finland CIF

France CIF

Germany CIF

Italy CIF

Japan CIF

Netherlands CIF

Switzerland CIF

UK CIF

USA Soft Scrub

WAR N I N G ! 
The cleaning solvents ethanol and isopropanol are highly
flammable! Do not use open flames and do not smoke while
cleaning. Ventilate the room properly.

CLEANING COLUMN PARTS

All column parts are polished before the instrument is delivered. For this
reason only occasional light polishing is required to remove
contamination that may build up on components in the column and
specimen chamber as part of normal operation. Any part that is exposed
to the electron beam should be highly polished, and free of
contamination and / or scratches that can charge and thus degrade the
imaging.

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 Maintenance: Cleaning Procedures Overview

Parts that can be removed by the general Supervisor / User and polished
include the following:
• GSED / LFD components

Caution! 
Gold plated parts should not be polished with abrasives.

MATERIALS AND TECHNIQUE

To polish components, place a lint-free cloth on a flat surface (a glass
block is ideal) and apply a small amount of Soft Scrub or CIF and distilled
water to the cloth.
Place the part to be cleaned on the polish and rub with a circular motion
until all contamination has been removed. For inner surfaces, use a
cotton swab or wooden dowel as an applicator. A toothpick can be used
for small holes.
Lint-free nylon (not cotton) or latex surgical gloves should be worn while
handling parts to avoid contaminating just-cleaned surfaces. Tweezers
should be used to hold small parts.
After the part has been polished, remove the Soft Scrub/CIF cleaner by
washing in hot water. Inspect the part under a stereo microscope at 20×
magnification to ensure that there is no remaining contamination or
polish residue. Wash the part in de-ionized or distilled water in a beaker
with an ultrasonic cleaner for several minutes.Transfer the part to a clean
beaker with alcohol or isopropanol and clean ultrasonically again for
several minutes.
Note: 
Do not use an ultrasonic bath to clean the GSED or LFD detector.
When the components are dry (a compressed air ‘duster’ can speed
drying), reassemble and return to the column. If a part is stained, heat it
with hot water and immediately rinse with alcohol and dry using
compressed air.

Cleaning Tips
Parts exposed to the electron beam require periodic polishing. This will
ensure maximum performance of the instrument for many years.
Do not use metal polishes such as POL or WENOL to clean parts as
these can leave outgassing material. Be aware that threaded surfaces
should not be polished as these do not have contact to the beam and are
a source of outgassing if polish is trapped. Wash threads with alcohol or
isopropanol if absolutely necessary.
After cleaning, inspect all parts for residue and stains using a light
microscope.
Down time can be reduced by purchasing detector assemblies and
having them cleaned and stored in a safe place, where they can be
ready to be installed into the microscope.

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Maintenance: Accessing the Column

Accessing the Column

For Tungsten (W) systems the column opens at the emission chamber to
allow access to the Wehnelt assembly, anode assembly and liner tube
with apertures.

OPENING THE COLUMN

1. Switch off the filament current and the high voltage by clicking off the
Beam On button (the color changes from yellow to grey). The
emission will be reduced to zero.
2. Select the Vacuum module Vent button. This switches off the pump
system and admits air or nitrogen into the chamber and column after
confirmation.
3. When the column and specimen chamber have reached ambient
pressure, lift the upper part of the column using the lever until the
mechanical stop is reached. While holding it in this position, rotate a
quarter turn counter-clockwise. After releasing the lever the upper
part will stay in detent position. The Wehnelt assembly is now outside
the emission chamber and is grounded by the grounding contact.
Note: 
If venting with nitrogen, it is recommended to have a continuous flow of
nitrogen while the column is at ambient pressure. This can be done by
clicking the Vent button again when the nitrogen supply has stopped
automatically. Once components have been removed for maintenance,
the column should be closed again until the components are ready for
installing.

CLOSING THE COLUMN

1. Before closing the column, check that the o-ring seal between the two
parts is free of dust, hairs or other irregularities that might cause
deterioration of the vacuum.
2. Using the lever, rotate the upper part of the column clockwise to
position it over the lower part. Carefully lower the upper part in such a
way that it fits on top of the O-ring seal located in the lower part of the
column.
3. Select the Vacuum module Pump button. The color of the button
turns from grey to yellow. The automatic sequence returns the system
to the appropriate pressure condition.

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 Maintenance: Wehnelt cap and Filament

Wehnelt cap and Filament

COMPONENTS
The Wehnelt assembly consists of the following parts:
• The Wehnelt cap (1a) with a central hole called the Wehnelt
aperture (1b). This cap is fitted onto the upper part of the Wehnelt
cylinder (2a) using a bayonet catch mechanism.
• The upper part (2a) of the Wehnelt cylinder in which the screws (2b)
are located.
• The middle part (3a) of the Wehnelt cylinder in which the Filament
base (4a) is located.
• The lower part (5a) of the Wehnelt cylinder with an engraved scale
(5b) and arrow (5c).
• The filament securing ring (7a).

FIGURE 6-1 PARTS OF THE WEHNELT CYLINDER

Caution! 
All the parts described operate in vacuum and should therefore be
handled carefully using clean gloves, and stored, when not being used,
in suitable containers or packed in aluminium foil.

REMOVING THE WEHNELT ASSEMBLY

The Wehnelt assembly is held in position inside the holder by a spring
ring. To remove it, grasp the Wehnelt assembly at the circular groove
using the thumb and fingers of one hand. Apply a force sufficient to
overcome the spring pressure in a downward direction, thus detaching
the Wehnelt assembly. Lower the upper column back down to keep the
emission chamber free of airborne dust.

WA R N I N G ! 
If the microscope was used for imaging recently, the Wehnelt could
be very hot. To handle, use caution and wear gloves made of
appropriate heat resistant material, or wait for the Wehnelt to cool.

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Maintenance: Wehnelt cap and Filament

REMOVING THE FILAMENT

1. Place the Wehnelt assembly in the plastic carrier such that the lower
part (5a) of the Wehnelt cylinder can no longer be rotated with respect
to the tool. This makes mutual rotation of the two pieces easier when
wearing gloves.
2. Rotate the upper part (2a) of the Wehnelt cylinder 3 scale divisions
counter-clockwise (in the direction opposed to the arrow (5c)). In this
way the filament is retracted from the Wehnelt cap (1a).
3. Using the special screwdriver (6), loosen the three screws (2b) by
turning them counter-clockwise over half a turn. This unlocks the
bayonet catch so that the Wehnelt cap (1a) can be removed.
4. Unscrew the filament securing ring (7a) using the special tool (8) and
remove it from the upper part of the Wehnelt cylinder. The filament
(4a) is now free and can be removed and replaced.

CLEANING THE WEHNELT CAP 

AND FILAMENT SECURING RING
After a period of operation, an evaporated film from the emitter can be
observed on the inside of the cap and around the Wehnelt aperture. After
2 or 3 filaments the Filament securing ring also becomes discolored, this
can also be cleaned.
1. Remove the film using cotton wool on the end of a wooden stick,
dipped Soft Scrub/CIF and distilled water.
2. Rinse with tap water.
3. Clean in an ultrasonic cleaner for 5 minutes using distilled water in the
beaker.
4. Transfer to a new beaker.
5. Clean in an ultrasonic cleaner for 5 minutes using alcohol p/a. or
isopropanol.
Caution! 
Do not place parts together in the beakers. Wash separately, as damage
can occur to the metal surfaces.
6. First blow dry with a compressed air, then dry thoroughly under an
infra-red lamp (15 min. to 1 hr.) at a temperature of between 80°C and
100°C. Do not bake in an oven.
7. Inspect cleanliness using a light microscope.
Note: 
It is not necessary to clean the remainder of the Wehnelt assembly
unless severe contamination of the gun chamber has occurred due to
another problem.

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 Maintenance: Wehnelt cap and Filament

INSTALLING FILAMENT, WEHNELT CAP

Caution! 
When mounting a filament, great care should be taken in handling it,
particularly when adjusting the filament-to-Wehnelt cap distance. If the
filament tip is allowed to touch the Wehnelt cap, it can very easily be
damaged.
1. Locate the filament unit (4a) in the body of the middle part (3a) of the
Wehnelt cylinder, ensuring that the slot on the filament base (4b)
engages with the pin (3b).
2. Screw down the filament securing ring (7a) with a spring washer to
secure the filament. The ring should be finger-tight only. Too tight a fit
might cause the base to crack when heated up during use.
3. Fit the Wehnelt cap (1a) onto the upper part (2a) of the Wehnelt
cylinder using the bayonet-catch. This can only be done in the correct
orientation.
Note: 
Since it might be necessary to clean the Wehnelt aperture, it can be
useful to have one spare Wehnelt cap in store. This enables the user to
mount a clean Wehnelt cap without losing operating time.

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Maintenance: Wehnelt cap and Filament

SETTING THE FILAMENT POSITION

FIGURE 6-2 ADJUSTING THE FILAMENT POSITION

1. Using a binocular microscope equipped with an illuminated support

platform, centre the filament tip in the Wehnelt aperture (1b) by
carefully shifting the Wehnelt cap (1a) over the upper part (2a) of the
Wehnelt cylinder.
2. Carefully turn the three screws (2b) finger-tight to secure the Wehnelt
cap with respect to the Wehnelt cylinder.
3. Turn the upper part of the Wehnelt cylinder clockwise (in the direction
of the arrow) over 1 division with respect to the lower part, to move
the filament tip towards the Wehnelt cap. Check that the filament tip
does not touch any part of the Wehnelt cap. If necessary repeat steps
1 and 2 with care.
4. Continue this procedure until the tip of the filament is level with the
front face of the Wehnelt cap. This can be observed clearly by tilting
the Wehnelt assembly and viewing the Wehnelt aperture obliquely.
5. Turn the upper part of the Wehnelt cylinder counter-clockwise (in the
direction opposed to the arrow (5c) until the tip of the filament is set to
a position between 0.2 and 0.3 mm below the front face of the
Wehnelt cap. 
This can be measured using the scale (5b) on the lower part of the
Wehnelt cylinder. Each division represents 0.05 mm.
6. Recentre the filament tip if necessary (see steps 1 and 2 above).

INSTALLING THE WEHNELT ASSEMBLY

Lift and swing away the gun head assembly, using the handle provided,
so that the Wehnelt can be repositioned. Replace the Wehnelt assembly
inside the holder attached to the upper part of the column. Ensure that
the slots on the assembly engage with the pins inside the holder. A small
force, resulting in a ‘click’, is required to overcome the spring pressure.
Close the top of the column.
Pump down the system using the Vacuum module Pump button. If the
vacuum status is not PUMPED (green icon) within 10 minutes, the gun o-
ring may need to be reseated or replaced.
Column alignment may be required after this procedure.

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 Maintenance: The Anode Assembly

The Anode Assembly

COMPONENTS
Figure 8-3 shows the basic components of the anode assembly. To
access the anode assembly see above.

FIGURE 6-3 THE ANODE ASSEMBLY

Extractor Electrode Extractor
Electrode Screw
Spring Loaded Ball (2 pcs.)

Anode Body Retaining Screw

Access Hole (2
Ceramic Insulator (3
pcs.)
pcs.)

Slotted Holes for Spring Loaded

retaining Screws Ball

Caution! 
The parts described operate in vacuum and should therefore be handled
carefully, using clean gloves and stored, when not being used, in suitable
containers or packed in aluminium foil. Under no circumstances
should the Anode Assembly be dismantled as it requires factory
alignment and sealing.

REMOVING THE EXTRACTOR ELECTRODE

It is not necessary to remove the entire anode assembly if only the
Extractor Electrode needs to be cleaned. It can be removed separately
from the complete Anode Assembly. To do this, remove the two Extractor
Electrode screws using the anode tool (a 2.5 mm hex wrench can also
be used for this), then remove the Extractor Electrode. The anode body
will remain in the column.

FIGURE 6-4 THE ANODE TOOL

CLEANING THE EXTRACTOR ELECTRODE

To clean the extractor electrode, use the same instructions given for the
Wehnelt Cap (see above).
A 500 µm aperture is located in the extractor electrode and is fixed with a
c-clip. This aperture should be closely inspected and cleaned or replaced
as needed. See the text with Figure 8-8 (Removing/installing Apertures)
for instructions on mounting apertures with a c-clip.

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Maintenance: The Anode Assembly

REPLACING THE EXTRACTOR ELECTRODE

With dust free gloves replace the EXTRACTOR ELECTRODE onto the ANODE
BODY locating the 2 screw holes. Replace the two EXTRACTOR ELECTRODE
SCREWS using the ANODE TOOL (a 2.5 mm hex wrench can also be used
for this). With the Wehnelt in place close the column.
Pump down the system using the Vacuum module Pump button. If the
vacuum status is not PUMPED (green icon) within 10 minutes, the gun o-
ring may need to be reseated or replaced.
Column alignment is required after this procedure.

REMOVING THE ANODE ASSEMBLY

The following Anode removal and cleaning is a Service Engineer level
procedure unless the Supervisor / User has received specific
maintenance training. The procedures start with the complete Anode
Assembly removal.
1. To remove the entire anode assembly (i.e., to access the column
liner), loosen, but do not remove, the two ANODE ASSEMBLY RETAINING
SCREWS using the ANODE TOOL shown in Figure 8-4 (a 2.5 mm hex
wrench can also be used). The screws are at the base of the
assembly and are accessible through the two RETAINING SCREW
ACCESS HOLES in the top of the assembly.
2. Grasp the anode assembly with a gloved hand, gently push, then
twist counter clockwise until it stops and pull up.

Anode Body
The anode body does not require regular cleaning. If cleaning the anode
body becomes necessary, clean only those areas near the beam path
that require cleaning. Use a minimal amount of cleaner, and a minimal
amount of liquid, and try not to wet the three porous ceramic insulators
while rinsing. If the ceramic insulators are cleaned, bake the anode
assembly in a clean oven for five hours (or overnight) at 60C (140 F).

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 Maintenance: The Anode Assembly

INSTALLING THE ANODE ASSEMBLY

Ensure that the liner tube along with its apertures and upper o-ring have
been correctly installed.
Figure 8-5 shows the inside of the column, looking down in from the top.
Refer to this picture for the following instructions.

FIGURE 6-5 INSTALLING THE ANODE ASSEMBLY

Gun Chamber Interior from the Top

HV feedthrough

Spring loaded ball contact

Anode Assembly

Retaining screw access hole

(2 pcs.)

Turn Anode Assembly CW.

The spring ball makes contact
with the HV.

1. With a gloved hand, place the anode assembly into the gun chamber
so the spring loaded ball contact is near the HV feedthrough and align
the slotted holes with the retaining screws on the bottom of the
chamber.
2. Push in and twist the anode assembly clockwise to lock it into the
place. The spring loaded ball contact should rotate into position
against the HV feedthrough. Use the anode tool to tighten the
retaining screws. With a Wehnelt installed close the column.
3. Pump down the system using the Vacuum module Pump button. If
the vacuum status is not PUMPED (green icon) within 10 minutes, the
gun o-ring may need to be reseated or replaced.
A column alignment should proceed after this procedure.

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Maintenance: The Column Liner and Apertures

The Column Liner and Apertures

COMPONENTS
The following Column Liner removal and cleaning is a Service Engineer
level procedure unless the Supervisor / User has received specific
maintenance training.
The Column liner tube contains four apertures:
• A - 500 µm platinum aperture mounted in a holder at the top
• B and C - two 1.0 mm spray apertures in the middle
• D - open-type spray aperture at the base
The aperture tool is used to install the apertures at the correct positions
inside the tube. The column liner tool is used to remove and install the
column liner. Instructions are given in the following sections.

FIGURE 6-6 LINER TUBE, APERTURES, TOOLS

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 Maintenance: The Column Liner and Apertures

REMOVING THE LINER TUBE

1. Vent the system and remove the anode assembly (see above).
2. Insert the COLUMN LINER TOOL into the end of the liner tube and tighten
the PLUNGER KNOB.
3. Raise the tube carefully until it is clear of the column. The upper
COLUMN LINER O-RING should come out with the tube. If it doesn’t,
remove the o-ring from the gun chamber.
4. Loosen the plunger knob to remove the column liner tool from the
tube.

FIGURE 6-7 REMOVING THE COLUMN LINER TUBE

Column
Liner
Tool

Plunger
Knob

Column
Liner
o-ring

New column
Cap

Removing Apertures from the Liner

Mounting positions are critical and the following instructions should be
carefully followed. The apertures are removed and installed using the
APERTURE TOOL.

Extract the apertures by inserting the APERTURE TOOL into the lower
(tapered) end of the liner tube and pushing it forward as far as it will go.
The apertures should slide out easily.

Removing Aperture (A) from Holder

1. Place the aperture holder with its open slotted end on a flat surface
and grasp it firmly with one hand.
2. Insert one blade of a pair of needle-pointed tweezers under the 
c-clip, making use of the slots in the holder, and then carefully pull out
the c-clip.
3. Remove the aperture either by lifting out with the tweezers, or by
inverting the holder over filter paper, a Petri dish, or other suitable
surface.

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Maintenance: The Column Liner and Apertures

PLATINUM APERTURES CLEANING

• Method 1:
Heat the aperture (held in special tweezers with platinum points) in a
clean gas flame until red-hot (for 4–20 seconds). Take care that the
aperture does not melt or become stuck to the tweezers.
• Method 2:
Connect a V-shaped molybdenum foil boat (about 2 cm long) across
the low voltage / high current contacts of a Vacuum Evaporator unit.
Use a pressure of 1.3x10-3 Pa (1x10-5 Torr) and heat until white hot
to flash decontaminate. Do not allow the Vacuum Evaporator to
contact the atmosphere until the foil boat is cool. When the aperture
has cooled down, place it on the foil, vacate, and reheat the foil to red
heat on the aperture (for 4–20 seconds). Take care that the aperture
does not melt or become stuck to the foil. Again, do not allow the
Vacuum Evaporator to contact the atmosphere until the foil boat and
aperture is cool.

Caution! 
Do not attempt to clean apertures just by washing in solvent, as this can
have an adverse affect just by shifting contamination back onto the
aperture. 
Polishing scratches the soft material and makes the aperture unusable
for high resolution. All apertures must be cleaned and must not have
scratches at the center hole. The top aperture should not have any
scratches or defects.

