Rev 2.

05
11062003

USB2000
Fiber Optic Spectrometer
Operating Instructions

Offices: Ocean Optics, Inc.

380 Main Street, Dunedin, Fla., USA
Phone 727.733.2447
Fax 727.733.3962
8:30 a.m.-6 p.m. EST

Ocean Optics B.V. (Europe)

Nieuwgraaf 108 G, 6921 RK DUIVEN, The Netherlands
Phone 31-(0)26-3190500
Fax 31-(0)26-3190505

E-mail: [email protected] (General sales inquiries)

[email protected] (European sales inquiries)
[email protected] (Questions about orders)
[email protected] (Technical support)
Copyright © 2001-2003 Ocean Optics, Inc.
All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, by any means, electronic,
mechanical, photocopying, recording, or otherwise, without written permission from Ocean Optics, Inc.
This manual is sold as part of an order and subject to the condition that it shall not, by way of trade or otherwise, be lent, re-sold, hired out or
otherwise circulated without the prior consent of Ocean Optics, Inc. in any form of binding or cover other than that in which it is published.

Trademarks
Microsoft, Windows, Windows 95, Windows 98, Windows ME, Windows NT, Windows 2000, Windows XP and Excel are either registered
trademarks or trademarks of Microsoft Corporation.
Limit of Liability
Every effort has been made to make this manual as complete and as accurate as possible, but no warranty or fitness is implied. The
information provided is on an “as is” basis. Ocean Optics, Inc. shall have neither liability nor responsibility to any person or entity with respect
to any loss or damages arising from the information contained in this manual.
Table of Contents
1 USB2000 Introduction .................................................................................................................. 1
Product Overview ...................................................................................................................................................1
Interface Options ....................................................................................................................................................3
Shipment Components ...........................................................................................................................................3
2 USB2000 Specifications ............................................................................................................... 5
How the USB2000 Works .......................................................................................................................................5
USB2000 Specifications .........................................................................................................................................7
3 Installing the USB2000 ............................................................................................................... 10
USB2000 Installation ............................................................................................................................................10
External Triggering Options ..................................................................................................................................13
4 USB2000 Compatible Products.................................................................................................. 14
5 Troubleshooting ......................................................................................................................... 18
USB2000 Connected to PC Prior to OOIBase32 Installation ...............................................................................18
Troubleshooting the Serial Port Configuration......................................................................................................21
Older Version of OOIBase32 Installed .................................................................................................................21
6 Sample Experiments................................................................................................................... 22
Preparing for Experiments ....................................................................................................................................22
Absorbance Experiments......................................................................................................................................24
Transmission Experiments ...................................................................................................................................26
Reflection Experiments.........................................................................................................................................28
Relative Irradiance Experiments...........................................................................................................................30
Time Acquisition Experiments ..............................................................................................................................32
Appendix A: Calibrating the Wavelength of the USB2000 .......................................................... 35
About Wavelength Calibration ..............................................................................................................................35
Calibrating the Spectrometer ................................................................................................................................35
Appendix B: USB2000-FLG Spectrometer ...................................................................................... 40
About the USB2000-FLG......................................................................................................................................40
Using the USB2000-FLG ......................................................................................................................................40
Index .....................................................................................................................................................................42
USB2000 Introduction

1 USB2000 Introduction
The following chapter contains introductory information about the USB2000 Spectrometer, shipment information,
and spectrometer connectivity.

Product Overview
The USB2000 Spectrometer connects to a notebook or desktop PC via USB port or serial port. When connected
to the USB port of a PC, the USB2000 draws power from the host PC, eliminating the need for an external power
supply.

Figure 1-1: Ocean Optics USB2000 Fiber Optic Spectrometer

System Requirements
You can use the USB2000’s USB connectivity with any PC that meets the following requirements:
• Windows 98/Me/2000/XP operating system (or Windows CE 2.11 or later for palm-sized PCs)
• Ocean Optics OOIBase32 software application installed and configured for use with the USB2000
(OOIPS2000 software if using a palm-sized PC). Consult the “Configuring the USB2000 in OOIBase32”
section of Chapter 3: Installing the USB2000 for specific configuration instructions.
Alternately, the USB2000 has a serial port for connecting to PCs, PLCs, and other devices that support the RS-
232 communication protocol. However, this connection method requires an external power supply to power the
USB2000.

EEPROM Utilization
An EEPROM memory chip in each USB2000 contains wavelength calibration coefficients, linearity coefficients,
and a serial number unique to each individual spectrometer. The OOIBase32 software application reads these
values directly from the spectrometer, enabling the ability to “hot-swap” spectrometers between PCs without
entering the spectrometer coefficients manually on each PC.

USB2000 Operating Instructions 1

USB2000 Introduction

About OOIBase32
OOIBase32 is the latest generation of operating software for all Ocean Optics spectrometers and is available free
to all customers. OOIBase32 is a user-customizable, advanced acquisition and display program that provides a
real-time interface to a variety of signal-processing functions. With OOIBase32, you have the ability to perform
spectroscopic measurements (such as absorbance, reflectance, and emission), control all system parameters,
collect and display data in real time, and perform reference monitoring and time acquisition experiments.
Note: When using a palm-sized PC, you will use the OOIPS2000 software instead of OOIBase32. The
functionality of OOIPS2000 is similar to OOIBase32, but it is specifically for the palm-sized PC.

Sampling System Overview

Ocean Optics fiber optic spectrometer systems consist of low-cost, modular data acquisition components. A
typical USB2000-based sampling system contains four core elements:
• USB2000 Spectrometer
• OOIBase32 operating software
• Light source
• Sampling optics (varying, depending on application requirements)

How Sampling Works

The following list explains the function of Ocean Optics sampling components in the sampling process:
1. The user stores reference and dark measurements to correct for instrument response variables.
2. The light transmits through an optical fiber to the sample.
3. The light interacts with the sample.
4. Another optical fiber collects and transmits the result of the interaction to the spectrometer.
5. The spectrometer measures the amount of light and transforms the data collected by the spectrometer
into digital information.
6. The spectrometer passes the sample information to OOIBase32.
7. OOIBase32 compares the sample to the reference measurement and displays processed spectral
information.

Modular Sampling Accessories

Ocean Optics offers a complete line of spectroscopic accessories for use with the USB2000. Most of our
spectroscopic accessories have SMA connectors for application flexibility. Accordingly, changing the sampling
system components is as easy as unscrewing a connector and replacing an accessory.
Chapter 4 contains a list of Ocean Optics spectroscopic accessories, including accessories designed for use
specifically with the USB2000 Spectrometer.

USB2000 Operating Instructions 2

USB2000 Introduction

Interface Options
The USB2000 has both USB and serial port connectors, enabling you to connect the spectrometer to a desktop or
notebook PC via a USB port or to a desktop, notebook, or to a palm-sized PC via a serial port.
Computer Operating System
Part Needed Description of Part
Interface Requirements
Desktop or
Windows 98/Me/ USB-CBL-1 Cable that connects from USB port on USB2000 to USB port on
Notebook PC
2000/XP (included) desktop or notebook PC
via USB Port
Desktop or Any 32-bit Adapter block that enables connection from serial port on
USB-ADP-PC
Notebook PC Windows operating USB2000 to serial port on desktop or notebook PC; comes with
(not included)
via Serial Port system 5 VDC power supply (required when connecting to serial port)
Adapter block that enables connection (with standard 9-pin
Palm-sized PC Windows CE 2.11 USB-ADP-H serial cable) from serial port on USB2000 to serial port on palm-
via Serial Port or higher (not included) sized PC; comes with 5 VDC power supply (required when
connecting to serial port)

Shipment Components
The following information and documentation ships with the USB2000 Spectrometer:

Packing List
The packing list is inside a plastic bag attached to the outside of the shipment box (the invoice arrives separately).
The packing slip lists all items in the order, including customized components in the spectrometer (such as the
grating, detector collection lens, and slit). The packing list also includes the shipping and billing addresses, as well
as any items on back order.

Wavelength Calibration Data Sheet

The bag containing the spectrometer also contains the Wavelength Calibration Data Sheet. The information on
both the Wavelength Calibration Data Sheet and in the file on the Spectrometer Configuration Diskette is
identical, and this information is unique to each individual spectrometer.

Spectrometer Configuration Diskette

The Spectrometer Configuration Diskette ships with the Wavelength Calibration Data Sheet. When you install
OOIBase32 Spectrometer Operating Software onto a PC, OOIBase32 prompts you to insert this diskette.
OOIBase32 reads the spectrometer calibration data from the diskette, eliminating the need to enter the data
manually.
Note: Due to the importance of the data contained in both the Wavelength Calibration Data Sheet and the
Spectrometer Configuration Diskette, you should store each item for reference after initial use.

USB2000 Operating Instructions 3

USB2000 Introduction

Software and Resources Library CD

Each order ships with the Ocean Optics Software and Resources Library CD. This disc contains software,
operating instructions, and product information for all Ocean Optics software, spectrometers, and spectroscopic
accessories. You will need to install Adobe Acrobat Reader version 5.0 or higher to view these files, and Ocean
Optics includes Adobe Acrobat Reader 5.0 on the Software and Resources Library CD.
With the exception of OOIBase32 Spectrometer Operating Software, all Ocean Optics software requires a
password during the installation process. You can locate passwords for the other software applications on the
back of the Software and Resources Library CD jewel case.

Other Documentation
You can find detailed instructions for the OOIBase32 Spectrometer Operating Software at
http://www.oceanoptics.com/technical/ooibase32bit.pdf.

Note: You can find instructions for the OOIPS2000 Operating Software for the palm-sized PC at the following
location: http://www.oceanoptics.com/products/ooips2000.asp.