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 Maintenance: The Column Liner and Apertures

INSTALLING APERTURE (A) IN HOLDER

FIGURE 6-8 REMOVING / INSTALLING APERTURE A

1. Place the aperture holder with its open slotted end on a flat surface
and grasp it firmly with one hand.
2. Using tweezers, carefully insert the aperture, sharp edge uppermost,
into the seating on the upper end of the holder.
3. Again using the tweezers, insert the c-clip into the tube of the injector
provided.
4. Depress the plunger slightly until the plane of the c-clip within the tube
is approximately at a right angle to the axis of the tube. Release the
plunger.
5. Place the injector vertically into the aperture holder, so that the tube
rests on top of the aperture.
6. Depress the plunger to push out the c-clip. The pressure must be
continued while retracting the body of the injector so that the c-clip
remains in place in the holder seating.
7. Remove the injector and check that the aperture is properly clamped
by the c-clip. This can be done either by inverting the holder over a
Petri dish and tapping lightly; or by observing the position of the c-clip
with a magnifying glass.
Note: 
Always check the mounted aperture under a binocular microscope or
with a magnifying glass to make sure that no hairs or other contaminants
are on the aperture or between the aperture and the c-clip. 
Be careful not to lose a small parts, especially the c-clip!
The following additional instructions on inserting the apertures should
also be noted:
• The platinum apertures must be installed so that the polished side
faces up, or towards the electron beam source.
• Installing the c-clip into the insert is done using both the aperture tool
and the injector / plunger tool. Use tweezers to insert the c-clip into
the injector tool, then use the injector tool to install the c-clip into the
aperture insert.

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Maintenance: The Column Liner and Apertures

• To put on the o-ring, push it onto and over the top of the insert,
making sure not to roll or deform it in any way.

APERTURE POSITIONING IN THE LINER

1. Insert spray aperture D into the top of the liner tube and push it all the
way to the bottom with the aperture tool. The open end of the
aperture faces down.
2. Insert aperture C (1 mm spray aperture) into the top of the liner tube.
The top of the column liner is flared outward and the 1mm hole of the
aperture should face up.
3. The aperture tool has a knurled end and three grooves cut into it.
Hold the aperture tool by the knurled end (top) and push the aperture
into the liner tube until the groove nearest the knurl (top) is exactly
level with the top of the liner.
4. Repeat step 2 for aperture B (1mm spray aperture) but use the next
groove down on the tool to place the aperture. (Aperture B and C are
identical and can be interchanged.)
5. Repeat step 2 for aperture A. The platinum aperture should face up
and the third groove down should be used to place this aperture.

FIGURE 6-9 APERTURE MOUNTING

Note: 
Take care not to drop or jar the tube during or after this procedure, as
this may move the apertures from their correct positions. The apertures
are held in place by spring clips. If an aperture feels loose going into the
liner or slips from its position, then the spring clip can be opened up
slightly to increase tension against the liner tube inside wall.

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 Maintenance: The Column Liner and Apertures

CLEANING THE LINER TUBE

1. Clean the inside of the tube with a pipe cleaner or a wooden stick with
cotton wool wrapped around it, using Soft Scrub/CIF cleaner.
2. Rinse in tap water.
3. Clean in an ultrasonic cleaner for 5 minutes using distilled water in the
beaker. The liner is long, so it may be necessary to reverse it in the
beaker and give it a further five minutes cleaning time.
4. Rinse with de-ionized or distilled water.
5. Transfer to a new beaker.
6. Clean in an ultrasonic cleaner for 5 minutes using alcohol p/a. or
isopropanol. The liner is long, so it may be necessary to reverse it in
the beaker and give it a further five minutes cleaning time.
7. Rinse with alcohol p/a. or isopropanol.
Caution! 
Do not place parts together in the beakers. Wash separately as damage
can occur to the metal surfaces.
8. First blow dry with a compressed air, then dry thoroughly under an
infra-red lamp (15 min. to 1 hr.) at a temperature of between 80°C and
100°C. Do not bake in an oven.

INSTALLING THE LINER TUBE

1. Ensure that the apertures are correctly mounted in the liner and that
the column liner upper o-ring is on the liner.
2. With a gloved hand, carefully push the liner down into the column until
it seats on the bottom o-ring. The column liner tool can be used to re-
insert the liner tube, also.
3. Refer to section ‘Installing the Anode Assembly’ to complete the
column installation procedure.
4. With a Wehnelt installed close the column.
5. Pump down the system using the Vacuum module Pump button. If
the vacuum status is not PUMPED (green icon) within 10 minutes, the
gun o-ring may need to be reseated or replaced.
Column alignment will need to be performed after this procedure.

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Maintenance: The Standard Insert

The Standard Insert

The following tools and procedures are used to install and remove the
standard insert from the lens pole and to assemble Pressure Limiting
Apertures and the Insert body.

REMOVING AND DISASSEMBLING

The following instructions describe how to remove and disassemble the
standard insert assembly.

FIGURE 6-10 STANDARD INSERT COMPONENTS

1. Insert the universal detector tool pins into the matching slots in the insert
assembly, as shown in Figure 6-12. Once the pins are engaged, twist
counter-clockwise to unscrew the insert from the pole-piece.

FIGURE 6-11 INSERT REMOVAL TOOL

2. Use the Apertures Removal Tool to remove the C-clip and the final
aperture from the insert. To do this, insert the pin of the tool into the
wide end of the insert and push the parts out of the narrow end of the
insert. Be sure the parts have a safe, clean place to drop onto.

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 Maintenance: The Standard Insert

FIGURE 6-12 REMOVING AND DISASSEMBLING THE INSERT

Aperture removal tool

Housing

Final Aperture + c-clip

3. Inspect the o-ring at the bottom of the insert. If the o-ring looks
deformed or damaged, replace it. This is a critical seal between EC1
and EC2 (which is under very low pressure). The surface of the o-ring
must be flush against the insert.
4. Inspect the threads on the insert for dirt, scratches on the threads,
etc. Clean the insert threads and if damaged, replace the insert.

HOUSING CLEANING
Once the entire assembly has been removed and taken apart:
1. Clean the standard insert housing with a toothbrush and Soft Scrub/
CIF or aluminium powder.
2. Rinse with de-ionized or distilled water.
3. Rinse in alcohol or isopropanol and dry with clean compressed air.
Under normal use, the insert should be inspected only when being
inserted. It should only be removed for cleaning when indicated by an
astigmatism.

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Maintenance: Gaseous Detectors

Gaseous Detectors

CLEANING THE GSED / LFD

FIGURE 6-13 REMOVING THE GSED ASSEMBLY

1. Vent the chamber.

2. Pull the end of the GSED detector head down to remove it from the
standard insert. The insert will remain inside of the pole-piece.
3. Pull the GSED pin contact board out of the signal connector mounted
to the chamber ceiling.
The PLA is part of the GSED detector and can be cleaned by inserting a
toothpick (or something similar) into the hole. The signal ring is
permanently attached to the underside of the detector, and can be
cleaned in a similar way.

CLEANING THE GBSD

1. Perform steps 1 and 2 above to remove the GBSD printed circuit
board from the chamber.
2. The GBSD is easily cleaned with a toothbrush, Soft Scrub/CIF
cleaner and water, as with the GSED. To access the PLA and
converter plate, remove the two screws holding the collector grid to
the printed circuit board. Scrub the SE grid gently, as this can be
easily damaged.

FIGURE 6-14 DISASSEMBLING THE GBSD

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 Maintenance: Stage Maintenance

Stage Maintenance

STAGE MECHANICS
Checking the condition of the stage should be a weekly exercise as
many differing samples may be exchanged in this time period. Some
samples may be powders or composite materials that inadvertently drop
particles on or in the stage. If a silicon wafer breaks in the chamber it can
shatter into hundreds of pieces. In this case the stage should be
thoroughly cleaned before attempting movement again.

Cleaning Stage parts

Abrasives and solvents must not be used on the moving stage parts.
Cleaning with a vacuum is the ideal method. If not available, cleaning
should be done by using dry nitrogen gas bursts around the stage
mechanics to blow out any foreign materials. Make sure the final lens
and detectors are protected from the turbulence. Do not use sharp metal
objects to scrape away debris. A fine pair of plastic tweezers can be
used to pick up difficult particles. Spillages on the stage should be wiped
up using a lint-free cloth, followed by vacuuming or blowing with clean
gaseous nitrogen.

SPECIMEN HOLDERS
Recommended cleaning procedures are given below for parts which
operate in vacuum and which are subject to possible contamination.
Frequency of cleaning is, in most cases, determined by necessity (image
quality or astigmatism level).

Cleaning
1. Clean these parts using a lint free cloth and a mild abrasive domestic
cleaner (see list of preferred cleaners at the end of this chapter).
2. Rinse in tap water.
3. Clean in an ultrasonic cleaner for 5 minutes using distilled water.
4. Clean in an ultrasonic cleaner for 5 minutes using alcohol p/a or
isopropanol.

Caution! 
Do not place parts together in the beakers. Wash separately as
damage can occur to the metal surfaces.
5. Rinse in alcohol p/a.
6. First blow dry with a compressed air, then dry thoroughly under an
infra-red lamp (15 min. to 1 hr.) at a temperature of between 80 °C
and 100 °C. Do not bake in an oven!

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Maintenance: Refilling Water Bottle

Refilling Water Bottle

The water bottle in the instrument typically needs to be filled about once
a month if the instrument is used on a regular basis at a Low Vacuum /
ESEM (option) mode. The water reservoir is located on the left side of
the microscope console, behind the cover. To fill the bottle, do the
following:
Note: 
The heating plate under the bottle should be warm.
1. Run the 154 - Water Bottle Venting alignment procedure 
(see Chapter 4).

Caution! 
Be aware of the gas type connected to the gas inlet before the Vent
water bottle button is clicked! If you are not sure, disconnect the
gas pipes from the gas inlet coupling.
2. Disconnect the quick-coupler and pull out the water bottle.
3. Remove the rubber plug and refill with distilled water (not de-ionized)
until 1/3 full.
4. Mount the rubber plug and install the water bottle in the reverse order
of that described above.
5. Pump the system. Switch to Low Vacuum / ESEM mode to force
automatic purging to flush any air out of the bottle and connecting
tubes.
Note: 
The first time the system is pumped in LoVac / ESEM mode after filling
the bottle, Auto-purging may be erratic until the bottle vacuum has
steadied. The removal of all the gas from the liquid must be
accomplished before good imaging is possible. This is done correctly
when no bubbles are produced in the water when increasing the
pressure in the chamber. It is recommended to use 6 to 8 purging cycles
20 to 200 Pa (where applicable) after refilling the bottle.

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 Maintenance: Pre-Vacuum Pump Maintenance

Pre-Vacuum Pump Maintenance

The Rotary pump supplied with the system is used to directly pump parts
of the vacuum system (such as the specimen chamber after a sample
exchange) and for backing the main pumping system – Turbo Molecular
Pump (TMP).

PERIODIC CHECK
Because the pump has to process large volumes of air, loss of oil level
over time is inevitable. The oil level check should be planned every 3
months. The level indicator window is usually found on the front end of
the Rotary pump, and shows minimum and maximum level markers.
Venting the chamber shuts off the rotary pumps. Although it is necessary
when changing the total oil reserve (Service function) it is not absolutely
necessary when only topping up the oil level.

Caution! 
Do not allow the pre-vacuum pump to emit gases into the work
place, as this can be a health hazard. 
The Rotary pump may become very hot while in use, be careful not
to touch the main frame of the pump. Venting the chamber will shut
off the rotary pump.

Topping-Up
The filling position is a plastic hand screw stopper on the top of the same
end as the level indicator.
1. Switch off the pump if necessary by venting the chamber.
2. Unscrew the stopper.
3. Clean around the stopper hole with a lint-free cloth.
4. Fill with the recommended oil to the upper level.
5. Clean up any spillage on the pump.
6. Replace the stopper.
7. Switch on the pump by pumping the chamber.

Caution! 
Never fill the pump through the exhaust hole by removing the
exhaust pipe, as this results in the oil being removed from the pump
by pressure build-up. Excessive back pressure in the exhaust pipe
eventually over-heats the pump, so it is important to allow good
passage for the exhaust gases, preferably via an installed factory
exhaust system.

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Maintenance: Troubleshooting

Troubleshooting

TABLE 6-2 POSSIBLE PROBLEMS AND CORRECTIVE ACTIONS

Problem Possible solution

Not possible to switch the microscope • Check the mains switch and the mains unit circuit breakers
or the PC on placed at the microscope back.
• Check the mains and the mains circuit breaker.
Server crashes at the Start-Up • Restart the PC.
• If this doesn’t help, restart the whole system.
• If this doesn’t help, run the Diagnostics Auto Report and
Simple TAD utilities (see below).
No signal / illumination • Check the Status module / Emission Current to be about
100 µA (see Chapter 3).
• Check the Beam Blank not to be on (see Chapter 3).
• Set the Enhanced Image / Digital Brightness / Gamma /
Digital Contrast values to the default.
• Set the highest Detector Contrast value (see Chapter 3).
• Select the Scan menu / Full frame (see Chapter 3).
• Use a different detector (see Chapter 5).
Astigmatism exceeds the UI control • Remove the Standard Insert, set the HiVac mode and
limits (bad image, not possible to check the image quality. If this helps, clean or replace the
focus) Standard Insert aperture (see above).
Image shift when focusing • Run the Final Lens Alignment (see Chapter 4). If this
does not help, run the 1 - Gun Alignment procedure (see
Chapter 4).
Not possible to adjust the  • Check there is only one Gun Tilt position with maximum
1 - Gun alignment illumination. If there are more of them, place the Gun Tilt
cross among them (see Chapter 4).
• If illumination is lost during a Gun Shift adjustment
(Modulator is on), re-adjust the Gun Tilt position
(Crossover mode) to find the illumination again (see
Chapter 4).
• Run the Diagnostics Auto Report and Simple TAD
utilities (see below).
Poor ETD image • Select the ETD. Open the Detectors menu / Detector
Settings. Select the Mode: Custom. Change the Grid
Voltage from maximum to minimum (see Chapter 5).
• There should be a visible change of the contrast (an image
is getting darker with lower voltage). If not, run the
Diagnostics Auto Report and Simple TAD utilities (see
below).
Alternating lighter and darker image • Run the Purging procedure (see Chapters 3).
bands visible in the ESEM / LoVac • Check the water bottle to be sealed properly (see above).
mode
Discharging and white stripes  • Decrease the Detector module / Contrast value (see
in ESEM / LoVac mode Chapter 3).

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 Maintenance: Troubleshooting

TABLE 6-2 POSSIBLE PROBLEMS AND CORRECTIVE ACTIONS

Water interlock failure • When cooling water does not flow, the Application
Status… window with the respective message pops up
(see Chapter 3). Check the cooling water flow.
Note: 
The system is designed to work without the cooling water.
However, if the air speed near the column is higher than 
5 m/min, it may cause an image drift due to the temperature
fluctuation.
Emission is missing • Check the filament condition.
• If this doesn’t help, run the Diagnostics Auto Report and
Simple TAD utilities (see below).
Pressure doesn’t reach the target • Check the water bottle to be sealed properly, to be filled
value when using the water in the with the water and the heating plate is warm (see above).
ESEM / LoVac mode
Frozen system • Restart the PC.
Touch Alarm is active • Remove the specimen holder away from the chamber.
• Check the presence of a short connection between the
specimen holder and the stage.
Other problems • Run the Diagnostics Auto Report and Simple TAD
utilities (see below).

There are two powerful tools for any system troubleshooting (e.g. flags in
the image, software problems etc.) accessible to a Supervisor:
• The Diagnostics Auto Report saves a zip file with all the logs,
system information, user’s description and screen shots.
• The Simple TAD (Simple Test And Diagnostics) performs many tests
(communication with microscope modules, supply voltages and
electronics boards test for instance) and saves a file with the results.
Generated files are intended to be sent to a local Field Service Engineer.
Note: 
If Simple TAD procedure is run prior to Diagnostics Auto Report, the
Simple TAD output file is collected by Diagnostics Auto Report and
zipped together with the logs. Then it’s enough to send only the
Diagnostics Auto Report output file.

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Maintenance: Troubleshooting

DIAGNOSTICS AUTO REPORT

When performing this utility the xT Microscope Server can either be
stopped or running.
1. Run the system Start / Programs / FEI Company / User Tools /
Diagnostics Auto Report. Click the Start button.

2. Write down how to reproduce the problem and choose a problem

class (when prompted by the tool).
3. Arrange the screen that you want to capture, e.g. flags in the image
(when prompted by the tool).
4. The tool proceeds with collecting of the system information.
5. The tool creates a file on the PC’s desktop. Send it to a Field Service
Engineer.

6. Close the window.

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 Maintenance: Troubleshooting

SIMPLE TAD
If the xT Microscope Server is running, the Simple TAD automatically
performs all the tests (communication, optics, supplies etc.). If it is exited,
only the communication tests proceed.
1. Run the system Start / Programs / FEI Company / Supervisor
Tools / Simple TAD. Click the Start button.

2. The tool proceeds with the collecting of the system information. A file
is saved to the location specified by the software. Send it to a Field
Service Engineer.

3. Exit the window.

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Maintenance: Old Pump maintenance

Old Pump maintenance

The dry pre-vacuum pump is used to directly pump parts of the vacuum
system (for instance the specimen chamber after a sample exchange)
and for backing the Turbo Molecular Pump (TMP). It also controls the
pressure in the specimen chamber when operating in the LoVac mode.

PERIODIC CHECK
The Rotary pump may become very hot while in use, be careful not to
touch the main frame of the pump. Venting the chamber will shut off the
rotary pump.

Caution! 
When using GIS’s (option), do not allow the pre-vacuum pump to
emit gases into the work place, as this can be a health hazard.

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7 SYSTEM OPTIONS

This chapter covers hardware and software that is an option either

integrated in, or accessory to the Quanta system (not all of them are
described here).
• The Manual User Interface (MUI) provides direct manual control of
microscope parameters such as focus, magnification, contrast,
brightness, beam shift and Stigmator.
• The Joystick brings another possibility to control the basic stage
movements.
• The Cooling Stage enables to image and analyse specimens (cooled
between 0 and 10 °C) of very diverse nature at relative humidity
conditions up to 100% (typical chamber pressures required are in the
range 300 - 1 000 Pa). Humidity experiments could characterize the
sample morphology and phase distribution. The stage is cooled by water.
• The Waterless Cooling Stage uses copper belt to detract heat
excess.
• The 1 000 °C Heating Stage is used to view heated samples (up to
1000 °C) and record in-situ morphological changes.
• The 1 400 °C Heating Stage enables to heat samples up to 1 400 °C.
This option includes two 1 400 °C and one 1 000 °C heating stages.
• The Compressor 120 V / 230 V, 50 / 60 Hz 4-litre Tank
• The Acoustic Enclosure for Pre-vacuum Pump
• The Specimen Holder Kit
• The Set of 20 Specimen Stubs for SEM’s
• The Keithley picoamper meter
• The Picoamper meter Switch Box
• The Electrostatic Beam Blanker
• The Mains Matching and Isolation Transformer provides a
galvanic isolated AC-regulated power source with the 115 / 230 V, 50
/ 60 Hz output.
• The Uninterruptible Power Supply
• The CryoCleanerEC + spare vessel – anti-contamination device
• The WetSTEM detector enables in connection with the Cooling Stage
to observe wet samples in a STEM mode.
• The Gaseous Back-Scatter Electron Detector (GBSD) allows BSE
imaging in ESEM™ mode, i.e. at a high chamber pressure (it uses a
gas amplification to compensate a signal loss). Other back-scattered
electron detectors (solid-state or scintillate-type BSE detectors)
typically work with a pressure up to 100 Pa, but tend to get very noisy
at this condition.
• The small diameter, low voltage Back-Scatter Electron Detector
(BSED)
• The low-voltage, High-contrast Detector (vCD)
• The Gaseous Analytical Detector (GAD) is the low voltage BSED
with an additional X-ray cone with a 500 µm Pressure Limiting
Aperture which seals to the objective pole piece.
• The solid state STEM I detector allows detection of electrons
transmitted through the sample. Regular voltage range is from 30 kV
down to around 5 kV, which is of course dependent on the sample

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System Options:

thickness.
• The Annular STEM II detector allows detection of electrons
transmitted through the sample. Regular voltage range is from 30 kV
down to around 5 kV, which is of course dependent on the sample
thickness.
• The Centaurus Detector with back-scatter tip is a retractable,
scintillate-type BSE detector. Atomic number discrimination allows a
resolution better than 0.1 Z (when Z = 30).
The Cathodoluminiscence Tip for the Centaurus Detector enables
to convert it to a cathodoluminiscence detector.
• The ESEM GAD needle detector
• The set of three apertures 200 µm, 3 mm diameter
• The set of ten Tungsten filaments
• The Thermal Printer Kit
• The Beam Deceleration mode is used to observe samples, when
electron energy is very low and under very low accelerating voltages.
• The WDX Completion Kit relocates the GSED detector connector
(bracket) and GSED pre amplifier bias feed-through to another
position in the SEM specimen chamber, to avoid geometrical conflicts
with the wavelength spectrometer.
• The Quick Loader
• The Nav-Cam
• The Remote Control / Imaging
• The SIS Scandium Image software
• The SIS Scandium desktop license
• The SIS Scandium webRacer allows regular users with ID /
passwords (provided by the supervisor) to view and retrieve
worldwide database data, using any internet browser and any
computer system (PC, Apple, Sun…).
• The Basic SEM Course
• The Advanced Course SEM
• The On-site Training / Support
• The On-site Training / Support - 1 day – North America / China /
Japan
For further up-to-date information on system options please contact your
local FEI representative.

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 System Options: Manual User Interface

Manual User Interface

The Manual User Interface (MUI) provides knobs to perform functions
that can also be performed with the software. It is connected to the USB
connector located on the microscope controller.

FIGURE 7-1 MUI

The MUI offers additional flexibility for controlling magnification, beam

shift, focus, astigmatism, contrast and brightness.

Joystick

The Joystick provides knobs to perform stage functions that can also be
performed by the software. It is connected to the USB connector located
on the microscope controller.

FIGURE 7-2 JOYSTICK

• The Up / Down lever motion moves the stage in Y axis.

The Left / Right lever motion moves the stage in X axis.
The Left / Right lever rotation rotates the stage left / right.
• The button 1 is not used.
• The button 2 is used together with the lever motion:
- Up / Down moves the stage up / down 
(regardless the Link Z to FWD status).
- Left / Right tilts the stage left / right 
(available for stages with motorized tilt axis movements).
• The button 3 speeds up the stage motion:
- 10× in X / Y axis
- 5× in Z axis
- 2× in R / T axis

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System Options: Uninterruptible Power Supply (UPS)

Uninterruptible Power Supply (UPS)

If the power failures occur occasionally it is recommended to use the

microscope UPS, which maintains the vacuum in the electron source
section.
In case the microscope system is powered by the UPS and a mains
power failure happens, the system starts 10 minutes countdown to
switch to the safe mode. User is informed about the countdown progress
in the application status window. If the mains power is recovered within
this time, the countdown is cancelled and nothing happens.

After 10 minutes of continuous power off a shutdown to the safe mode

with following actions is activated:
• Chamber is vented
• UI is stopped
• xT Microscope server is stopped
• Microscope console is shut down
• Microscope controller and the support computer (if present) 
are switched off

WAR N I N G ! 
Because the Emitter IGP’s are supported by the internal batteries,
some parts of the microscope are still under power.
To return the system to an operation follow the startup procedure (see
Chapter 2). When the xT microscope Server is launched the first time
from the safe mode, a dialog is displayed to inform a user.

Note: 
A Supervisor must restart the system after a longer power failure. If the
Startup procedure fails, contact an FEI Service Engineer.

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 System Options: Nav-Cam

Nav-Cam

Beside the Sample Navigation / Navigation Montage… feature which

navigates across the sample surface this functionality represents a fast
method to navigate across a range of stage movement area. This is
convenient when investigating large area samples or several samples
with the use of any multi sample holder.

CAPTURING NAVIGATION IMAGE PROCEDURE

1. Vent the chamber, open the chamber door and insert a sample.
2. Close the chamber door and set the WD to 10 mm (top sample
surface) with the use of the CCD 10 mm Marker. At this position only
the Nav-Cam functionality is correct! Do not pump the system!
3. Open the chamber door and rotate the navigation camera to point to
the stage.
4. At this moment the beam and the detector changes to Nav-Cam and
a live imaging of navigation camera is obtained in the last time active
quad (with the resolution of 512 × 442 pixels only). Set the Detectors
module / Brightness slider in case the imaging is not satisfactory.
5. Select the Stage menu / Move Stage to Nav-Cam function to move
the stage to Nav-Cam position.
In case the Preferences… / General tab / Automatic move to Nav-
Cam position item is set to Yes, the stage moves to the 
Nav-Cam position automatically.

Caution! 
When the stage is moving to the Nav-Cam position, do not rotate
the camera until the stage reaches the final position! The alignment
setting (see below) could be lost.

WA R N I N G ! 
Be aware of a stage movement, do not put fingers to the trajectory! 

6. Capture an image (with the high resolution of 3072 × 2048 pixels) by

pressing the silver camera button on the top of its body or by using
Snapshot / Photo function (see Chapter 3). The image could be
saved or adjusted like any other image taken from the microscope
(image enhancement, process etc.).
If the sharpness of the captured image is not sufficient, try to find a Z-
coordinate (about ±1 mm from WD 10 mm) at which the image is
sharp enough and repeat steps 3 and 4.
7. Rotate the navigation camera back to its home position (the stage
moves to its last time position before venting the chamber), close the
chamber door and pump the system.
A green rectangle (or just a cross) represents a place, where electron
beam will aim.
Note: 
Nav-Cam operation is restricted for highly shiny and simultaneously
planar specimens (Si wafers, mirrors etc.).
Besides a Navigation image one can use also the Digital Zoom module
to navigate the stage (see Chapter 3).
When the Preferences… / General tab / Display Stage Map in
Navigation quads item is set to Yes, saved stage positions are
displayed in the Nav-Cam photo (see Chapter 3).

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System Options: Nav-Cam

In case a user log off and the sample and its stage loading position did
not change, use the Stage menu / Restore Last Nav-Cam Photo.

403 - NAV-CAM ALIGNMENT

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 System Options: Optional Detectors

Optional Detectors

OPTIONAL DETECTORS CONNECTION

Detectors are connected to the feed-through connector panel.
Connectors have engraved names and they are used to connect
following detectors:
BSD • The STEM connector: STEM I / Wet STEM / STEM II
• The GAD connector: GAD / ESEM GAD
• The BSD connector: vCD / CBS / QUAD BSED
STEM
GAD Caution! 
Insert connectors gently without any force in order not to break its
pins!

INSTALLING / REMOVING 
LENS MOUNTED DETECTORS
This procedure is intended for the Lens Mounted CBS, Annular GAD,
ESEM GAD detectors.

Caution! 
Detector must be installed only to the Standard insert (see
Chapter 2), do not use the insert delivered with the ICD detector.
1. With your gloved hand grasp the detector in the protective box and
push the mounting collar gently up to the standard insert groove. The
part with connector cables face towards the chamber door.
2. Push the sides of the protective box and release the installed
detector.
3. Connect the detector to the appropriate connector (see Chapter 2).
When removing the detector, proceed in reverse.

Caution! 
Do not apply power, there is only one possible connection position! 
Secure the detector cable to the pole piece hook to prevent its catch
by a moving stage!

FIGURE 7-3 LENS MOUNTED DETECTORS INSTALLATION

1 2

When the detector is not installed, it is possible to leave it in the

protective box on the chamber bottom to prevent its pollution.

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System Options: Optional Detectors

GASEOUS BACK SCATTERED ELECTRON

DETECTOR (GBSD)
The GBSD is used in place of the standard Gaseous SE (GSED) detector
and Large Field Detector (LFD). It was specifically designed to image at
pressures above 4 Torr (534 Pa) (predominantly in the range of 6 to 9 Torr
(800 to 1200 Pa)). This makes the GBSD best suited for use with the
Peltier when both secondary and back scattered images are required.
This detector is integrated into a flexible PC board and plugs into the
signal connector behind the conical lens.

FIGURE 7-4 GBSD OPERATIONAL SCHEMA

The grid on the bottom of the GBSD board is used to collect all SE
signals from the gas. This grid, the surface of the board around the grid
and the PLA1 are connected to high voltages up to ± 600 V during ESEM
operation.

Installing and Settings the GBSD

Follow the same procedure as described for GSED (see Chapter 5).
Note: 
the GBSD or other gaseous detectors do not need to be removed to pump
to HiVac at the end of a day. They may be left in the place. However,
stages with water lines inside the chamber must be removed.
At the Detector Settings module the following options are possible:
• Mode list box with choices:
The Secondary Electrons (SE) mode: the converter plate voltage is
reversed and a second positive voltage is applied to the SE collection
grid. SE from the sample are collected directly and the SE image is
similar to the GSED image. All SE generated by BSE at the converter
plate are drawn back to the converter plate.
The Backscatter Electrons (BSE) mode: BSE generated by the
primary beam, strike the BSE converter plate and generate SE, which
are accelerated (repelled) by a negative voltage placed on the BSE
converter plate. A zero voltage potential is applied to the SE collection
grid. When the electrons strike a gas molecule with enough energy,
they ionize it. The two electrons are further accelerated, causing more
collisions. The SE signal is “amplified” in the gas with gains up to a few
thousand resulting in BSE image.

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 System Options: Optional Detectors

the MIX mode is a combination of a negative potential on the

converter plate and a positive potential on the SE grid, generating a
mixed SE-BSE image.
• Contrast adjuster: the GBSD, like other back scattered electron
detectors, works best with high beam currents and voltages. Since
back scattered electron yield is low for light atomic number elements,
using high voltages and high beam currents may not be a suitable
option for these samples. To solve this, an additional contrast
expansion circuit is provided.

Obtaining an images with the GBSD

1. Install the GBSD (if necessary, install the standard insert).
2. Pump down and flush the chamber.
3. In the Detector menu, select GBSD.
Secondary Electrons Mode
4. From the Mode list box select Secondary Electrons. The voltage
changes automatically for SE imaging.
5. Move the sample to a WD of 9.5 to 10.5 mm.
Backscatter Electrons Mode
1. From the Mode list box select Backscatter Electrons. The voltage
changes automatically for BSE imaging.
2. Move the sample to a WD of 8.5 to 9.5 mm. The closer the sample is
to the detector, the stronger the BSE signal is.
Mix Mode
1. Select the Detector menu / Mix mode. Slowly increase the contrast
until an images appears on the screen.

RETRACTABLE DETECTORS CONTROL

When any retractable optional detector is installed on the system, the
appropriate Insert / Retract button is added to the Detector Settings
module / Detector: CCD to enable the equipment control while
observing the optical quad. The same button is present on the
appropriate detector module also.

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System Options: Optional Detectors

LOW-VOLTAGE HIGH-CONTRAST DETECTOR

LENS MOUNTED / RETRACTABLE (vCD)
This is a solid State detector ideal for low accelerating voltages down to
about 200 V. The diode has an active area of approximately 100 mm2
and it is positioned directly above the sample (optimum WD should be
from 3.5 to 7 mm) to achieve maximum detection efficiency. Therefore it
causes some limitation in a tilt range (see below).

FIGURE 7-5 Lens Mounted / Retractable vCD

Caution! 
The diode is sensitive to mechanical damage so the active area
(shiny diode) should never be touched.
The detector could be mounted on a retractable arm which can be
inserted between the lens and the sample and it is parked to pole piece
to reduce vibration.
Select the Detector Settings module / Detector list box / vCD or from
the Detectors menu.

Installing / Removing Lens Mounted vCD Detector

Hold the detector by its sides and push up the back of the diode onto the
Standard Insert until it stops. The diode should by oriented so that its out
coming cables side should be faced towards the chamber door.

Inserting and Retracting vCD Detector

Before insertion the retractable version of vCD / CBS detector, the user
needs to check the following conditions:
• Chamber is pumped to HiVac or LoVac condition.
• The Link Z to FWD procedure must be done, the WD must be more
than 4.5 mm and the Tilt must be from - 0,5° to + 0,5°.
If the above mentioned conditions are not fulfilled, the Insert button is
not active (a tooltip occurs under the mouse cursor).
By clicking the Insert button the dialogue appears asking a confirmation
of detector insertion. The Tilt and the Z-axis stage movements are limited
to the above mentioned values.
Retracting the detector is automatic with the Stopping / Starting the
server or venting the chamber. Otherwise user can use the Retract
button.
When the detector is retracted, the information text is displayed in each
quad which uses it.

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 System Options: Optional Detectors

DIRECTIONAL BACKSCATTERED DETECTOR –

CONCENTRIC BACKSCATTERED DETECTOR
LENS MOUNTED / RETRACTABLE (CBS)
The CBS uses concentric segmentation of the detector diode to
distinguish between BS electrons scattered close to the beam axis –
inner segment (preferentially compositional contrast) and electrons
scattered far from the beam axis – outer segment (more topography
signal). Z-contrast mode provides signal collection from all detector
segments.

FIGURE 7-6 LENS MOUNTED / RETRACTABLE 

DIRECTIONAL BACKSCATTERED DETECTOR

Detector Settings
Select the CBS from the Detector Settings module / Detector list box.
Choose the required diode segment(s) by checking the relevant radio
button. The Custom mode is used to define the segments to be used for
detecting. Clicking the + / - sign over particular segment activates it to
add (yellow color) / subtract (blue color) the segment signal. When the
segment color is grey (double-clicking), it is switched off.
Distribution of electrons collected by detector segments changes with
setting of working distance, lens mode and Beam Deceleration mode
(option).
It is also possible to set different concentric segments in particular quads
and thereafter to use the Enhanced Image module / Mix 3 or Mix 4 tab
to mix color coded signals to create color images (see Chapter 5).

Installing / Removing Lens Mounted CBS Detector

See above.

Inserting and Retracting vCD / CBS Detector

Follow the procedure described for the vCD detector (see above). 
When the detector is retracted, the information text is displayed in each
quad which uses it.

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System Options: ESEM GAD

ESEM GAD

Needle GSED / Gaseous Analytical Detector

This detector has both GAD and GSED functionality. The GAD diode is
combined with the needle shaped gaseous SE detector, which could be
used at pressures above 200 Pa.

FIGURE 7-7 ESEM & GAD DETECTOR

The GAD two-segment low voltage silicon diode with an active area of
approximately 100 mm2 is combined with the needle shaped GSED
(gaseous SE detector), which could be used at pressures above 200 Pa.
It is positioned directly over the sample to obtain maximum detector
efficiency.
The GAD can be used down to a high voltage about 1 kV and works best
at a slow scan conditions. It works in parallel with the LVSED, which
allows simultaneous use of SE, BSE and X-ray detectors in a gaseous
environment. It should be used at the lower part of working pressure
range.
It can be used for HiVac but because it limits the minimum achievable
WD, it is disadvantageous for high resolution imaging. It has a 500 µm
PLA cone for the LoVac and ESEM (option) operation, especially the 
X-ray analysis. The cone extends down from the unit to 7.5 mm, which
reduces the gas path length for electrons to an efficient 2.5 mm at the
standard 10 mm analytical WD.

Installing / Removing
See above.
• The GSED connector comes to the upper connector socket above the
final lens.
• The GAD connector comes to the right part of the connector board
placed in the right bottom of the chamber.

Caution! 
The diode is sensitive to a mechanical damage so the active area
(shiny diode) should never be touched. 
The GAD is mounted close to the (optional) X-ray detector
collimator, which must not be touched when changing detectors. It
is advisable to retract the EDX collimator when mounting / removing
the detector on / from the objective lens insert.

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FIGURE 7-8 GAD / GSED CONNECTION

Detector Settings
Select the GAD from the Detector Settings module / Detector list box.
(a user can select also GSED detectors in a different quad - see
Chapter 5). Choose the required Mode by ticking the radio button:
• The Z Contrast is the normal BSE image with suppressed
topographical contrast and maximum atomic number contrast.
• The Topography is the pseudo-topographical image with suppressed
atomic number contrast and maximum topographical contrast.
• The Segment A / B uses shadows to create strong topographical and
atomic number contrast.

Obtaining Image in BSE Mode

1. Install the detector diode and select the Detector Settings module /
Detector: GAD.
2. Close the chamber door and pump down the chamber. Select No
Accessory / GAD cone in the PLA Configuration dialogue when this
appears.
3. When the Vacuum is Pumped, switch on the accelerating voltage and
slowly increase the contrast and brightness to obtain an image.
Note: 
Whenever the GAD is selected, the optical quad is paused (because the
CCD camera infra-red LED’s are switched off not to emit the photons
supersaturating the detector diode).