To find operating instructions on some of Ocean Optics’ most popular spectroscopic accessories (including light
sources, sampling chambers, sampling optics, and probes), consult the USB2000-compatible products list in
Chapter 4. You can also access operating instructions for Ocean Optics products from the Software and
Technical Resources CD that ships with the product.
For those engineers and programmers needing the serial port commands of the USB2000, consult the USB2000
Technical Datasheet on the Ocean Optics web site. You can find engineering-level documentation at
http://OceanOptics.com/Technical/EngineeringDocs.asp.

Modification and Repair Policy

In the event that you need to return an item for modification or service, you must obtain a Return Merchandise
Authorization (RMA) number prior to shipping the item back to Ocean Optics. Contact an Ocean Optics
Applications Scientist for specific instructions on returning an item.

USB2000 Operating Instructions 4

USB2000 Specifications

2 USB2000 Specifications
This chapter contains information on spectrometer operation, specifications, and system compatibility. It also
includes accessory connector pinout diagrams and pin-specific information.

How the USB2000 Works

The following diagram illustrates the movement of light through the optical bench of the USB2000 Spectrometer.
You can customize the items marked with an asterisk (*) when ordering the USB2000.

Note: The optical bench has no moving parts that can wear or break. Ocean Optics secures all components in
place permanently at the time of manufacture.

Figure 2-1: USB2000 Spectrometer with Components

The USB Component Table on the following page explains the function of each numbered component in the
USB2000 Spectrometer diagram (Figure 2-1).

USB2000 Operating Instructions 5

USB2000 Specifications

USB2000 Component Table

Ocean Optics permanently secures all components in the USB2000 at the time of manufacture. Only Ocean
Optics Technicians can replace interchangeable components, where noted.
Item Name Description
The SMA Connector secures the input fiber to the spectrometer. Light from the
1 SMA Connector
input fiber enters the optical bench through this connector.
The Slit is a dark piece of material containing a rectangular aperture, which is
mounted directly behind the SMA Connector. The size of the aperture regulates the
amount of light that enters the optical bench and controls spectral resolution.
2 Slit*
You can also use the USB2000 without a Slit. In this configuration, the diameter of
the fiber connected to the USB2000 determines the size of the entrance aperture.
Only Ocean Optics technicians can change the Slit.
The Filter is a device that restricts optical radiation to pre-determined wavelength
regions. Light passes through the Filter before entering the optical bench. Both
3 Filter* bandpass and longpass filters are available to restrict radiation to certain
wavelength regions.
Only Ocean Optics technicians can change the Filter.
The Collimating Mirror focuses light entering the optical bench towards the Grating
of the spectrometer.
4 Collimating Mirror
Light enters the spectrometer, passes through the SMA Connector, Slit, and Filter,
and then reflects off the Collimating Mirror onto the Grating.
The Grating diffracts light from the Collimating Mirror and directs the diffracted light
onto the Focusing Mirror. Gratings are available in different groove densities,
5 Grating* allowing you to specify wavelength coverage and resolution in the spectrometer.
Only Ocean Optics technicians can change the Grating.
The Focusing Mirror receives light reflected from the Grating and focuses the light
6 Focusing Mirror onto the CCD Detector or L2 Detector Collection Lens (depending on the
spectrometer configuration).
The L2 Detector Collection Lens (optional) attaches to the CCD Detector. It
focuses light from a tall slit onto the shorter CCD Detector elements.
The L2 Detector Collection Lens should be used with large diameter slits or in
L2 Detector
7 applications with low light levels. It also improves efficiency by reducing the effects
Collection Lens*
of stray light.
Only Ocean Optics technicians can add or remove the L2 Detection Collection
Lens.
The CCD Detector collects the light received from the Focusing Mirror or L2
Detector Collection Lens and converts the optical signal to a digital signal.
CCD Detector
8 Each pixel on the CCD Detector responds to the wavelength of light that strikes it,
(UV or VIS)
creating a digital response. The spectrometer then transmits the digital signal to the
OOIBase32 application.

USB2000 Operating Instructions 6

USB2000 Specifications

USB2000 Specifications
The following sections provide specification information for the CCD Detector in the USB2000, as well as the
USB2000 Spectrometer itself.