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System Options: ESEM GAD

SCANNING TRANSMISSION ELECTRONS

MICROSCOPY DETECTOR (STEM I)
The STEM I is a two segment solid-state diode mounted underneath the
STEM I holder. It can be used at any available working distance
(preferably close to the lens for high resolution) or at the eucentric
position for simultaneous use of the EDX. It works best at a slow scan
conditions.
The mounting pin below the detector locates into the standard conical
single stub mount. The detector is connected to an SSD pre-amplifier
input board.
Note: 
When the STEM I detector is mounted to the chamber, stage rotation is
disabled automatically for the safety, when the temperature stage is
installed. It is possible to unlock these stage movements manually, but
beware of possible detector cable damage while rotating or tilting the
stage.

FIGURE 7-9 STEM I DETECTOR

Settings for STEM I Detector

The A + B condition (default) can be used for the first time since the
entire detector is working, which facilitates to get an image. To switch BF
/ DF choose Segment A / B in the Detector Settings module.
Choosing A - B gives a negative image that although will not be used
frequently may highlight features by contrast not easily seen otherwise.
The STEM I holder has 8 positions for TEM sample grids. The following
table refers to the positions numbering and their related capabilities.
TABLE 7-1 STEM I HOLDER POSITIONS

Grid Position Observation Mode and Diode switching

1D and 5D The object is left / right of the segment separator: 
Segment A gives BF / DF 
Segment B gives DF / BF
2,3,4 BF – use Segment B only
6,7,8 BF – use Segment A only

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Loading samples
Materials or hard samples should be prepared as for the TEM by
appropriate thinning technique. The STEM I holder (which is a part of the
detector assembly) can either be loaded with samples while outside the
microscope chamber (which is more convenient) or when it is mounted
and fixed to the stage.
1. Remove the holder top (by loosening the central screw). This
exposes the 8 grid positions (round holes with tweezers slots).
2. Load the TEM grids with samples face-up into the grid holes. 
The holder top has raised rings to press down in the grid holes to hold
the TEM grids firmly in place. The holder top numbers should overlay
the same ones on the base plate.
3. Replace the holder top carefully and tighten down the central screw.
To remove sample grids proceed in the reverse order.

Obtaining Imaging
1. Switch on the accelerating voltage at 20 kV, set the spot size to 3.
2. Using a fast scan focus the top of the STEM I holder surface with SE
detector.
3. Link Z to FWD and bring the focused surface to a 5 mm WD.
4. Move to the appropriate sample position and focus the TEM grid bars.
The WD and Z position has now lengthened and re-setting of the Z-
axis value to 5 mm is necessary.
This procedure is necessary to prevent inadvertently bringing the
detector in contact with the final lens. The minimum safe distance to the
sample surface is 1 mm. Be aware that the STEM I holder surface is now
closer to the lens than the sample.
By moving off the grid bars and fine focusing most imaging corrections
(image rotation, astigmatism) can be performed in the SE Mode.
5. Choose the Detectors menu / STEM I detector and select the segment
mode, depending on the sample position in the holder. A transmission
sample image should be visible at a low magnification.
• The BF image: change the accelerating voltage to suit the contrast
necessary through the sample. For example light element materials
(such as silicon or silicon oxide) may work better with 5 - 10 kV to
create contrast, whereas dense materials (such as metals) may
require 10 - 20 kV or higher. Finally set the magnification, fine focus
and correct the astigmatism.
If the aperture adjustment is needed, it may be achieved more easily
by momentarily switching to ETD, because a faster scan speed can
be used.
• The DF image: the samples that reside in the 1D and 5D positions
can be observed in the dark field mode. The separator line of the two
diodes crosses vertically the positions of 1D and 5D. An area of
interest on the left / right side of the line can be observed with the
right-hand / left -hand diode for DF / BF observation.
DF observation may require higher HV to create a suitable image as
the angle subtended to the detection diode can be wide. Choosing 2×
the value used for BF is a good guide level.
Detector home position
While the detector is not used, it could be placed into a holder which is
mounted inside the specimen chamber, saving it from a mechanical
damage and pollutions.

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RETRACTABLE ANNULAR SCANNING

TRANSMISSION ELECTRONS MICROSCOPY
DETECTOR (STEM II)
This is a 8 segments solid-state diode mounted on a retractable arm. It
must be used only with a special sample holder, oriented in an exact
position monitored by a software (see below). It works best at a slow scan
conditions.

FIGURE 7-10 STEM II DETECTOR

Note: 
When the STEM II detector is inserted stage rotation is disabled
automatically for the safety when the temperature stage is installed. It is
possible to unlock these stage movements manually, but beware of
possible detector cable damage while rotating or tilting the stage.

Holder Arm Installation

1. Run the Home Stage (Shift + F3) procedure.
2. Remove all sample holders from the stage plate.
3. Screw the holder arm to the stage plate (the picture shows 110 mm
stage, for the 150 mm the stage plate is larger).

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Load In Row Holder

4. Place the row holder to the load base (the load base pin is beneath
the position you want to load in / out). Tighten it by the screw knob,
the pin lifts up the spring.
If the pin does not lift up the spring enough to put the sample in,
adjust the lifting height by turning the screw.
5. Insert a sample under the row holder spring.
6. Release the screw knob and the entire row holder from the load base.
7. Repeat steps No. 1 - 4 to load in / out another samples.
8. Put the row holder to the holder arm.

FIGURE 7-11 ROW HOLDER ON THE LOAD BASE / 

ROW HOLDER ATTACHMENT INTO HOLDER ARM

Inserting and Retracting STEM II Detector

Caution! 
Always take care of any stage movement which could cause a collision
with the STEM II detector. Any collision can cause its damage.
Before insertion the retractable STEM II detector, the chamber must be
pumped to HiVac or LoVac, otherwise the Insert button is not active (a
tooltip occurs under mouse cursor).
When clicking the Insert button the dialogue requires confirmation of the
correct sample holder installation to enable detector insertion. When the
stage is not in a correct position for insertion, another dialogue appears
requiring a confirmation of moving it to the safe position.

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System Options: ESEM GAD

The Tilt and the Z-axis stage movements are limited to enable safe stage
movements.
Retracting the STEM II is automatic with the Stopping / Starting the
server or venting the chamber. Otherwise a user can use the Retract
button. When the detector is retracted, the information text is displayed in
each quad which uses it.

Settings for STEM II Detector

1. Position the desired sample grid in the field of view using the ETD.
Focus and link Z coordinate to FWD.
2. Select the Detector Settings module / Detector list box / STEM II
detector.
3. Click the Insert button to insert the detector (see above).
Bright Field imaging
1. Select the Detector Settings module / BF radio button.
2. Adjust the contrast and brightness. An image should be visible at low
magnification.
3. Change the voltage to suit the contrast necessary through the
sample.
For example: light materials (poly-silicon or silicon oxide) may work
better with 5 - 10 kV to create contrast, whereas dense materials
(metals) may require 10 - 20 kV or higher.
4. Set the desired magnification, fine focus and correct the astigmatism.
Dark Field imaging
1. Obtain a Bright Field image first.
2. Select the Detector Settings module / DF radio button.
3. Adjust the contrast and brightness.
HAADF (High Angle Annular Dark Field) imaging
This mode may require higher voltage to create a suitable image as the
angle subtended to the detection diode can be wide. Choosing 2× the
value used for Bright field is a good guide level.
1. Obtain a Bright Field image first.
2. Select the Detector Settings module / HAADF radio button.
HAADF-P (High Angle Annular Dark Field - Partial) imaging
1. Select the Detector Settings module / HAADF-P radio button.
You can select any combination of HAADF segments by clicking it on
detector diagram. Active segments are highlighted in yellow. HAADF
segments cannot be combined with DF or BF.
Area of active segments can be “rotated” using the blue arrow buttons to
view orientation contrast changes etc.
Selecting the Detector Settings module / HAADF-PC radio button gives
the signal from complementary segments to those selected in HADF-P.
Note: 
There is also 14 segments solid-state diode modification, which is
obvious from the Detector Settings module. The detector has the same
handling and control as described.

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PHOTO MULTIPLIER TUBE / BACKSCATTERED

ELECTRON DETECTOR 
AUTRATA, CENTAURUS (PMT-BSE)
See separate manual.

FIGURE 7-12 AUTRATA / CENTAURUS DETECTOR

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OBSOLETE DETECTORS
These detectors are not provided any more, they are installed in some
older equipment.

Quad Backscattered Electrons Detector (Quad BSED)

These are four-segment low voltage silicon diode. Either diode has an
active area of approximately 100 mm2 and is positioned directly above
the sample to obtain maximum detector efficiency.

FIGURE 7-13 QUAD BSED DIODE UNITS

It can be used down to a high voltage about 1 kV and works best at a

slow scan conditions. It can be used in parallel with the LFD, which
allows simultaneous use of SE, BSE and X-ray detectors in a gaseous
environment. It is designated for a HiVac and LoVac imaging.
Installing / Removing
Hold the detector by its sides and push up the back of the diode onto the
Standard Insert until it stops. The diode should by oriented so that its out
coming cables side should be faced (and parallel) to the chamber door.
Detector home position
While the Quad BSED detector is not used, it could be placed into a
holder which is mounted on the upper edge of the pole piece, saving it
from a mechanical damage and pollutions.

Caution! 
The diode is sensitive to a mechanical damage so the active area
(shiny diode) should never be touched. 
The Quad BSED is mounted close to the (optional) X-ray detector
collimator, which must not be touched when changing detectors. It
is advisable to retract the EDX collimator when mounting / removing
the detector on / from the objective pole piece.
Detector Settings
Select the Quad BSED from the Detector Settings module / Detector
list box. Choose the required Mode from the list box.
• The Z Contrast (A+B+C+D) is the normal BSE image with suppressed
topographical contrast and maximum atomic number contrast.
• The Topography is the pseudo-topographical image with suppressed
atomic number contrast and maximum topographical contrast.
Adjusted segment setting could be left / right rotated by two buttons
with circular arrows. This changes a direction of the resulting image
illumination.
• The Custom mode is used to define the segments to be used for
detecting. Right-click over the particular segment and select Add

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(yellow color) / Substract (blue color) to add / subtract the segment

signal or Turn Off (grey color) to switch the segment off.
Obtaining Image in BSE Mode
1. Install one of the diodes and select the corresponding Detector.
2. Close the chamber door and pump down the chamber. 
When the Quad BSED diode is installed, No Accessory must be
selected in the PLA Configuration dialogue when this appears.
3. When the Vacuum is ready, switch on the accelerating voltage and
slowly increase the contrast and brightness to obtain an image.
Note: 
Whenever the Quad BSED is selected, the optical quad is paused
(because the CCD camera infra-red LED’s are switched off not to emit
the photons supersaturating the detector diode).

Dual BSED / Dual GAD

Back Scattered Electron Detector / Gaseous Analytical Detector
These detectors are replaced by the CBS and Annular GAD. Two-
segment low-voltage diodes has the 500 µm PLA cone for the Low
Vacuum and ESEM modes, especially for the X-ray analysis. The cone
extends down from the unit to 8.5 mm, which reduces the gas path
length for electrons to an efficient 1.5 mm at the standard 10 mm
analytical WD.
Either diode has an active area of approximately 125 mm2 per segment
and is positioned directly above the sample to obtain maximum detector
efficiency. Therefore it causes some limitation in the tilt range.
Both detectors are connected to an SSD pre-amplifier input board. They
can be used down to a high voltage about 1 kV and works best at a slow
scan conditions.
The detector can be used for all vacuum modes, but because it limits the
minimum achievable WD, it is disadvantageous for high resolution
imaging in HiVac mode. It can be used in parallel with the LFD, which
allows simultaneous use of SE, BSE and X-ray detectors in a gaseous
environment. They should be used at the lower part of a pressure range,
obtainable for a particular detector.

FIGURE 7-14 GAD DIODE UNITS

Installing
Hold the detector by its sides and push up the back of the diode onto the
Standard Insert until it stops. The diode should by oriented so that its out
coming cables side should be faced (and parallel) to the chamber door.

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Detector home position

While the GAD detector is not used, it could be placed into a holder
which is mounted on the upper edge of the pole piece, saving it from a
mechanical damage and pollutions.

Caution! 
The diode is sensitive to a mechanical damage so the active area
(shiny diode) should never be touched. 
The GAD is mounted close to the (optional) X-ray detector
collimator, which must not be touched when changing detectors. It
is advisable to retract the EDX collimator when mounting / removing
the detector on / from the objective pole piece.

FIGURE 7-15 GAD INSTALLATION AND HOLDER POSITION

Detector Settings
Select the GAD from the Detector Settings module Detector list box.
Choose the required Mode by ticking the radio button:
• The Z Contrast (A+B) is the normal BSE image with suppressed
topographical contrast and maximum atomic number contrast.
• The Topography (A-B) is the pseudo-topographical image with
suppressed atomic number contrast and maximum topographical
contrast.
• The Segment A / B (Left / Right) uses shadows to create strong
topographical and atomic number contrast.
Obtaining Image in BSE Mode
1. Install one of the diodes and select the corresponding Detector.
2. Close the chamber door and pump down the chamber. 
When the GAD diode is installed, No Accessory / GAD cone must
be selected in the PLA Configuration dialogue when this appears.
3. When the Vacuum is ready, switch on the accelerating voltage and
slowly increase the contrast and brightness to obtain an image.
Note: 
Whenever the GAD is selected, the optical quad is paused (because the
CCD camera infra-red LEDs are switched off not to emit the photons
supersaturating the detector diode).

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 System Options: Energy Dispersive X-ray (EDX) Analysis

Energy Dispersive X-ray (EDX) Analysis

The EDX (sometimes referred to also as EDS analysis) is a technique

used for identifying the elemental composition of the specimen, or an area
of interest thereof. It works as an integrated feature of a scanning electron
microscope (SEM), and cannot operate on its own without the latter.
The specimen is bombarded with an electron beam inside the
microscope column. These electrons collide with the specimen atoms'
own electrons, knocking some of them off in the process. Positions
vacated by ejected inner shell electrons are occupied by a higher-energy
electron from an outer shell, while giving up some of its energy by
emitting an X-ray. The amount of energy released depends on which
shell it is transferring from / to. The atom of every element releases 
X-rays with unique amount of energy, identifying it.
The output of an EDX analysis is an EDX spectrum, which is just a plot of
how frequently an X-ray is received for each energy level. The higher a
peak in a spectrum, the more concentrated the element is in the
specimen.

HIGH VACUUM
HiVac operation gives the most accurate X-ray results, but the sample
must be electrically conductive.

FIGURE 7-16 X-RAY IMAGING IN HIVAC MODE

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LFD EDX ANALYSIS

EDX analysis should be performed at the lowest possible gas pressure,
so it should be done with the LFD. Normally, X-ray analysis is performed
with a relatively high beam current so that there is enough signal for a
good SE image even at very low gas pressure.
The Hot Stage cone can also be used with the LFD for X-ray analysis
and has a field of view twice as large as the X-ray PLA.

FIGURE 7-17 LFD CONFIGURATION FOR THE EDX ANALYSIS

GSED EDX ANALYSIS

The ESEM mode allows observation of electrically insulating samples,
but care must be taken when using this mode to collect X-ray results.

FIGURE 7-18 X-RAY IMAGING WITH THE GSED

Some of the electrons are deflected due to interaction with the chamber
gas. The deflected electrons form a “skirt” around the main beam. The
skirt electrons will hit the sample at points that are remote from the area
of interest, and generate X-rays from these points.
The number of skirt electrons increases with chamber pressure and the
distance that the beam travels through the gas. The effect of these skirt
electrons can be minimized by reducing gas pressure, or by shortening
the distance between the sample and the final PLA.
The X-ray detector is designed for the sample to be at 10 mm WD, which
is too long for optimum imaging with a high pressure detector such as the
GSED. For this reason, the ESEM is supplied with a special X-ray PLA
which is used in conjunction with the LFD to give the best results.

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 System Options: Energy Dispersive X-ray (EDX) Analysis

GAD EDX ANALYSIS

Maximum detector response is around the 8,5 mm WD, providing an
atomic number contrast, when the resolving power is better than 0.1 (in
the Atomic number range around 20).

FIGURE 7-19 X-RAY GAD CONFIGURATION IN ESEM MODE

STEM EDX ANALYSIS

Set the sample surface to 10 mm WD.
Select the area of interest in the STEM mode and perform X-ray
analysis, mapping or line scans as appropriate.
Because the samples are not bulk in nature the beam spread normally
associated with SEM samples is greatly reduced and therefore higher
spatial resolution can be obtained with the STEM detector. This also
provides less background in the spectrum and allows better separation
of peaks as well as more accurate lower count rate mapping. The high
voltage chosen for the analysis still depends mainly on the composition
of the sample.

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System Options: Cooling Stage

Cooling Stage

The Cooling stage (CS) is used to control the sample temperature

± 20 °C around the ambient, uppermost from - 25 °C to +55 °C and to
observe it with the use of FEI electron microscope. In conjunction with a
specimen chamber water vapour pressure it can be used to create a
water condensation on the sample surface to keep it wet.

WAR N I N G ! 
Opening the microscope chamber does not switch off the cooling.
When operating the Cooling stage, please be aware that
neighbouring surfaces can become cold.

COOLING STAGE PARTS

• The Cooling stage assembly
• The Chamber feed-through plate
• The Cooling stage controller and cables
• The Water chiller, The Flow box and Cooling water hoses

FIGURE 7-20 COOLING STAGE SYSTEM BLOCK DIAGRAM

Cooling Stage Assembly

is mounted onto the microscope stage using the mounting adapter.

Caution! 
The presence of water hoses and cables inside the chamber causes
a risk of cooling stage and further the vacuum system damage (the
hoses could be pulled out of the stage and water could spill into the
vacuum port in the chamber bottom). Once the cooling stage
assembly is installed, it should be moved only by ±10 mm from the
home position in X- / Y-axis direction. Rotation and Tilting are
locked automatically. Tilt can be released by a user in the Stage
module / Coordinates tab / Tilt check box (see Chapter 5). Be
aware of the limitation!