CCD Detector Specifications

Detector: Sony ILX511 linear silicon CCD array
Number of elements: 2048 pixels
Pixel size: 14 µm x 200 µm
Pixel well depth: 62,500 electrons
Signal-to-noise ratio: 250:1 (at full signal)
A/D resolution: 12 bit
Dark noise: 2.5 RMS counts
Corrected linearity: >99.8%

USB2000 Spectrometer Specifications

Dimensions: 89.1 mm x 63.3 mm x 34.4 mm
Weight: 190 g (without cable)
Power consumption: 90 mA @ 5 VDC
Detector range: 200-1100 nm
Detector: 2048-element linear silicon CCD array
Gratings: 14 gratings; UV through Shortwave NIR
Entrance aperture: 5, 10, 25, 50, 100 or 200 mm wide slits or fiber (no slit)
Order-sorting filters: Installed longpass and bandpass filters
Focal length: f/4, 42 mm (input); 68 mm (output)
Optical resolution: ~0.3-10.0 nm FWHM (depending on grating and size of entrance aperture)
8
Dynamic range: 2 x 10 (system); 2000:1 for a single scan
Stray light: <0.05% at 600 nm; <0.10% at 435 nm; <0.10% at 250 nm
400 nm – 90 photons/count; 600 nm – 41 photons/count;
Sensitivity (estimate):
800 nm – 203 photons/count
Fiber optic connector: SMA 905 to single-strand optical fiber (0.22 NA)
Data transfer rate: Full scans into memory every 13 milliseconds
Integration time: 3 milliseconds to 65 seconds
Fiber optic connector: SMA 905 to single-strand optical fiber (0.22 NA)
Windows 98/Me/2000/XP when using the USB interface on a desktop or notebook
PCs
Operating systems: Any 32-bit Windows operating system when using the serial port on desktop or
notebook PCs
Windows CE 2.11 and above when using the serial port on palm-sized PCs

USB2000 Operating Instructions 7

USB2000 Specifications

System Compatibility
The following sections provide information on hardware and software requirements for the USB2000:

Compatibility for Desktop or Notebook PCs

To use the USB2000, you must have a PC that meets the following minimum requirements:
• IBM-compatible PC with Pentium (or higher) processor
• 32 MB RAM
• OOIBase32 Spectrometer Operating Software
• Windows 98/Me/2000/XP operating system (when connecting the USB2000 to a PC via USB port)
or
Any 32-bit version of Windows (when connecting the USB2000 to a PC via serial port)

Compatibility for Palm-sized PCs

In order to use the USB2000 with your palm-sized PC, the computer must meet the following requirements:
• Palm-sized PC running Windows CE 2.11 or higher
• 32 MB
• OOIPS2000 Spectrometer Operating Software
• Serial port connectivity

10-pin Accessory Connector Pinout

The USB2000 features a 10-pin Accessory Connector, located on the side of the unit as follows:

10-pin Connector

Figure 2-2: Location of USB2000 10-pin Connector

USB2000 Operating Instructions 8

USB2000 Specifications

10-Pin Accessory Connector Pinout Diagram

When facing the 10-pin Accessory Connector on the USB2000, pin numbering is as follows:

10 8 6 4 2
9 7 5 3 1

Figure 2-3: 10-Pin Accessory Connector Pinout Diagram

10-Pin Accessory Connector – Pin Definitions

The following table contains information regarding the function of each pin in the USB2000’s 10-pin accessory
connector:
Pin # Description
1 VUSB or 5V in
2 RS232 Tx
3 RS232 Rx
4 Lamp Enable
5 Continuous Strobe
6 Ground
7 External Trigger In
8 Single Strobe
2
9 I C SCL
2
10 I C SDA

10-Pin J2 Accessory Connector – Part Number and Compatibility

The part numbers for the USB2000 Spectrometer 10-pin accessory connector are as follows:
• The connector is Samtec model IPT1-105-01-S-D-RA.
• The mating right-angle connector is Samtec model IPS1-105-01-S-D-RA.
If you are customizing your USB2000 Spectrometer system or configuring an External Triggering configuration,
you may need these part numbers to complete your setup.

USB2000 Operating Instructions 9

Installing the USB2000

3 Installing the USB2000

This chapter contains instructions in parallel for connecting the USB2000 via both USB and serial modes.
Note: You must install the OOIBase32 software application prior to connecting the USB2000 Spectrometer to
the PC. The OOIBase32 software installation installs the drivers required for USB2000 installation. If you
do not install OOIBase32 first, the system will not properly recognize the USB2000.

If you have already connected the USB2000 to the PC prior to installing OOIBase32, consult Chapter 5:
Troubleshooting for information on correcting a corrupt USB2000 installation.

USB2000 Installation
USB Mode Serial Port Mode
To connect the USB2000 to a PC via the USB port, To use the serial port capacity of the USB2000
the PC must be running the Windows 98/ME/2000/XP Spectrometer, the PC must be running a 32-bit
operating system. version of the Windows operating system (or Windows
CE 2.11 or higher for palm-sized PCs).
Note: The USB port on a PC can power up to five
USB2000 spectrometer channels. Systems Follow the steps below to connect the USB2000 to the
with more than five channels require a PC via serial port:
powered USB hub. 1. Connect the serial cable adapter block to the
USB2000.
Follow the steps below to connect the USB2000 to a
PC via the USB port: 2. Connect one end of the 9-pin serial cable to
the adapter block on the USB2000, and then
1. Install OOIBase32 on the destination PC.
connect the other end to a serial port on the
2. Locate the USB cable (USB-CBL-1) provided PC.
with the USB2000.
3. Note the number of the serial port (COM Port)
3. Insert the square end of the cable into the to which you connected the USB2000 (some
side of the USB2000. PCs may not have numbered ports; palm-
sized PCs typically have only one serial port).
4. Insert the rectangular end of the cable into the
USB port of the PC. 4. Plug the 5 VDC external power supply into an
outlet and connect it to the USB2000.
If you installed OOIBase32 prior to connecting the
USB2000, the Add New Hardware Wizard appears
and installs the USB2000 drivers. If the drivers do not
successfully install (or if you connected the USB2000
to the PC before installing OOIBase32), consult
Chapter 5: Troubleshooting.

USB2000 Operating Instructions 10

Installing the USB2000

Configuring the USB2000 in OOIBase32

Once you install the USB2000, you must configure OOIBase32’s Configure Spectrometer options so that
OOIBase32 recognizes the USB2000 Spectrometer.
Note: Consult the OOIBase32 Spectrometer Operating Software Manual for detailed instructions on configuring
the spectrometer in OOIBase32. You can find these instructions on the Software and Technical
Resources CD or on the Ocean Optics web site at the following location:
http://www.oceanoptics.com/technical/ooibase32bit.pdf.

The following sections contain instructions on initially configuring the USB2000 the first time you start OOIBase32:

Operator and Serial Number Dialog Box

The Operator and Serial Number screen prompts you to enter a user name and software serial number into
OOIBase. Some data files created by OOIBase32 during sampling procedures use this information in the file
headers.

Default Spectrometer Configuration File

The Default Spectrometer Configuration File screen prompts you to select a spectrometer configuration
(.SPEC) file for use with the USB2000. The unique serial number of the USB2000 precedes the file extension (for
example, USB2J0162.SPEC).
Navigate to the OOIBase32 installation directory and select the spectrometer configuration file.

Configure Hardware Screen

The Configure Hardware screen prompts you to enter spectrometer-specific information into OOIBase32 the first
time you run the program. Typically, you will only enter this information the first time you run OOIBase32.
However, you can alter the hardware configuration at any time using the Spectrometer Configuration screen.
Select Spectrometer | Configuration from the OOIBase32 menu bar to access the Spectrometer Configuration
screen.
Follow the steps on the next page to configure the USB2000:
Note: You do not need to configure the spectrometer hardware in the OOIPS2000 palm-sized PC operating
software. Most palm-sized PCs have only one serial connector and do not have USB ports. Thus,
OOIPS2000 will communicate with the spectrometer via this port at a fixed baud rate. There is no way to
customize the USB2000 configuration with OOIPS2000.

USB2000 Operating Instructions 11

Installing the USB2000

Configure Hardware Screen - Continued

USB Mode Serial Port Mode

1. Specify USB2000 in the Spectrometer Type 1. Select the USB2000 option from the
drop-down menu. Spectrometer Type drop-down menu.
2. Specify USB2000 in the A/D Converter Type 2. Select the Serial (RS-232) A/D option from the
drop-down menu. A/D Converter Type drop-down menu. This
selection enables serial-specific options in the
3. Specify the serial number of the USB2000
lower portion of the Configure Hardware
under the USB Serial Number drop-down
screen.
menu.
3. Select the COM port that the USB2000 is
Note: The system pre-fills this drop-down connected to in the Serial Port drop-down
menu with the serial numbers of all menu. Consult Chapter 5: Troubleshooting for
discovered USB2000 Spectrometers. information on identifying serial ports.
4. Click the OK button to accept the selected 4. Select the speed at which the USB2000 will
options. operate from the Baud Rate drop-down menu
(115,200 baud is recommended).
5. Specify the pixel resolution (from 1 to 500) in
the Pixel Resolution box. This value specifies
that every nth pixel of the spectrometer will
transmit from the USB2000 to the PC.

Note: You can sacrifice pixel resolution to

gain speed. The transfer of one
complete spectra requires ~0.3
seconds at 115,200 baud.
6. Enable the Compress Data function to
minimize the amount of data transferred
over the RS-232 connection. The
transmission of spectral data over the serial
port is a relatively slow process. Enabling
this function ensures that the USB2000
compresses every scan that it transmits.
This greatly increases the data transfer
speed of the USB2000.
7. Click the OK button to complete setup.

The spectrometer should now be able to acquire data and respond to light. Exit and restart OOIBase32 to save
configuration data to disk.

USB2000 Operating Instructions 12

Installing the USB2000

Spectrometer Configuration Screen

The Spectrometer Configuration screen prompts you to configure specific channel-level spectrometer information,
if necessary.
Select Spectrometer | Configure from the menu and set system parameters. In the Wavelength Calibration
tab, OOIBase32 pre-fills the coefficients for the USB2000 from information on a memory chip in the spectrometer.
Verify that the calibration coefficients match the coefficients from the Wavelength Calibration Data Sheet that
accompanied the spectrometer. If necessary, modify these values using the USB Programmer utility. Additionally,
ensure that you select both the Master and Channel Enabled boxes.
In the A/D Interface tab, enter the same values as in the Configure Hardware dialog box. OOIBase32 stores this
information for future use once you close the program.