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FIGURE 7-21 COOLING STAGE ASSEMBLY

• The mounting adapter enables to attach the Cooling stage to the

microscope stage.
• The Cooling stage base holds the thermoelectric module and the
specimen holder with the use of a thermal grease. Water hoses and
the inner cable are connected permanently to the base.
• The thermoelectric module is a small wafer composed of PN
semiconductor layers. When current passes through these elements,
one side of the wafer heats and the opposite one cools. Reversing the
polarity switches cold and hot sides. This is referred to as the Peltier
effect.
• The thermistor is placed near the sample (inside of the Specimen
holder – a plate into which the Sample holder is inserted), thus
giving accurate temperature readings.
• The Delrin cover keeps the entire assembly together.
• The cooling stage comes with different Sample holders, which are
used for various sample types (see the consumable table below).
– The Flat holder should be used for flat samples (sheets, powders,
etc.). It can also be used for bulk samples up to 4 mm.
– The Dual cup holder is reversible. It has a shallow cup on one side
(for powders, tiny particles, or beads). A larger cup on the other side
should be used for thick liquids, and bulk samples between 4 mm and
8 mm.
– The Deep cup holder should be used for all other liquids and bulk
samples larger than 8 mm.
– The WetSTEM holder could fit the sample grid for a STEM
observation.
Note: 
All of the sample holders have a groove cut beneath the cup bottom.
This allows a condensation to escape from beneath the holder, so
that the liquid do not force the sample holder out from the specimen
holder.

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System Options: Cooling Stage

FIGURE 7-22 COOLING STAGE ASSEMBLY 

MOUNTING ADAPTER WITH MOUNTING SCREW

Chamber feed-through Plate

provides feed-through connectors for the cables and water hoses.

FIGURE 7-23 CHAMBER FEED THROUGH PLATE 

INSIDE / OUTSIDE

Heating Stage connector

Water hoses flanges

(blue color)

Cooling Stage connector

Cooling Stage Controller

This microprocessor-controlled board provides accurate and stable
automatic temperature control of the cooling stage and interfaces with
the xT microscope Control software.
The temperature measurement accuracy is determined by the thermistor
and the controller. These specifications are as follows:
• thermistor accuracy: ± 0.1 °C
• normal / limit temperature range: 
± 20 °C from an ambient temperature / from - 25 to + 55 °C
Additionally, accuracy of a temperatures readout depends on sample
conductivity, thickness, shape and general thermoelectric properties that
vary by sample and mounting method.
Cables
• The Outer Cable connects the outer feed-through plate side with the
controller board.
• The Inner Cable connects the inner feed-through plate side with the
cooling stage (to which the cable is permanently attached).

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FIGURE 7-24 OUTER AND INNER CABLES

Water Chiller, Flow Box and Cooling Water Hoses

Note: 
In case the waterless Cooling stage is installed the following devices are
not available.
An external water chiller is provided to efficiently remove excess heat
from the temperature stage.

WA R N I N G ! 
The temperature stage water chiller is powered by the individual
power cord directly. The hazardous voltages may be present even
when the microscope power plug is disconnected!

FIGURE 7-25 THE WATER FLOW BOX CONTROL BOARD

The water flow box is installed between the water chiller and the
chamber feed-through plate. It monitors a water flow via a sensor on
each line and closes both solenoid valves if a failure is detected to
protect the system against a water leak into the chamber.
Cooling water hoses are delivered: the shortest set of hoses is
connected to the stage on one end, the other end goes to the inside of
the feed-through plate. One set of hoses goes from the outside of the
chamber feed-through plate to the water flow box. Next one connects the
water chiller with the water flow box.

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COOLING STAGE INSTALLATION

The chamber feed-through plate should be in place and remain installed.
1. Vent the specimen chamber and open the door.
2. Remove any sample holder from the stage rotation head.
3. Place the mounting adapter on the stage rotation head and fix it
through the center using the mounting screw (finger tight).
4. Slacken off the mount locking screw on the stage body side using a
metric 0.5 mm hex wrench, then place the stage on and over the
mounting screw.
5. Tighten the mount locking screw. The water hose connectors go
towards the rear of the chamber.

Cables and Water Hoses connection

6. The loose end of the inner cable (9-pin D-type connector) should be
installed on the corresponding connector on the feed-through plate.
Also plug the water hoses.
7. One end of the outer cable goes to the outside of the Chamber feed-
through plate on the connector labeled Cooling stage and the other
end to the rear of the CS controller.

Water Flow Box installation and operation

8. Check that the water dam is fitted into the HiVac port in the chamber
bottom.
9. Put the Water Flow Box between the chiller and the feed-through
plate. The larger hose should connect from the chiller Outlet to the
Flow Box input marked From Chiller. The water flow path should
make a loop between the chiller, through the water flow box and
stage, then back.
Note: 
It is important to keep the water chiller away from the microscope
console to prevent vibrations.

FIGURE 7-26 CONNECTING THE WATER FLOW BOX

10.Plug the water flow box power cable but leave the power switched off.
(The other end of this cable goes to the + 24 V power supply inside
the microscope console. This should have been connected by a
service).
11.Turn on the water chiller. Water does not flow at this point, since the
valves in the Flow Box are closed when it is off.
12.Turn on power to the Flow Box. An alarm sounds, indicating that there
is no flow through the box.
13.Press and hold the Start Flow button down until all the air is out of the
water lines (this can be seen as water flows through them).
Thereafter release the button.

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14.Make sure that the Flow OK light on the Flow Box is on. This
indicates that water flow is working; i.e. that there are no leaks in the
system. The light remains illuminated until there is a leak, or if the
Stop Flow button is pressed, which could be done at any time to
close the valves and shut off the water flow, for whatever reason,
which is indicated by an alarm sound. The Start Flow button must be
pressed and held again to re-establish flow through the system.

Caution! 
Never pump the specimen chamber without checking for water
leaks first.

WetSTEM

The WetSTEM II is used to observe objects dispersed in thin liquid layer

by transmitted electrons. It is the cooled sample holder which does not
include any solid state detector - it is compatible with the retractable
STEM detector. The WetSTEM assembly consists of the following parts:
• The WetSTEM assembly
• The Chamber feed-through plate
• The Cooling stage controller and cables
• The Water chiller, The Flow box and Cooling water hoses

FIGURE 7-27 WETSTEM SET

It is mounted onto the microscope stage the same way as the Cooling
Stage (see above). The software control corresponds to the one
described for the Cooling Stage and the STEM I detector (see above).
The software control corresponds to the one described for the Cooling
Stage and the STEM I detector (see above).

WetSTEM Basic operations

The WetSTEM experiments are very dynamic and proper observation
conditions can be stable for a few minutes only.
Note: 
Precise control of sample humidity is essential in WetSTEM
experiments. Therefore, it is highly recommended to execute the cooling
stage calibration procedure (see above).
1. Plug the GSED detector on. Alternatively, the GAD, the Low kV PLA

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System Options: WetSTEM II

or the X-Ray PLA can be used.

2. Insert the TEM grid (ideally holey carbon coated grid) into the
WetSTEM Sample holder.
3. Insert the WetSTEM Sample holder with the grid into the WetSTEM
assembly and tighten it by Fixation sleeve.
4. Pre-cool empty grid to 1.5°C for 15 minutes.
5. When it is cold, put a droplet of liquid with specimens on the grid.
6. Use a filter paper to siphon the liquid off the grid until only a thin liquid
layer remains.
7. Add water droplets in the 4 indentations.
8. Set pressure to 750 Pa, set purging to 800-1 000 Pa in two cycles
(see Preferences / ESEM tab), move the stage away of the beam
axis and pump the chamber.
9. When the vacuum status is Pumped (750 Pa), move the stage back
to the observing position and switch the Beam On 
(15 – 30 kV, spot size 4 – 5).
10.Set the GSED / LVSED for Quad 3, go to a working distance 
5 –10 mm (depends on the detector / lens insert cone plugged on)
and optimize the imaging.
11.Set the STEM I detector segment A for Quad 1 and segment B for
quad 2.
12.Liquid stays on grid meshes during the observation. If there is no or a
poor STEM detector sample imaging, the liquid layer could be too
thick. Decrease pressure slightly until the liquid layer becomes
correctly thick.

WetSTEM II

The WetSTEM II is used to observe objects dispersed in thin liquid layer

by transmitted electrons. It is the cooled sample holder which does not
include any solid state detector - it is compatible with the retractable
STEM detector. The WetSTEM assembly consists of the following parts:
• The WetSTEM assembly
• The Chamber feed-through plate
• The Cooling stage controller and cables
• The Water chiller, The Flow box and Cooling water hoses
It is mounted on the specimen stage the same way as the row bar holder
of the retractable STEM (see above). The software control corresponds
to the one described for the Cooling Stage and the STEM I detector (see
above).

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FIGURE 7-28 WETSTEM II SET

WetSTEM Basic operations

The WetSTEM experiments are very dynamic and proper observation
conditions can be stable for a few minutes only.
Note: 
Precise control of sample humidity is essential in WetSTEM
experiments. Therefore, it is highly recommended to execute the cooling
stage calibration procedure (see above).
1. Plug the GSED detector on. Alternatively, the ESEM GAD, the Low
kV PLA or the X-Ray PLA can be used.
2. Move the stage rotation to -90° and Z to the lowest position.
3. Mount the Wet STEM II to the stage with cable pointing to the left and
hoses pointing towards the back side of the chamber.
4. Connect cables and hoses to cooling stage feedthrough.
5. Insert the TEM grid (ideally holey carbon coated grid) into the
WetSTEM II Sample holder.

FIGURE 7-29 WET STEM II SAMPLE HOLDER, OPEN / CLOSED

6. Insert the WetSTEM II Sample holder with the grid into the WetSTEM
II assembly.

FIGURE 7-30 WET STEM SAMPLE HOLDER INSERTION

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System Options: WetSTEM II

7. Pre-cool empty grid to 1.5°C for 15 minutes.

8. When it is cold, put a droplet of liquid with specimens on the grid.
9. Use a filter paper to siphon the liquid off the grid until only a thin liquid
layer remains.
10.Add water droplets in the 4 indentations.
11.Set pressure to 750 Pa, set purging to 800-1 000 Pa in two cycles
(see Preferences… / ESEM tab), move the stage away of the beam
axis and pump the chamber.
12.When the vacuum status is Pumped (750 Pa), move the stage back
to the observing position and switch the Beam On (15 - 30 kV, spot
size 4 - 5).
13.Set the GSED / LVSED for Quad 3, go to a working distance5 -10 mm
(depends on the detector / lens insert cone plugged on) and optimize
the imaging.
14.Set the STEM II detector Bright Field for Quad 1 and Dark Field for
quad 2. Press insert button of retractable STEM on detector page of
user interface. Before insertion the retractable STEM detector, the
chamber must be pumped to HiVac or LoVac, otherwise the Insert
button is not active (a tooltip occurs under mouse cursor). When
clicking the Insert button the dialogue requires confirmation of the
correct sample holder installation to enable detector insertion. When
the stage is not in a correct position for insertion, another dialogue
appears requiring a confirmation of moving it to the safe position.

FIGURE 7-31 STEM II INSERTION DIALOGUES

15.Liquid stays on grid meshes during the observation. If there is no or a

poor STEM detector sample imaging, the liquid layer could be too
thick. Decrease pressure slightly until the liquid layer becomes
correctly thick.
16.Retracting the STEM II is automatic with the Stopping / Starting the
server or venting the chamber. Otherwise a user can use the Retract
button.
17.After STEM detector retraction stage is lowered by 10mm when
chamber is being vent.

WetSTEM II vibration suppression

Cooling water flowing through WetSTEM II assembly causes vibrations
visible in the imaging at higher magnification, which can be suppressed
in two ways.
1. It is possible to switch off flow of cooling water for experiments not
exceeding several minutes, sample temperature will remain stable for
a short certain period of time (grabbing an image) without cooling
water flow.
2. It is possible to use docking feature of WetSTEM II for long time
experiments requiring keeping the cooling water circuit switched on.

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 System Options: WetSTEM II

3. Docking pins of two different heights can be mounted on Wet STEM II

assembly to be docked to retractable detector docking bracket in
order to suppress vibrations caused by cooling water significantly.
Two lengths of docking pin enable user to dock in eucentric working
distance (longer version) or working distance of approximately 5.5mm
(shorter version).
4. It is needed to find the place of interest first and then move in Z axis to
position close to the docking bracket by small increments. The
moment when docking is achieved can be checked in image of CCD
camera or by small shift of the observed area which occurs after
docking pin makes firm contact to docking bracket.
5. Small movement of WetSTEM II docked to docking bracket is
possible, for larger movements it is necessary to lower Z coordinate
of the stage first.
6. WetSTEM II holder is automatically lowered by 10mm from actual
position when stage is vented. This prevents damage of docking pin
during stage door opening.

Cooling Stage Consumable

v
TABLE 7-2 COOLING STAGE CONSUMABLE PARTS
Item Part #
Sample holder
Flat 4022 290 08612



Sample holder
Deep 4022 290 08592



Sample holder
Dual  4022 290 08602
(possible to use both sides)


Sample holder for 

WetSTEM: assembled



Sample holder for  

WetSTEM: parts
base 4022 290 32101
lid  4022 290 32111

Sample holder for  1019490

WetSTEM: 


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System Options: WetSTEM II

SOFTWARE CONTROL

Temperature Stage Control Module

The cooling / heating stage is software controlled using the xT
microscope Control software / Temperature Page (added when any
temperature stage is installed) / Temperature Stage Control module.
Cooling / Heating button
activates the Cooling / Heating stage software control. When the stage is
active / inactive the corresponding button is Yellow / Grey.

Temperature tab
• The Actual read-out box displays the actual temperature measured
by the temperature stage hardware (the same value is used in the
databar).
• The Target edit box sets the target temperature. It is active when
either stage is enabled and no profile is running.
• The Ramp edit box sets the speed of the temperature change. It is
active when either stage is enabled and no profile is running.
• Clicking the Go To button starts to proceed to the target temperature.
It is active when no profile is running and after any change in the
Target / Ramp edit box.
Temperature / Pressure Profile
Edit boxes are used to define temperature / pressure profiles or cycles.
Each row pertains to a single heating cycle.
• Temp. / Pressure - desired target temperature / pressure
• Ramp - speed of a temperature / pressure increase / decrease
• Soak time - specifies time (hours : minutes : seconds) for how long
the target temperature / pressure should be held after it is reached
Edits are active when the profile is not running. When the profile is
running the box mark at the end of the actual step line is displayed in
yellow.
• The Start / Stop toggle button starts / stops the Temperature /
Pressure profile. The profile starts with step one. The first step with an
empty or a zero Ramp or a zero Temp. value stops execution of the
profile.
• The Next / Clear toggle button: when profile is running the caption is
Next and clicking the button bypasses an actual cycle in a multiple
set immediately. When no profile is running the caption is Clear and
clicking the button resets all values. The button is disabled when the
Hold button is active.
• The Hold button switches keeping of the Actual temperature /
pressure invariable on / off. Clicking the button turns it to yellow. It can
be used to interrupt a ramping cycle and maintain the controller at the
actual set-point. When clicking the Hold button during a ramping
cycle, the controller holds the actual temperature indefinitely, until the
button is clicked again.
Note: 
Edited values are checked for limits, values out of limits are not
accepted.

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 System Options: WetSTEM II

Humidity tab
The Humidity tab is displayed only when the CS is connected to the feed-
through plate connector.
This application controls humidity of wet samples during ESEM
microscope operations with the FEI Cooling Stage installed. It is possible
to do so manually by the sample temperature and specimen chamber
water vapour pressure control. User can set a desired sample humidity
directly via the Humidity tab.
Note: 
A humidity value can also be displayed in the databar.
To start the work and control the humidity follow the steps:
1. Vent the chamber. Install the GSED, if it is not.
2. Insert a wet sample and add water drops when needed.
3. Close the door and pump down the chamber to the LoVac / ESEM
mode.
4. Set the Column module / Pressure (usually 400 Pa).
5. Click the Cooling button.
6. Set the Temperature tab / Target temperature (usually 2 - 5 °C) and
click the Go To button
7. Set Humidity tab / Target humidity (usually 90 - 100%) and click the
Go To button.
Any pressure change causes a target temperature change and vice
versa to keep a desired humidity constant.
Three phase diagram shows a pressure (vertical axis) against actual
temperature (horizontal axis). If the Go To button either at Temperature
or at Humidity tab is active (which is represented by its yellow color),
moving red line appears in the graph to depict actual pressure /
temperature values.
If the system is at the stable condition, changing target humidity causes a
pressure change.

Calibration
For precise humidity control a calibration of each sample must be
performed. By obtaining condensation on a sample surface and
correction of the theoretical 100% relative humidity value to the actual
conditions, a temperature difference between thermistor readout and
real sample surface temperature can be minimized (assuming pressure
readout is precise).
Calibration procedure
1. Set the sample pressure and temperature appropriate to 90%
humidity.
2. Obtain a GSED image of your sample surface.
3. Slowly increase pressure (humidity) until water drops start to grow on
the surface.
4. Right-click & drag over the humidity graph area to call the popup
menu.
5. Click the Calibrate item. 
The Restore item sets calibration values to pure theoretical ones.

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System Options: WetSTEM II

153 - Cooling Stage Calibration

For precise humidity control this alignment procedure must be
performed.
By obtaining condensation on a sample surface and correction of the
theoretical 100% relative humidity value to the actual conditions, a
temperature difference between thermistor readout and real sample
surface temperature can be minimized (assuming pressure readout is
precise).

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COOLING STAGES BASIC OPERATIONS

Condensation Point
When determining the Cooling stage condensation point, use the flat
sample holder. This positions the sample closer to the thermistor, thus
giving a more accurate reading. Use carbon paint or carbon tape to hold
samples onto the holder. Better contact between the sample and the
holder yields better heat transfer.
Pressure and Temperature control
It is better to control the condensation by a pressure control, as opposed
to temperature control. Firstly, the thermoelectric module heat pumping
capability is very small; therefore a temperature is hard to control
accurately. Secondly, it is easier to keep the pressure below the
condensation point, which prevents water condensate from raising the
sample temperature (cooling water takes longer time to reach the set
point). As a general rule, condensation is achieved by the following
procedure:
1. Set the pressure to 540 Pa (4.0 Torr).
2. Bring the sample to 5 °C.
3. Raise the pressure until water condenses on the sample. Keep the
pressure below the condensation point 860 Pa (6.5 Torr).
Keeping sample wet
Water in the sample tends to evaporate during the pump-down cycle.
The simplest way to keep the sample wet is to accurately control sample
temperature and pressure conditions. Another method is to cool
mounted sample to its operating temperature before it is put into the
chamber. Then add several drops of water to the stage base; this
displaces air faster during pump-down. There is an indentation on each
corner of the base for this purpose.
Once the system enters Low Vacuum / ESEM mode and the chamber
pressure has reached the set point value, the chamber automatically
Purges. It repeats this process 5 times. Wait until the pressure returns to
the set point.