Note: For information on using the USB2000 with the OOIPS2000 Operating Software for the palm-sized PC,
visit http://www.oceanoptics.com/technical/palmspec.pdf.

Connect Spectroscopic Accessories

To find operating instructions for USB2000-compatible products (such as light sources, sampling chambers, and
probes), consult the Software and Technical Resources CD or the Ocean Optics web site at:
http://www.oceanoptics.com/technical/operatinginstructions.asp
Chapter 4 contains a list of USB2000-compatible products with links to corresponding operating instructions.

External Triggering Options

You can trigger the USB2000 using a variety of External Triggering Options through the 10-pin Accessory
Connector on the spectrometer.
Consult the External Triggering Options document located at the following address:
http://www.oceanoptics.com/technical/externaltriggering.pdf
If you do not have web access, you can retrieve this document from the Software and Technical Resources CD
included with your spectrometer shipment.
The External Triggering PDF contains instructions on configuring External Triggering Options for the USB2000.
Note: Only the external software triggering option is available when using a palm-sized PC.

USB2000 Operating Instructions 13

USB2000 Compatible Products

4 USB2000 Compatible Products

Ocean Optics offers a complete range of spectroscopic accessories -- such as light sources, sample chambers,
probes, fibers, and software -- to complete a spectrophotometer system. Below is a list of products compatible
with the USB2000.

USB2000 Direct-attach Accessories

USB-ADP-DT Adapter block connecting the USB2000 to the DT-Mini
USB-ADP-H Adapter package to connect USB2000 to palm-sized PCs; European version
USB-ADP-PC Adapter package to connect USB2000 to PCs; European version
USB-ADP-PX2 Adapter block to connect the USB2000 to the PX-2 Pulsed Xenon Light Source
USB-BP Lithium-ion Battery Pack for USB2000
USB-CBL-1 1 meter USB cable
USB-CBL-H1 Serial cable connects palm-sized PCs to other serial devices
USB-CBL-H2 Serial cable and power cable for USB2000 to DB9
USB-CBL-PS +5 VDC, 2.4 Amp power supply
USB-FHS Filter Holder System
USB-ISS-T Integrated Sampling System with test-tube holder
USB-ISS-UV-VIS Integrated Sampling System with UV Light source
USB-ISS-VIS Integrated Sampling System with Visible light source
USB-LS-450 LS-450 Light Source
USB-LS-450-4/20 4-20 mA output module for the USB-LS-450 LED module
USB-LS-450-TP RTD temperature probe for USB-LS-450 (1/8" x 6")
USB-SPEC-CODE USB stand-alone spectroscopy firmware
USB2000-02CODE Stand-alone oxygen sensing firmware

USB2000 Operating Instructions 14

USB2000 Compatible Products

Software
The USB2000 is compatible with all Ocean Optics software.
• OOIBase32 Spectrometer Operating Software Manual
• OOIChem Chemistry Teaching Software Manual
• OOIColor Color Measurement Software Manual
• OOIIrrad Absolute Irradiance Software Manual
• OOIPS2000 Palm-SPEC Operating Software Manual
• OOISensors Sensor Software Manual

Device Drivers
The USB2000 is compatible with all Ocean Optics device drivers.
• OOIWinIP Windows Interface Package
• OOILVD LabVIEW Software Device Driver Package
• OOIHIP Palm-sized Interface Package
• OOIHSD High-speed Driver Library

A/D Converters
The USB2000 has an A/D converter integrated with the spectrometer. Thus, it does not require an external A/D
Converter.

Light Sources
• D-2000 Deuterium Source
• DH-2000 Deuterium Tungsten Halogen Source
• HG-1 Mercury Argon Calibration Source
• LS-1 Tungsten Halogen Source
• LS-1-CAL Calibrated Source
• LS-1-CAL-INT Calibrated Source
• LS-450 Blue LED Pulsed Source
• Mini-D2T Deuterium Tungsten Source
• PX-2 Pulsed Xenon Lamp

USB2000 Operating Instructions 15

USB2000 Compatible Products

Integrated Sampling Systems

• ISS-2 Integrated Sampling System
• ISS-UV-VIS Integrated Sampling System
• USB-ISS-UV-VIS Integrated Sampling System