FIGURE 7-32 ADDING WATER TO COOLING STAGE BASE

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Condensation and Detector

When imaging with the GSED, water droplets on the sample appear
darker than the surrounding features. One exception to this occurs when
imaging an oil / water emulsion, in which case the oil always appears
darker than water.

Caution! 
When using shorter working distances, water from the sample can
splash onto the GSED. To avoid this, start with a longer working
distance until the sample has equilibrated, then move to a shorter
working distance to optimize the image.

Using bulk samples

For more accurate temperature readings, bulk samples should be placed
as flat as possible on the holder. The further away from the holder
surface the sample is, the less accurate the temperature reading is.
Another way to ensure accuracy with bulk samples is to maintain the
temperature of the sample for about 5 minutes before condensing. This
equilibrates the sample so that the temperature is the same throughout.

High magnification imaging

At magnifications above 20 000×, water moving through the CS causes
small vibrations. To prevent this, shut the water off temporarily using the
valve on the water hose line attached to the chiller. The Stage continues
to cool the sample for about 15 minutes without water cooling. After this
time the sample temperature rises.

Caution! 
If the cooling stage is used without a heat sink connection, severe
damage may result to the thermoelectric module. Do not operate
the CS for longer than 15 minutes without cooling water, else
damage occurs to the device.

Cooling below Ice Point

In most cases, the power of the thermoelectric module is not sufficient to
freeze large quantities of bulk water. Small water drops can be frozen on
the stage using the following procedure:
1. One can set the external water chiller to 5 °C. Allow the chiller time to
cool the water. Keep the pressure in the chamber below 800 Pa
(6 Torr) to keep water from condensing on the cooling lines.
2. Set the temperature of the cooling stage to -5 °C. As the temperature
drops, decrease the pressure gradually to 400 Pa (3 Torr) at the same
time as the temperature reaches -5°C. If the pressure is dropped too
quickly, the bulk water in the sample evaporates; conversely, if the
pressure is reduced too slowly, water condenses onto the sample and
raise the temperature.

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WATER COOLED TEMPERATURE STAGE

OPERATION TERMINATION
1. Let the stage compensate for the room temperature.
2. Shut down the water chiller.
3. Disconnect one of the water hoses coming out the water flow box to
the chamber.
4. Push START FLOW button and push the water out from the lines with
the use of the compressed air (breath).
Make sure the system is drained before disconnecting the inner
hoses. This prevents excess water from dropping into the chamber
and slowing the time it takes for the chamber to pump down again.
5. Install one water line plug into each water fitting on the inside of the
Chamber feed-through plate.
The water fittings on the inside of the feed-through plate are designed
to create a pressure seal whenever the water lines on stage are not
connected. If there is any debris in the cooling water, it can collect on
the fitting o-ring seals and cause a leak. To prevent this, water plugs
must be installed over the fittings on the inside of the feed-through
plate whenever the stage is removed.

FIGURE 7-33 CHAMBER FEED-THROUGH PLATE (INSIDE)

6. Once the stage has been drained and both water lines have been
removed, blot out any remaining water from the connectors using a
cotton swab or paper towel. Another way to remove water from the
connectors is to pump down directly to Low Vacuum / ESEM mode
(this causes the pump down to take longer than usual).
Note: 
When pumping the chamber to Hivac mode after the stage use,
always enter Low Vacuum / ESEM mode first, otherwise the system
may not pump down to Hivac mode on the first attempt.

Caution! 
To avoid water leaks in the chamber, the stage must be removed
and water plugs installed before going into HiVac mode.
7. Once the water lines are disconnected and the water plugs installed,
the temperature stage can be removed from the chamber in the
reverse order of as described in the Installation procedure.

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System Options: Heating Stage 1 000 °C / 1 400 °C

Heating Stage 1 000 °C / 1 400 °C

The Heating stage (HS) is used to control the sample temperature from
40 °C to 1 000 °C / from 200 °C to 1 400 °C and to observe sample with
the use of FEI electron microscope.

WAR N I N G ! 
Opening the microscope chamber does not switch off the heating.
When operating the Heating stage, please be aware that
neighbouring surfaces can become hot.

HEATING STAGES PARTS

• The Heating stage assembly
• The Chamber feed-through plate
• The Water chiller, The Flow box and water hoses
• The Heating stage controller and cables
• The High temperature GSED
• The HS 1 400 Heat shield assembly
• The HS 1 400 Heat shield and Sample bias (SSB)

FIGURE 7-34 HEATING STAGE SYSTEM BLOCK DIAGRAM

Heating Stages Assembly

is mounted onto the microscope stage using the dovetail stage adapter.
The HS 1 000 and the HS 1 400 have the same construction and look
similar. Each stage is appropriately labeled (engraved) on the top
surface.

Caution! 
The presence of water hoses and cables inside the chamber causes a
risk of heating stage and further the vacuum system damage (the
hoses could be pulled out of the stage and water could spill into the
vacuum port in the chamber bottom). Once the heating stage
assembly is installed, it should be moved only by ±10 mm from the
home position in X- / Y-axis direction. Rotation and Tilting are locked
automatically. Tilt can be released by a user in the Stage module /
Coordinates tab / Tilt check box (see Chapter 5). Be aware of the
limitation!

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 System Options: Heating Stage 1 000 °C / 1 400 °C

FIGURE 7-35 HEATING STAGE ASSEMBLY

• The dovetail mounting adapter enables to attach the Heating stage

to the microscope stage.
• The Heating stage base (5) holds all components.
• The Top and Bottom Insulators (2 and 3) are disk-shaped pads
made of aluminous foam, placed inside the assembly.
• The Heater sits between the top and bottom insulators. It is a micro-
furnace in which samples are heated from the sides, allowing uniform
temperature gradients. It includes the heating element, thermocouple,
ceramic connectors (4) and crucible, in which the sample is placed.
• The Cover Plate (1) holds the heating stage components in place.
• Two ceramic papers (Heater cover and Heater cover 2) sit at the top
of the top insulator; they reduce heat losses from the heater and
protect the insulators.
To remove the crucible from the stage assembly, grasp the edge of
the crucible with a pair of tweezers and lift it out. There is a hole in the
bottom of the stage which can be used to remove the crucible, should
it become stuck in the heater. Use a small rod or wooden stick to
access the crucible through this hole.

Chamber Feed-through Plate

See the description above (the Cooling stage).
Water Chiller, Flow Box and Cooling Water Hoses
See the description above (the Cooling stage).

Heating Stage Controller

This microprocessor-controlled board provides accurate and stable
automatic temperature control of the heating stage and interfaces with
the xT microscope Control software. It has an internal temperature limit
for either stage to protect the equipment.
The temperature measurement accuracy is determined by the
thermocouple and the controller. These specifications are as follows:
• HS sensor accuracy: ± 1 °C
• HS 1 000 normal operating range / limit temperature: 
up to 1 020 °C
• HS 1 400 normal operating range / limit temperature: 
up to 1 400 °C
Additionally, accuracy of temperatures readout depends on sample
conductivity, thickness, shape and general thermoelectric properties that
vary by sample and mounting method.

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System Options: Heating Stage 1 000 °C / 1 400 °C

Cables
The Outer Cable is 4-ended cable connecting the outside of the
chamber feed-through plate with the HS controller and SSB board. The
greater / lesser spherical connector connects to the connector labeled
Heating stage / Cooling stage (this is used in case your system enables
both stages, to use only one cable). The 25-pin / 9-pin connector
connects to the HS Controller / SSB.
The Inner Cable is 3 or 4-ended cable connecting the inside of the
Chamber feed-through plate with the heating stage assembly. The 15-pin
connector goes to the appropriate inner feed-through plate connector,
the other ones connect connectors ascribed to the Heater, to the Sample
Bias and to the Thermocouple.

FIGURE 7-36 OUTER CABLE AND INNER CABLES

High Temperature GSED

The High Temperature GSED must be installed if the heating stage is
going to be operated above 500 °C (up to 1 400 °C), as the standard GSED
could be damaged at these conditions. It is a cap containing the cone with
aperture (PLA) which is pressed onto the ESEM insert. A printed board
adapter plugs into the signal connector inside the chamber. On the other
end of this board is a wire which clips onto the cap.
The detector is located just over the heat shield. Any working distance
can be used.

FIGURE 7-37 HIGH TEMPERATURE GSED

Note: 
The operating characteristics of the GSED and the high temperature
GSED are slightly different.
Installing High Temperature GSED
1. Vent the specimen chamber and open the stage door.
2. Snap the wire hook on the printed circuit board onto the cap.

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 System Options: Heating Stage 1 000 °C / 1 400 °C

3. Plug the printed circuit board adapter into the connector on the
chamber ceiling.
4. Press the cap onto the final lens ESEM insert (see Chapter 2).

1 000 °C Heating Stage variances

Heat Shield
is a small part sitting on the HS assembly top. The heat shield is most
effective above 600 °C, where the sample is more prone to a radiant heat
loss. In this environment the heat shield creates an “oven” effect helping
to keep the temperature consistent throughout the sample.
Crucibles
Crucibles have a finite lifetime, and are meant to be disposable when it
becomes too contaminated and can no longer be cleaned.
Ceramic crucibles also shrink after some time of use. This could cause
vibrations, if the crucible does not fit tightly in the heater. A Ceramic
paper pad provided with the HS option is used to fix the crucible. Place
the paper (or a part of it) by tweezers between the heater and the
crucible.
• The Standard MgO crucible is used for thin samples and powders.
• The Low MgO crucible is provided for tall or bulky samples (it sits
lower into the heater for more uniform sample heating).
The MgO crucibles can be used for all atmospheres.
• The Graphite crucible is to be used only in an inert or reducing
atmosphere below 900 °C.

1 400 °C Heating Stage variance

1 400 °C heating stage assembly has a limited lifetime and has not
accurate temperature readings below 800 °C. Because of these reasons
two 1 400 °C heating stage assemblies and one 1 000 °C heating stage
assembly are supplied within the FP 2300/06 option.
The inner cable for each stage type is different and marked by a label:
HS 1 000 / HS 1 400.
Heat Shield Assembly
is attached to an individual feed-through plate. The shield (comprises
multiple layers of aluminous paper supported by netting stainless steel
disks) is attached to the end of the Swing Arm (for a large chamber it is
necessary to use the extender). The Swing Arm is used to move the
shield away by a knob on the outside of the feed-through plate.

FIGURE 7-38 1 400 °C HEAT SHIELD ASSEMBLY

Caution! 
When the Heat shield is installed, the stage tilt is limited, even if the
arm is pushed away.

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System Options: Heating Stage 1 000 °C / 1 400 °C

Adjusting Heat Shield

If the heat shield touches the high temperature GSED or sits farther than
2 mm from it, the arm needs to be adjusted. It must be centred in the X /
Y directions too (this typically need not be adjusted).
1. Loosen the Z adjustment hex screw and move the heat shield up so
that the tip of the GSED sits in the heat shield hole.
2. Use the X / Y adjustment screws to make any necessary centring
adjustments.

FIGURE 7-39 ADJUSTMENT OF THE 1 400 °C HEAT SHIELD

3. Move the arm to the 2 mm distance from the GSED and re-tighten the
Z adjustment screw.
Note: 
For the 150 mm stage the extender must be installed.
Heat Shield and Sample Bias (SSB) board
This board provides voltages used for the following features:
• A heat shield bias voltage (0 - 300 V) draws the electrons from the
sample through a small opening in the heat shield.
• At low temperatures, the sample bias (± 50 V) is negative (with
respect to ground) and pushes the electrons to the detector. At higher
temperatures, this bias is positive to suppress the thermal electrons
which are generated by a sample.
Note: 
The safety interlock causes the bias voltages to switch off whenever the
specimen chamber is vented; however make sure the supply is turned off
before changing any connection.
Crucibles
The crucible types and its application see above (HS 1 000).
MgO crucibles are coated with a conductive platinum paste and a
platinum wire runs inside it, allowing a sample bias to be applied directly
under the sample.
Crucibles have a finite lifetime, the platinum coating wears out after
some time.
Before inserting the crucible into the heater always check the sample
bias wire shape to avoid a poor electrical contact.
The Platinum (the heating element is made of) reacts with the silicon,
therefore always avoid free silicon.

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 System Options: Heating Stage 1 000 °C / 1 400 °C

HEATING STAGE INSTALLATION

1. Remove an actual (if any) sample holder adapter.
2. Install the dovetail included onto the stage rotation base (if it is not in
place) parallel to the door opening direction.
3. Slide the stage module onto the dovetail base from the rear forward,
until it stops (1). The stage has a pin which ensures the sample is
centred beneath the beam.
Note: 
Hoses must be oriented towards the chamber back always.
4. Tighten the locking screw on the stage assembly right side (2).

FIGURE 7-40 INSTALLING THE HEATING STAGES

Cables and Water Hoses connection

5. Connect the 15-pin connector of the 4-ended Inner / Outer cable to
the appropriate feed-through plate connector.
Note: 
Check the inner cable corresponds with the stage type.
6. Connect the Heater power, Thermocouple and Sample Bias (for
HS 1 400) connectors. Also plug the water hoses.

FIGURE 7-41 CONNECTIONS TO THE HEATING STAGE

7. The greater spherical Chamber Interface 4-ended cable connector fits

to the outside of the Chamber feed-through plate, on the connector
labeled Heating stage. (The lesser spherical connector works with the
CS.)
8. The 25-pin connector fits to the HS Controller and the 9-pin connector
to the SSB (only for HS 1 400).
Water Flow Box installation and Operation
See description above (the Cooling stage).

C O N F I D E N T I A L – FEI Limited Rights Data 7-47

System Options: Heating Stage 1 000 °C / 1 400 °C

SOFTWARE CONTROL

Temperature tab
See description above (the Cooling stage).

Advanced tab
The Advanced tab is displayed only when the HS is connected to the
feed-through plate connector.
• The Auto Power check box is cleared, the Power slider becomes
active and user can apply desired power directly to the heater. The
functionality is useful when working at temps above 1300 °C, when
regulation can be affected by a sample outgassing or a leakage
current.

Caution! 
The slider button shows % of maximum allowed power. Apply just
as many Watts as needed in order not to exceed 50 °C/min ramp
speed, otherwise your heater lifetime shortens. For advanced
users ONLY.
Additional HS 1 400 features
• The Bias Presets check box allows a user to apply sample and
shield bias values according to settings in the alignment procedure
150 (see below).
• The Heat Shield and Sample Bias sliders are used for the manual
sample and shield bias values setting.
• The power and biases can also be controlled via Manual User
Interface (MUI) modified knobs, which is a part of the 1 400 °C
heating stage option. The MUI performance could be set in the
Preferences… / General tab, where the following line appears:
MUI knobs assignment (Default / Heating stage) 
The Default setting always keeps the original functionality. The
Heating Stage setting assigns MUI knobs another functionality when
the Temperature Control module / Heating button is clicked. When
the HS is turned off or removed, the habitual functionality is restored
(see above).

FIGURE 7-42 MUI BUTTONS NEW FUNCTIONALITY

• the Stigmator X knob changes to the Power knob

• the Stigmator Y knob changes to the Enhanced Contrast knob
• the Shift X knob changes to the Sample Bias knob
• the Shift Y knob changes to the Heat Shield Bias knob

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 System Options: Heating Stage 1 000 °C / 1 400 °C

150 - Heating Stage Settings

This is the supervisor alignment procedure. Follow the Instructions. There
are different Alignments modules (Step 1) for 1 000 / 1 400 °C stages.
• Step 1 (HS 1 000): the Temperature Ramping Limit 
could be set up to 300 K/min (default value is 50 K/min).
• Step 1 (HS 1 400): the Maximum Ramp Speed enables to set
different limits for 3 temperature ranges (see image below) 
up to 300 / 50 / 20 K/min (default values are 50 / 10 / 10 K/min).
• Step 2 (HS 1 400): allows to preset values of Sample Bias and Heat
shield Bias (see above) and to set the Switching Point between
these two values.

Caution! 
Ramp speeds higher than 50 K/min strongly decreases the heater
lifetime and leads to regulation instability. When operating in higher
temperature ranges, high Ramp Speeds wear the heater much
more out.

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System Options: Heating Stage 1 000 °C / 1 400 °C

151 - Temperature Calibration

This is the supervisor alignment procedure. The HS 1 000 assembly is
calibrated by melting the silver sample (962 °C), the HS 1 400 assembly
is calibrated by melting the gold sample (1 064 °C). The calibration
samples are a part of accessory.
The HS assemblies are factory calibrated with the standard ceramic
crucible, at 400 Pa chamber pressure, under a water environment and
with the ramp rate 10 K/min. At these conditions the temperature shift
should be less than 50 K. In other case, contact your local FEI service
representative.
Note: 
Different pressure, environment and fast ramp speeds lead to a less
accurate sample temperature readout and to incompatible results.
Checking Calibration
The HS assembly calibration typically does not change over the heater
lifetime. However, if greater precision is required in the actual
temperature read-out follow the procedure:
1. Put a small piece of calibration sample onto the standard ceramic
crucible.
2. Move the stage by 10 mm from the center position to protect the
sample to be blown away during pumping the chamber.
3. Pump down the chamber. Obtain the sample image onscreen.
4. Start the 151 - Temperature Calibration alignment.
5. Reach the temperature 100 K below the expected melting point 
(50 K/min ramp rate can be used).
6. Slower the ramp rate to 10 K/min and set the target temperature to
10 K above the expected melting point.
7. Observe the sample and stop ramping just when the sample melts. 
Enter obtained temperature to the Ag / Au melting point: /
Measured edit box.
By finishing the procedure, the temperature readout is corrected to
match the theoretical value. A readout at 273 K is not influenced and a
linear interpolation is applied between these points.
Other samples with a verified Theoretical melting temperature (note the
vacuum and chamber environment conditions could influence it) can be
used in the User-defined calibration point: edit boxes. This introduces
another point to the calibration profile, so the linear interpolation starts at
273 K, proceeds to the 1. calibration point and from this point starts
another linear interpolation to the second calibration point. After reaching
the 2. calibration point the calibration correction remains constant to the
end of the temperature range.
Note: 
Maximal temperature correction is restricted to the (- 100 + 100) °C.