Sampling Accessories
• 74-90-UV Right Angle Reflector
• 74-ACH Adjustable Collimating Lens Holder
• 74-OPM Optical Post Mount
• Collimating Lenses
• CUV-ALL-UV 4-way Cuvette Holder
• CUV-CCE Electrophoresis Sample Cell
• Cuvettes
• CUV-FL-DA Direct Attach Cuvette Holder
• CUV-UV, CUV-VIS Cuvette Holders
• CUV-UV-10, CUV-VIS-10 Cuvette Holders
• FHS-UV In-line Filter Holder
• FIA Flow Cells
• FOIS-1 Integrating Sphere
• FVA-UV Variable Attenuator
• ISP-REF Integrating Sphere
• LED-PS Power Supply
• LPC Long Pass Flow Cells
• NANO-1 Surface Tension Microcell
• PIP-10 SpectroPipetter Microcell
• RPH-1 Reflection Probe Holder
• STAN-ABS-UV and STAN-ABS-VIS Absorbance Standards
• WS-1 Diffuse Reflectance Standard

USB2000 Operating Instructions 16

USB2000 Compatible Products

Fiber Optic Probes

• CC-3 Cosine-corrected Irradiance Probes
• FL-400 Flame-resistant Probe
• R200 and R400 Reflection Probes
Also see operating instructions for the RPH-1 Reflection Probe Holder
• T200-RT-VIS-NIR Transflection Dip Probe
• T300-RT-UV/VIS Transflection Dip Probe
• TP300-UV-VIS Transflection Dip Probe

Optical Fiber Assemblies and Accessories

• Fiber Care and Operation
• "C" Mount Adapter & SMA Connector
• Fiber Wrenches
• Splice and Bulkhead Bushings

USB2000 Operating Instructions 17

Troubleshooting

5 Troubleshooting
The following sections contain information on troubleshooting issues you may encounter when using the
USB2000 Spectrometer.

Note: For issues encountered when using a palm-sized PC, consult the OOIPS2000 manual.

USB2000 Connected to PC Prior to OOIBase32 Installation

If you connect your Ocean Optics USB or PCI device to the computer prior to installing your Ocean Optics
software application, you may encounter installation issues that you must correct before your Ocean Optics
device will operate properly.

Follow the applicable steps in this document to remove the incorrectly installed device, device driver, and
installation files.

Note: If these procedures do not correct your device driver problem, you will need to obtain the “Correcting
Device Driver Issues” document from the Ocean Optics website. Visit the following web address:

http://www.oceanoptics.com/technical/engineering/correctingdevicedriverissues.pdf

Remove the Unknown Device from Windows Device Manager

1. Open Windows Device Manager as follows:

Windows 98/ME:

• Go to the desktop and right-click on My Computer.

• Select Properties from the pop-up menu.

• Click on the Device Manager tab.

Windows 2000/XP:

• Click Start | Settings | Control Panel | System.

• Select the Hardware tab.

• Click on the Device Manager button.

2. Locate the Other Devices option and expand the Other Devices selection by clicking on the "+" sign to
the immediate left.

Note: Improperly installed USB devices can also appear under the Universal Serial Bus Controller
option. Be sure to check this location if you cannot locate the unknown device.

USB2000 Operating Instructions 18

Troubleshooting

3. Locate the unknown device (marked with a large question mark). Right-click on the Unknown Device
listing and select the Uninstall or Remove option.

4. Click the OK button to continue. A warning box appears confirming the removal of the Unknown Device.
Click the OK button to confirm the device removal.

5. Disconnect the USB2000 from your computer.

6. Locate the section in this chapter that is appropriate to your operating system and perform the steps in
the “Remove Improperly Installed Files” section.

Windows 98:

Remove Improperly Installed Files:

1. Open Windows Explorer.

2. Navigate to the Windows | INF directory. If the INF directory is not visible, you will need to disable the
“Hide System Files and Folders” option on in Windows Folder Options.

Note: If the INF directory is not visible, you will need to disable the “Hide System Files and Folders” and
“Hide File Extensions for Known File Types” options in Windows Folder Options.

You can access Windows Folder Options from Windows Explorer, under the View | Options
menu selection.

3. Delete the OOI_USB.INF file in the INF directory.

4. Navigate to the Windows | System32 | Drivers directory.

5. Delete the EZUSB.SYS file.

6. Reinstall your Ocean Optics application and reboot the system when prompted.

7. Plug in the USB device.

The system will now be able to locate and install the correct drivers for the USB device.

USB2000 Operating Instructions 19

Troubleshooting

Windows 2000/XP:

Remove Improperly Installed Files:

1. Open Windows Explorer.

2. Navigate to the Windows | INF directory. If the INF directory is not visible, you will need to disable the
“Hide System Files and Folders” option on in Windows Folder Options.

Note: If the INF directory is not visible, you will need to disable the “Hide System Files and Folders” and
“Hide File Extensions for Known File Types” options in Windows Folder Options.

You can access Windows Folder Options from Windows Explorer, under the Tools | Folder
Options menu selection.