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 System Options: Heating Stage 1 000 °C / 1 400 °C

HEATING STAGES BASIC OPERATIONS

Setting up Temperature Profile

The temperature profile is a series of heating cycles consisting of a set
point temperature, ramping rate and soaking time. The controller
performs each cycle in succession, starting with the first set point and
going through each one until finished. This feature is useful for
performing dynamic experiments with specific temperatures and heating
times.
In the temperature profile example (see below) there are four setpoints
defined, each with its own ramp and soak time. The ramp (Rn) and soak
(Sn) periods are pointed out.

FIGURE 7-43 TEMPERATURE PROFILE

When the last cycle is finished, the controller holds at 600 °C (the last set
point) indefinitely until further action is taken.

Temperature Conductivity
The sample crucible temperature matches the thermocouple reading.
The actual sample temperature however varies, depending on the
sample thermal conductivity and its thickness.
The temperature at the conductive sample surface is closer to that at the
crucible, as heat is more likely to spread throughout. The temperature at
the non-conductive sample top surface is lower than that at the bottom.
This difference increases with a sample thickness.
With large samples, the exposed surface area provides a great deal of
heat loss through radiation; therefore the exposed surface is cooler than
the bottom, which is in contact with the crucible. Also, higher chamber
pressures causes more heat loss through convection.
HS 1 400 contains MgO crucibles with Pt wire in its center and Pt paint at
the top and bottom. The Pt wire leads heat from the crucible bottom to its
top (sample), thus the wire and its surrounding has slightly higher
temperature comparing to the rest of the crucible.
Both Heating stages have the same heater design which is intended to
minimize a sample temperature discrepancies. The heater is essentially
a micro-furnace which provides heating from the bottom and from the
sides.
To obtain accurate heat conduction through the sample, it should be
cemented or otherwise firmly mounted onto the crucible with a good
thermal contact. Use conductive carbon paint for temperatures below
900 °C; and a high temperature adhesive for temperatures above
900 °C.

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System Options: Heating Stage 1 000 °C / 1 400 °C

FIGURE 7-44 TEMPERATURE AND CONDUCTIVITY

Outgassing Samples
Some types of samples may contain compounds which evaporates
under high temperatures. This does not affect the pressure in the
chamber. However, if large quantities of compounds are given off, they
may condense and get on the aperture inside of the GSED assembly
(PLA), and then astigmatism could result. If this happens, the detector
must be cleaned.

Using HS with EDX Detectors

There is a number of variables to be taken into account when selecting
operating temperatures for EDX detectors. Some of these include
window materials, window thickness, window support structure and the
closeness of the window.
Above 400 °C the sample begins to radiate infrared light, and this blinds
the EDX detector, preventing further analysis. For this reason, do not
perform elemental analysis above 400 °C. It is also advisable to retract
the EDX detector fully when temperatures above 400 °C are to be
attempted.

Caution! 
Be very careful when determining operating temperatures. To avoid
damaging a detector, always consult the EDX manufacturer for
guidelines and operating limits.
Once cooled, swing the heat shield out of the way of the stage. (the
optical image may be helpful to see into the chamber.) Raise the stage to
a working distance of 12 mm (the GSED is 8 mm), then collect X-rays as
usual.
Positioning High Temperature GSED
The high temperature GSED must be installed so that the collection ring
does not interfere with the angle of the EDX detector. This can be done
by simply rotating the detector so that one of the gaps in the ring faces
the EDX detector. In the following photo, note that the bars on the
collection ring are oriented so that the path from the EDX detector to the
GSED is clear.
Also note that the working distance given may be longer than the
recommended (10 mm). It has been found that different EDX
manufacturers may have optimum collection below 10 mm. Each system
should be tested to find the optimum working distance before using the
heating stage.

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 System Options: Heating Stage 1 000 °C / 1 400 °C

FIGURE 7-45 POSITION OF THE HIGH TEMPERATURE GSED

Inclined Crystal EDX Detectors

The detector comes in at a take-off angle (TOA) of 35°, and the sample is
not tilted. This illustration is shown with the high temperature GSED
installed.
EDX Performance
Elemental analysis can be performed while heating; the heat radiated
from the heating stage to the EDX detector is very small (under the
400 °C) and generally does not affect the EDX detector.
The sides of the crucible and the top edges of the stage interferes with
the collection of x-rays from the sample. Therefore, all EDX analysis
should be performed on the sample opposite to the EDX detector:
Tilting the stage by no more than 5° toward the EDX detector will
improve x-ray signal collection as well. Count rates for EDX analysis may
be slightly lower than normal using this heating stage.

FIGURE 7-46 INCLINED CRYSTAL EDX DETECTOR CONFIGURATION / 

POSITIONING FOR EDX PERFORMANCE

Window Contamination
Upon heating, certain samples may evolve gases or burn off various
residual components such as binders or fillers. If the EDX detector is
located close to the sample, these evaporated components may
condense onto the EDX window. To prevent this, keep the EDX detector
retracted away from the stage until it is needed.

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System Options: Heating Stage 1 000 °C / 1 400 °C

Water Cooled Temperature Stage Operation Termination

See description above (the Cooling stage).

HS MAINTENANCE

Cleaning
The Heating stage could be polluted after a long term use or when using
highly outgassing samples. To prevent another samples contamination
remove and clean the stainless steel cover plate. The ceramic paper
heater cover should be replaced together. Use Heater cover 2 (harder
paper) always on the top.
The Heat shield isolation should be replaced as well (for HS 1 400 only).

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 System Options: Heating Stage 1 000 °C / 1 400 °C

HS Consumables

TABLE 7-3 HS 1 000 / 1 400 CONSUMABLE PARTS

Item Part #
HS 1 000
Standard crucible (10 pcs) 4022 298 00681
Low crucible (10 pcs) 4022 298 00691


HS 1 400
Standard crucible (10 pcs) 4022 298 00711
Low crucible (10 pcs) 4022 298 00721


HS 1 000 and 1 400

Graphite crucible (50 pcs)  4022 298 00701



HS 1 000 and 1 400

Heater cover (20 pcs) 4022 298 00731 
Heater cover 2 (20 pcs)  4022 298 00871


HS 1 400
Heat shield isolation  4022 298 00741
(20 pcs)


Old version HS 1 000

Specimen cup (10 pcs) 4022 298 00751



HS 1 000 and 1 400

Detector Cap  4022 293 22561



HS 1 000 and 1 400

Hook Wire adapter 4022 293 22521




HS 1 000 and 1 400

Ceramic paper pad (50 pcs) 4022 298 00831

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System Options: Remote Imaging

Remote Imaging

The Remote Imaging enables to connect to the Microscope PC via

network using the VNC application and to control the microscope
operation remotely.
For information how to install this functionality, see Installation
Instructions available on the installation CD. For more details on the
remote connection and its possibilities, see VNC documentation
available on the installation CD.

CONNECTION TO MICROSCOPE PC
Follow the steps below to connect to the Microscope PC.
1. Double-click the VNC Viewer icon on the remote PC desktop to
launch the VNC Viewer application.
2. In the Connection Details dialogue, type the computer name of the
Microscope PC you want to connect to, followed by colon (:) and the
port number 5905, into the Server field.

In case your configuration consists of both Microscope PC and

Support PC, you need to connect to the Support PC. Type the
Support PC name, followed by the colon (:) and the port number
5905, into the Server field. Click the OK button.
3. Some secure key and signature related dialogues may appear.
Confirm all of them by clicking OK or Yes button.

4. In the Authentication dialogue, fill in your microscope Username

and the corresponding Password. Click the OK button.

When this step successfully passes, you are connected to the

Microscope PC and the VNC window with its desktop opens.

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 System Options: Remote Imaging

When connecting remotely, be aware of the fact that there might be

some person operating the microscope locally, i.e. working directly with
the Microscope PC.
To close the remote connection to the Microscope PC, just close the
VNC Viewer window.

MICROSCOPE PC’S DESKTOP SHARING

Several users can connect to the Microscope PC at the same time and
thus share its desktop on the remote PC's. This can be used e.g. for the
educational purposes. The typical scenario is that a dedicated user/
supervisor controls the microscope (locally or remotely) and the other
connected users can only view the Microscope PC's screen over the
network.
1. In FEI User Management application, create a non-active user
account for the view only purpose.
2. Open the VNC Viewer application on the remote PC of the person
who is intended to control the microscope and connect remotely to
the Microscope PC as user/supervisor.
3. Other users will then open the VNC Viewer application on their
remote PC's and connect remotely as 'view-only' users.
Note: 
The desktop sharing must be enabled in the VNC Server application on
the Microscope PC. For instructions how to do so, see VNC Server
documentation available on the installation CD.

CONTROLLING MICROSCOPE REMOTELY

After connecting remotely to the Microscope PC, you can do all the tasks
as if you work directly with that computer. It is possible to control the
microscope operation, run the supportive applications, backup or restore
user data, view the log files etc.
In general, expect slower response on your commands and actions. This
limitation comes from the amount of data that have to be transmitted and
from the network bandwidth.
In case the xT microscope Control user interface stops responding or the
Server Busy dialogue appears, the Microscope PC is probably
overloaded and may have problems with the actual conditions being
operated remotely. If such a problem occurs, wait till the Microscope PC
recovers; or restart it yourself when necessary.
Here are some recommendations for the remote control operation:
• Be very careful when navigating the stage. Always keep in mind that
what you see in the CCD camera image is not the exact position of
the stage (because of delay in imaging data transmission).
• You can improve the performance / response time by setting the more
convenient scanning conditions: quad instead of full screen, single
quad running instead of more quads active; lower resolution; slower
scan (i.e. higher dwell time).
• Benefit from the automatic functions that are not affected by the
delayed response problem (Auto Contrast Brightness, Auto Focus,
Auto Stigmator). In case you prefer to focus or correct astigmatism
manually, it is better to do so in the reduced area.

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System Options: Beam Deceleration

Beam Deceleration

STAGE MODIFICATION
When extending the system capabilities with the Beam Deceleration
mode, it is necessary to make the stage modification by mounting the BD
attachment on the stage head. For systems acquired with the Beam
Deceleration this procedure is not carried out.
1. Open the specimen chamber and remove the specimen holder.
2. Place holding screw to the free stage position (use M3 or M4 thread
according to which is available).
3. Place the BD attachment on the stage (holding screw is under the
cable output part to keep it stable while rotating the stage) and tight
the central screw to fix the attachment (use the socket-head screw).

4. Set maximum X,Y and Tilt coordinates to ensure the cable does not
limit stage movement. Put the cable into the holder, be sure the cable
is not placed in CCD camera field of view!
5. Plug the connector from the BD attachment to the chamber
feedthrough and slightly rotate it to lock.

6. Place the specimen holder back.

Be aware (before closing the chamber door) the specimen height
increases after mounting the BD attachment!
The BD attachment could be left in the chamber or removed, when larger
specimens should be observed.

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 System Options: Beam Deceleration

BEAM DECELERATION
The Beam Deceleration mode (BDM) method is based on a negative
voltage Stage Bias (bias) applied to a stage (i.e. a sample). The
electrical field between the sample and the nearest surface above 
(a column bottom or a detector) is formed, acting as the additional
electrostatic lens. Its power is described by the Immersion Ratio
(imRatio) parameter (see below).

Detection Principles
The Beam Deceleration influences both primary and signal electrons.
As the sample is at the negative potential according to the ground and
detectors, the initial SE and BSE energy (when leaving the surface) is
accelerated by the Stage Bias before the detection. The higher is the
Immersion Ration, the lower is the difference between SE and BSE
energies when detected.
Signal electrons are accelerated upwards and deflected towards the
column axis. The SE have a low initial speed and they are usually
absorbed into the detector central hole, equally like the BSE heading
upright. Conversely the BSE heading nearly parallel to a surface (which
normally cannot be detected) are driven to a detector.
By changing the Stage Bias an output angle distribution of electrons
leaving a surface could be obtained.

FIGURE 7-47 TYPICAL TRAJECTORIES OF SECONDARY (RED)

AND BACK SCATTERED (GREEN) ELECTRONS

Detectors most convenient for the Beam Deceleration are BSE ones,
placed closely under or directly inside the column. Their efficiency
depends on their active area: the smaller is the inner diameter of the
active area, the better. The standard ETD could also be used, but its
efficiency is low.
Beam Deceleration Applications
• The BDM enables detection of the BSE when the electron energy is
under the detection limit of the detector.
• The BDM expands the electron energy range under the minimum HV
limit.
• The BDM improves the microscope resolution at low accelerating
voltages. A conventional microscope resolution is limited by a
chromatic aberration at low electron energies. The higher is the
Immersion Ratio, the smaller are the aberrations and a loss of
resolution at low electron energies is well compensated.
• The BDM enables to detect electrons heading nearly parallel to a
surface which accentuates a surface roughness.

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System Options: Beam Deceleration

Application Restrictions
• In the gaseous mode the chamber environment is rather electrically
conductive and the BDM is not available.
• The sample tilt causes an electrical field deformation, which adds not
correctable aberrations (a chromatic aberration and an image
distortion). An acceptable sample tilt is about a few degrees, for a
higher immersion ratios preferably less.

FIGURE 7-48 SIGNAL DISTORTION AND IMAGE ABERRATIONS

FOR TILTED AND ROUGH SAMPLE (TIN BALLS) 
AT HIGH IMMERSION RATIO

Beam Deceleration Module

The Beam Deceleration module is accessible from the Beam Control
and Detectors pages. It has following features:
• The On button switches the BDM on / off. This is available only in the
HiVac mode and with the Beam On. When switching the beam off, the
BDM switches off automatically.
• The Stage Bias (bias) reflects the negative voltage applied to a
stage. Minimal value is 50 V, maximal is 4 kV.
When the BDM is on, a hook mark is placed behind the HV. In this case
this value represents energy of electrons reaching a sample surface (it is
also stored within the TIF file header).
The imRatio = (HV + bias) / HV.

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 System Options: Beam Deceleration

Beam Deceleration Mode Imaging Procedure

1. Put the sample into the chamber and pump to the HiVac.
In the BDM a sample becomes the electrode. Its position, size, tilt and
surface roughness influence an imaging quality. At optimal conditions
the sample should be symmetrical, planar, have a size comparable
with the detector size, and placed perpendicular to the column axis. In
other conditions a distortion, an astigmatism and a blurring caused by
the chromatic aberration appear. This is even worse when the
Immersion Ratio is higher.
2. Select the suitable HV and find an area of interest. Set the Eucentric
Position and tune an imaging. In various quads get the SE and BSE
images to observe different imaging simultaneously.
3. Click the Beam Deceleration module / On button. Gradually raise the
Stage Bias, the SE / BSE image is getting dark / light.
At low magnifications an ETD image should become dark
symmetrically around the window center, in other case the sample
could be tilted.
When a dark area is shifted with an Stage Bias change, the sample is
possibly not parallel with the detector. With the use of the
Compucentric stage rotation / stage tilt try to keep the dark are in the
center of the screen.
Note: 
When the retractable vCD detector is inserted, stage tilt is restricted via
the UI. Override it by manual control to keep the dark area in the center
of the screen (for Quanta 450 / 650 only).
Note: 
An image shift when changing the Stage Bias could be caused by
imaging near the sample edge or any other edge.

4. Set the Stage Bias considering the sample material (charging

compensation, material contrast) and to optimize the signal. Set the
brightness, contrast and WD according to the requirement.
5. Tune an imaging.
6. Repeat steps 4. and 5. to get the best result.

C O N F I D E N T I A L – FEI Limited Rights Data 7-61

System Options: Quick Loader

Quick Loader

The Quick Loader was designed for:

• Easy Sample transfer
• Faster sample through-put
• Contamination free chamber environment
• Materials applications

Caution! 
Minimize a Quick Loader usage with the CryoCleaner (see below)
filled with LN2! This is because each Load cycle adds small layer of
gas and ice onto the Nitrogen Vessel surface, thus decreasing the
CryoCleaner efficiency and increasing the amount of gas released
into the specimen chamber in case the LN2 dries out.

GENERAL DESCRIPTION
The loader module can manually load and unload small samples into the
SDB / SEM. The loader module is connected to the specimen chamber
of the SDB / SEM and it has its own pumping system.

The loader consists of a loading rod with set slide and parking position, a
loader chamber for loading and unloading the sample carrier (with
sample) onto a bayonet fitting located at the end of the rod. A gate valve
seals the vacuum of the SDB / SEM specimen chamber and can only be
opened when the vacuum of the loader chamber is correct, this being
indicated by the OK labeled LED prompted by an electrical and
mechanical interlock.
The sample carrier can be entered into the main SDB / SEM specimen
chamber by way of the rod and released by the rotating motion of the rod
at a predetermined position on the stage adapter.

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 System Options: Quick Loader

Loading rod
The loading rod has a pre-machined slot to move in to load or unload a
sample. At each end there is a side slot. There are 2 side slots at the
further end from the vacuum chamber. One is for loading and unloading
the sample carrier in the loader chamber and the other is a parking
position (prevents the rod to be sucked in by the vacuum).

Caution! 
Do not unload the sample carrier with gate valve opened! The
sample carrier could drop down from the rod.
At the end of the rod closest to the loader chamber is a large slot for
coupling and de-coupling the bayonet into or out of the sample carrier
when positioned on the carrier adapter.
The bayonet is designed to make a positive and secure connection to the
sample carrier so that it remains horizontal and in a straight line to
connect with the carrier adapter within the specimen chamber.

Gate valve
The Gate Valve has positions that are defined by the following status:
• rotated position of the Gate Valve Lever: LOCK / UNLOCK
The position has to be turned from LOCK to UNLOCK to be able to
move the loading rod IN and OUT
• colored strips on the side of the exposed barrel axis: 
one / two when IN / OUT

• Position 1 - IN and LOCK

• Position 2 - IN and UNLOCK
• Position 3 - OUT and UNLOCK
• Position 4 - OUT and LOCK (prevents vacuum closing valve).
The Gate Valve has a two safety movements.
• it can be placed over the entry hole on the slide
• it can be locked in place by a turn of the connecting knob (securing
the closure of the valve)
A system interlock takes care of correct conditions (system vacuum,
accelerating voltage) for loading and unloading cycles (movement of the
gate valve).

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System Options: Quick Loader

Controls
There are 2 buttons (illuminated while in operation) and 1 indicator lamp:
• The P (pump) labeled button is pressed to pump the loader chamber
to the required vacuum, the stage moves to a loading position at the
same time. If the system reaches appropriate vacuum level, the lever
interlock is released and the gate valve can be opened. The pump
cycle is automatically terminated when the required vacuum is
reached.
• The V (vent) labeled button is pressed once to vent the loader
chamber. The vent cycle continues till the P button is pressed or it is
terminated by time-out.
• The indicator lamp labeled OK lights up when vacuum is reached
after pumping. When it goes out this means the wait time has been
exceeded and the appropriate vacuum for a transfer has been lost.
Pressing the P button again will bring the system to vacuum OK
status.
Control buttons are not shining when the system is recovering from
vacuum status transition (e.g. immediately after the load/unload sample,
during venting the chamber...). After finishing the state transition the
control buttons will be in operation again.

Sample Carrier, Sample Gate and Stage Adapter

A sample carriers (2 pcs.) are used to hold and transport the sample
from the loader to the specimen stage of the SDB / SEM. The carrier sits
in the stage adapter with a dovetail joint. It is fixed to the loading rod via a
bayonet coupling. The loading rod is disjoined at the bayonet coupling
when the sample carrier is located in the adapter and withdrawn leaving
the sample carrier ready for sample observation.

The Stage Adapter is connected to the rotation base of the FEI stage by 3
hexagonal headed screws. The base of the adapter has 3 high points for a
firm 3-point contact to the rotation base to prevent vibration transmission.
The height of the stage adapter is distinct to the SDB /SEM system it is
used with. The top of the adapter has a dovetail slot for the acceptance
of the sample carrier from the rod loading mechanism.
Sample Height
Before mounting the Stage Adapter the stage must be homed with the
chamber door opened.
Only samples that fit the Sample Gauge can be loaded. One sample stub
of diameter up to 32 mm (1 1/4 ") can be used, although standard sizes
of 25 mm and 12.5 mm can also be used. Height can be no greater than
9 mm.
The shuttle clamps with a spring in the dovetail shaped slot of the adapter.
It is fixed to the loader arm via a bayonet coupling. The maximum pin
length of the stubs that can be used is 11 mm (most common commercial
FEI type stubs have a pin length no greater than 8 mm).

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 System Options: Quick Loader

INSTALLATION
The Quick loader is pre-installed in FEI factory. No special adjustment is
needed only the loading rod was uninstalled for transport.
1. Unpack the lead glass lid.
2. Remove four screws holding the cover of the loading rod feedthrough.
3. Use the same screws to attach the loading rod to the loader chamber.

Loading position
The load / unload position is preset from factory. If a calibration is
needed, run the Quick Loader Alignments at first.

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System Options: Quick Loader

OPERATIONS

Loading a sample
1. Mount the sample with fast drying adhesive medium onto the stub.
Allow to dry.
2. Check the sample satisfies the sample limits imposed by placing the
top of the mounting tool over the base mount.

Caution! 
If the sample proves to be too large this has to be addressed before
the sample and carrier should be allowed into the loader chamber.
3. If the sample satisfies the limits, the sample loaded carrier can be
loaded into the loader chamber. A user can either remove from or
place a mounted carrier in the loader chamber by using tweezers for
stubs which will fit around the stub rim.
Note: 
Loading samples this way is an easier and safer than trying to mount
the sample directly into the sample carrier while in the loader
chamber.

Rod Loading Sequence

1. While holding the sample carrier on the loading table in the loader
chamber move the rod out of the Parking position to the far left, to the
back of the slot and forward to engage the bayonet into the sample
carrier. Place the rod back into the Parking position after coupling to
prevent the rod slowly creeping forwards.
2. Switch OFF the electron beam accelerating voltage. Retract the GIS
or STEM modules (if present) to a safe state (can not be used in
combination with loader).
3. Close the loader chamber lid. After the lid is properly closed the P
button starts to shine.
4. Press the P button, the button stops to shine and the pumping cycle
starts, the stage moves to the loading position at the same time.
When the vacuum in the loader chamber is correct the pump light
starts to shine and the OK button lights up indicating operation can
continue. The gate valve lever interlock is released.
5. Turn the Gate Valve knob lever from LOCK to UNLOCK position.
Then carefully pull the knob bar fully out from the first mark on the
knob drum to the second mark. Turn the knob bar to (anti-clockwise)
to the LOCK position.
6. Move the loading rod from the Parking position into the chamber
while still holding the rod bar. The Sample Carrier will engage with the
Stage Adapter at the end of the rod travel.
7. Turn the rod bar to the left (anti-clockwise) to the base of the slot; pull
back on the rod bar so it travels along the base of the slot, then turn to
the right (clockwise) so that the rod bar is vertical and withdraw it
back to the PARK slot at the far end of the rod guide.
8. Close the Gate Valve by turning the knob bar to the UNLOCK position
and press the knob in to engage the valve over the opening, this can
be seen through the lead glass lid, then turn the knob bar to the
LOCK position to secure the valve. Good practice is to leave the
loader chamber under vacuum.

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 System Options: Quick Loader

Unloading a sample
1. If there is a sample carrier in the loader chamber attached to the
bayonet, remove it (the chamber needs to be vented and the carrier
removed).
2. Switch OFF the electron beam accelerating voltage. Retract the GIS
or STEM modules (if present) to a safe state (can not be used in
combination with loader).
3. Close the loader chamber lid. After the lid is properly closed the P
button starts to shine.
4. Press the P button, the button stop to shine and the pumping cycle
starts, the stage moves to the loading position at the same time.
When the vacuum in the loader chamber is correct the pump light
starts to shine and the OK button lights up indicating operation can
continue. The gate valve lever interlock is released.
5. Turn the Gate Valve knob lever from LOCK to UNLOCK position.
Then carefully pull the knob bar fully out from the first mark on the
knob drum to the second mark. Turn the knob bar to (anti-clockwise)
to the LOCK position.
6. Move the unloading rod from the Parking position into the chamber
while still holding the rod bar. When resistance is found turn the rod
bar to the left (anti-clockwise) to enter the bayonet. Push forward and
turn the rod to the right (clockwise) and the bayonet will engage with
the Sample Carrier on the Stage Adapter close to the end of the rod
travel.
7. Withdraw the rod back to the far end of the rod guide and place in the
Parking position. The rod, bayonet and sample carrier are now out of
the chamber and sit in the Loader chamber.
8. Close the Gate Valve by turning the knob bar to the UNLOCK position
and press the knob in to engage the valve over the opening. This can
be seen through the lead glass lid, then turn the knob bar to the
LOCK position to secure the valve.
9. Press V button once. The chamber will be vented and the lid can be
opened. The sample carrier can be released by turning the rod bar to
the far left and pulled back then returned to the parking position.
Remove the sample carrier.
10.Close the loader chamber lid.
11.Press P button to evacuate the loader chamber.
Note: 
In case the sample carrier falls from the loading rod, vent the chamber
with gate valve opened, put the carrier back to a correct position and
close the gate valve. Proceed from the step No. 1.

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System Options: CryoCleanerEC

CryoCleanerEC

These equipment allow to decrease the contamination level in the

system. The CryoCleanerEC can be efficient to approximately 24 hours.
The kit consists of: Vacuum vessel, Vacuum vessel lid, Nitrogen vessel
(Dewar) with cap (including proper warning labels), Nitrogen vessel
stand and Nitrogen vessel safety Pliers.

WAR N I N G ! 
This option uses liquid Nitrogen (LN2), which may cause serious
cold burns.

Caution! 
It is strongly recommended to vent the specimen chamber and
replace the Nitrogen Vessel with a clean one after completing cca
20 subsequent Load Lock (see above) load cycles with the cool
CryoCleaner! 
If the chamber is vented with the CryoCleaner filled with LN2 (or
empty but still significantly below the ambient temperature), the
Nitrogen Vessel should be removed and baked before it is used again.

PARTS AND ACCESSORIES

The CryoCleanerEC consists of a Nitrogen vessel that is surrounded by
an outer container - the Vacuum vessel, which is connected to one of the
specimen chamber ports by a vacuum seal. The space between is then
pumped by the microscope vacuum system.

FIGURE 7-49 NITROGEN VESSEL 

VACUUM VESSEL WITH ACCESSORIES

When the specimen chamber (together with the CryoCleaner) is

pumped, liquid Nitrogen is introduced to the Nitrogen vessel. Its outside
cold surface absorbs contaminating products from the specimen
chamber. The vacuum in the specimen chamber improves over a short
period and contamination is now reduced.
When LN2 runs out, a pressure burst inside the chamber could cause
the system to vent and to be at atmosphere for long periods of time if
unattended. In this case the system switches the beam off, but it is
protected from venting (about 30 min). After this period an automatic
vacuum recovery procedure tries to pump the chamber, only if it is not
successful the system is vented.

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 System Options: CryoCleanerEC

Flanges
The Vacuum vessel has special flange enabling to mount it to different
chamber ports with the use of interlink with a desired shape (depending
on the port to be used and the vicinity).

FIGURE 7-50 CRYOCLEANER FLANGES

The interlink flanges can be mounted on by means of the 3 screw-hole

fittings on the perimeter of the vacuum flange. Care must be taken that
the 'O' ring held in the end of the flange is secure, free of dirt and is not
crimped when mounting.

CRYOCLEANER OPERATION
Once mounted the Nitrogen vessel can be placed in the Vacuum vessel.
Secure the two components by fixing the clips to the top of the Nitrogen
vessel and locking the clips down. Take care that the 'O' ring seal on the
Vacuum vessel is secure when joining the two components together.

Dewar Vessel Refilling

WA R N I N G ! 
The handling of LN2 should be performed wearing face and hand
protection in the form of a protective shield and a pair of thermal
protective gloves. 
Users must not touch the cold surfaces of the Dewar as this could
result in burns. Use the Safety Pliers provided, when handling the
Nitrogen Vessel.
1. Pump the specimen chamber, the Vacuum vessel is pumped along
with it.
2. When the specimen chamber vacuum is ready (Pumped status),
partially fill the Dewar with the use of funnel (the plastic cap upside
down) and wait until boiling stops.
3. Then fill the Dewar and place the plastic cap at the top of the
CryoCleaner. The volume of liquid Nitrogen needed is approximately
500 ml.
Note: 
The LN2 stops boiling very quickly so that no vibration is seen from this
device. If the CryoCleaner needs to be used for longer periods it can be
refilled with LN2.
Note: 
Before re-filling it is recommended to perform Baking procedure (see
below).

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System Options: CryoCleanerEC

FIGURE 7-51 PLASTIC CAP FILLING POSITION 

PLASTIC CAP OPERATION POSITION

Removing Nitrogen Vessel

WAR N I N G ! 
Use the Safety pliers provided when handling the Nitrogen vessel.
Removing the Nitrogen vessel depends on the level of contamination
found in the specimen chamber. If the level is unusually high then the
CryoCleaner could work continuously till improvement is seen, otherwise
normally after approximately 2 to 3 hours the Nitrogen vessel can be
removed.
Note: 
It is not recommended to leave it inside the vacuum vessel after all
nitrogen evaporates, because contamination evaporates back to the
chamber.
1. Vent the specimen chamber (the excess LN2 starts to boil).
2. Unclip the Nitrogen vessel from the Vacuum vessel. Lift the Nitrogen
vessel out of the Vacuum vessel by the Safety pliers placed under the
ring on the neck of the Dewar cylinder.

3. Place the Lid over the Vacuum vessel to seal it from the atmosphere
(fix the clips). Pump the specimen chamber again, however the
microscope vacuum remains cleaner than before and sample
contamination is still reduced.
4. Remove the cap from the Nitrogen vessel and pour out the excess
LN2 into a suitable container.

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 System Options: CryoCleanerEC

WA R N I N G ! 
When the LN2 is removed from the nitrogen vessel, the bottle still
remains at a very low temperature.
5. Place the Nitrogen vessel onto the Stand ready for baking.

Baking Nitrogen Vessel

1. Place the Nitrogen vessel Stand on a suitable heat resistant surface.
2. Place the Nitrogen vessel onto it and use an Infra-red lamp to bake
the base of the bottle. Baking should take place for approximately
2 hours.
Alternatively the Nitrogen vessel can be baked in an oven at 90 °C for
2 hours.
Regenerating the Dewar by heat allows removal of condensed
contamination and subsequent reuse of the vessel.
Note: 
The oven that is used must have a venting system to extract any harmful
fumes. Alternatively it should be baked in a fume cupboard using an
infra-red lamp.

Replacing Nitrogen Vessel

1. Vent the specimen chamber. Allow the Nitrogen vessel to cool down
before handling.
2. Unlock two clips holding the Vacuum vessel Lid. Remove the Lid from
the Vacuum vessel.
3. The Nitrogen vessel can be placed in the Vacuum vessel, taking care
that the 'O' ring seal on the Vacuum vessel is secure when joining the
two components together. Secure the two components by fixing the
clips to the top of the Nitrogen vessel and locking the clips down.
4. Pump the specimen chamber. The Vacuum vessel is pumped along
with the specimen chamber.

MAINTENANCE
• Keep the 'O' rings clean of dust and fibre particles by inspecting the
Vacuum vessel main 'O' ring on a regular basis. If the Vacuum vessel
is removed frequently from the specimen chamber, inspect the
specimen chamber 'O' ring seal each time.
• Keep the sealing surfaces of the Nitrogen vessel and the Vacuum
vessel Lid clean and free of dust and fibre particles.
• Do not use any kind of vacuum grease on the 'O' rings.
• Wipe outsides of the stainless steel parts to remove finger stains with
a lint free cloth dampened with pH neutral soap solution.

SPARE VESSEL
It is possible to obtain secondary nitrogen vessel kit, which contains:
• Nitrogen Vessel
• Vessel Stand
• Vessel Plug

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System Options: Specimen Holder Kit

Specimen Holder Kit

The Specimen Holder Kit is Universal. The interfacing parts allow the
fitting of all the common components to the system. Major holders in the
kit locate with a 2 pin system originating from the stage rotation head,
through the interface piece, to the holder. All interfacing parts have a 3
point contact to minimize vibration. The Specimen Holder Kit comprises
of:
• Older type 50 mm stage adapter
• Interface pillar for all multi-fittings
• 16 Position stub holder (spring held)
• Angled stub holder, 4 at 45°, 2 at 0°
• Analytical holder 2× 1 inch samples
• 25 mm and 32 mm diameter Polished mount holders
• 2× Clamp stubs
• Eucentric stub holder Quanta 450
• Eucentric stub holder Quanta 650
• 1× No.10 Torx driver
• 1× No.6 Torx driver

FIGURE 7-52 SPECIMEN HOLDER KIT OPTION

OLDER INTERFACE ADAPTER

This adapter is used on pre-Quanta 50 mm stages that had no 2 pin
locating holes. The old centre rotation head needs to be removed from the
stage and this component should replace it. It is available for those who
have pre-Quanta 50 mm stage XL30 instruments and want to use this kit.

FIGURE 7-53 OLDER INTERFACE ADAPTER

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 System Options: Specimen Holder Kit

LOCATION POSITIONS
The interface parts and all fitting holders have a 2 pin / 2 hole location
system. This is present so that holders can be positioned in the same
orientation each time they are fitted. All stages have 2 holes, one is
round and the other is a slot. This will allow the stage location system to
work with a holder for precise specimen position.
This works directly from the Home condition of the stage. The stage
needs to be homed before fitting of the Holder interface components.

FIGURE 7-54 QUANTA 450 LOCATION POSITIONS

Location
slot

Single
holder
threaded
hole

Location
hole

INTERFACE PILLAR
This component is used to attach the 3 multi-holders individually to the
stage. It is fixed to the stage by the captive centre screw.

FIGURE 7-55 INTERFACE PILLAR FOR MULTI-HOLDERS

Analytical
holder screw
positions

Location pins
top

Location pins
bottom

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System Options: Specimen Holder Kit

MULTI-HOLDERS
The Multi-Holders fit individually on the Interface pillar using the same
pin location system. Numbers 1 and 2 have a captive centre screw for
fixing to the Interface pillar, where as number 3 has two captive screws
offset from the centre.

FIGURE 7-56 THE MULTI-HOLDERS

16 Position Stub Holder (1)

This can be used for 12.5 mm pin stubs, the Clamp stubs, the Polished
mount holders or any pinned small holder. The pins are held by spring
pressure to prevent vibration or falling out. Using the location pin
position, with homing of the stage, each time will allow one to map the
holder into the stage location system. The 16 Position Stub Holder fits to
the Interface pillar by a captive centre screw.

Angled Stub Holder (2)

This holder can be used for a pre-tilt condition where either there is no
wish to tilt the stage, or additional tilt is needed beyond the stage tilt
capabilities. The set angle is 45° and holds 4× 12.5 mm stubs at this
angle. There are also 2 positions on the top of the holder for 2× 12.5 mm
stubs. All stubs are screw fixed. The Angled Stub Holder fits to the
Interface pillar by a captive centre screw.

Analytical Holder (3)

The Analytical Holder is use in conjunction with an EDX system. 2
polished 1inch mounts can be slotted from below into the retaining holes
until they become flush to the top of the holder. Here they can be locked
in place by screws in the holder side wall. This gives the specimens a
common height with a Faraday cup position drilled into the top of the
holder and therefore can be common during x-ray analysis.
There are also 2 positions for 12.5 mm stubs or for standards necessary
for the analysis. The 2 stubs are each held by a screw in the side wall.
The Analytical Holder fits to the Interface pillar by two captive screws
equally off-set from the centre.
All screws are either Torx or Hex-key ended.

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 System Options: Specimen Holder Kit

POLISHED MOUNT HOLDERS

These comprise of 2 shallow cup holders of different diameters. The
sizes are 25 mm and 32 mm. These are the general size of encapsulated
mounts either for Metallurgy or Geology. The holders have a split in the
side of the cup so as to grip the mount when it is pushed in. They have a
simple pin the same as the 12.5 mm stubs, therefore can be mounted on
any of the same fittings as the standard stub.

FIGURE 7-57 POLISHED MOUNT HOLDERS / CLAMP STUBS

CLAMP STUBS
These are generally used for holding thin objects such as a piece of IC
wafer. Also can be used when adhesive is prohibited. They have Hex-
key screws that clamp with Nylon bushes onto the object. Grounding of
the specimen may need to be made by another method other than just
touch contact.

TORX DRIVERS
Within the kit are two Torx drivers to complete the fitting of the interfacing
parts. All screws for interfacing connections are Torx. All screws for
clamping sample stubs are the Hex-key type (the appropriate Hex-key
tool is a standard facility).

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System Options: Specimen Holder Kit

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