3. Delete the OOI_USB.INF and OOI_USB.PNF files in the INF directory.

4. Navigate to the Windows | System32 | Drivers directory.

5. Delete the EZUSB.SYS file.

6. Reinstall your Ocean Optics application and reboot the system when prompted.

7. Plug in the USB device.

The system will now be able to locate and install the correct drivers for the USB device.

USB2000 Operating Instructions 20

Troubleshooting

Troubleshooting the Serial Port Configuration

Occasionally, you may encounter problems with the serial port connection and/or software. Perform the following
steps to troubleshoot the serial port connection:
1. Cycle the power on the USB2000 and restart the OOIBase32 software. This ensures that the software
and the USB2000 are synchronized.
2. Determine the serial port (COM port) number:
Operating System Instructions
1. Right-click on My Computer
Windows 95/98/ME 2. Select Properties
3. Click on the Device Manager tab
1. Select Start | Settings | Control Panel | System
Windows 2000/XP 2. Select the Hardware tab
3. Click the Device Manager button.
1. Select Start | Programs | Administrative Tools (common) NT
Windows NT
Diagnostics

3. Double-click on the Ports (COM & LPT) option to display COM port numbers. Ensure that no warning icon
appears next to the USB2000’s COM port.
4. Verify that the COM port to which the USB2000 is interfaced is active. If the ports on the PC are not
labeled and you do not know the COM port number, use trial-and-error to find the correct COM port.

Open OOIBase32 and view the displayed graph. If the correct COM port is selected, you will see a
dynamic trace responding to light near the bottom of the graph. If the correct COM port is not selected,
you will see a straight line at zero counts.
5. Disable virus protection to ensure timely and complete data transfer (optional – some computers require
this step).

Older Version of OOIBase32 Installed

If the PC you want to use to interface to your USB2000 already has an older version of OOIBase32, you need to
install the latest version of OOIBase32. You can download the latest version of OOIBase32 from the Software and
Technical Resources CD or from the Ocean Optics web site at the following URL:
http://www.oceanoptics.com/technical/softwaredownloads.asp.
You do not need to uninstall previous versions of OOIBase32 when upgrading to the latest version.

USB2000 Operating Instructions 21

Sample Experiments

6 Sample Experiments
The following sections contain information on conducting sample experiments using the USB2000 and
OOIBase32. For information on experiments with OOIPS2000, consult the OOIPS2000 Operating Instructions.

Preparing for Experiments

Follow the steps below to configure the USB2000 and OOIBase32 for experiments:
1. Double-check that you have correctly installed the USB2000, installed OOIBase32, and configured the
light source and other sampling optics.
2. Open the OOIBase32 application, select Spectrometer | Configure from the menu bar, and double-
check that A/D Interface settings are correct.
3. Check your spectrometer setup configurations in OOIBase32:

Locate the Wavelength Calibration Data sheet that came with the USB2000. Select Spectrometer |
Configure from the menu and choose the Wavelength Calibration page. For each spectrometer
channel in the system, enable the channel and make sure the First Coefficient, Second Coefficient, Third
Coefficient and Intercept correspond to those of the system.
4. Adjust the acquisition parameters using the Acquisition Parameters dialog bar or select Spectrum |
Configure Data Acquisition from the menu.
If you have followed the previous steps and started OOIBase32, the spectrometer is already acquiring
data. Even with no light in the spectrometer, there should be a dynamic trace displayed in the bottom of
the graph. If you allow light into the spectrometer, the graph trace should rise with increasing light
intensity. This means the software and hardware are correctly installed.
Once you install the hardware, configure the software, and establish your sampling system, you are ready to take
measurements.
There are four basic optical measurements from which to choose:
• Absorbance
• Transmission
• Reflection
• Relative irradiance
The type of measurement you will take determines the configuration of the sampling optics for your system.
Furthermore, your choice of reference and data analysis determines how the OOIBase32 presents the results.
Note: For each measurement, you must first take a reference and dark spectrum. After you take a reference
and a dark spectrum, you can take as many measurement scans as needed. However, if you change any
sampling variable (integration time, averaging, smoothing, angle, temperature, fiber size, etc.), you must
store a new dark and reference spectrum.

USB2000 Operating Instructions 22

Sample Experiments

Application Tips
If the signal you collect is saturating the spectrometer (intensity greater than 4000 counts), you can decrease the
light level on scale in scope mode by:
• Decreasing the integration time
• Attenuating the light going into the spectrometer
• Using a smaller diameter fiber
• Using a neutral density filter with the correct optical density

If the signal you collect has too little light, you can increase the light level on scale in scope mode by:
• Increasing the integration time
• Using a larger diameter fiber
• Removing any optical filters

USB2000 Operating Instructions 23

Sample Experiments

Absorbance Experiments
Absorbance spectra are a measure of how much light a sample absorbs. For most samples, absorbance is
linearly related to the concentration of the substance. OOIBase32 calculates absorbance (Aλ) using the following
equation…

Sλ - Dλ
Aλ = - log10 ( R -D )
λ λ

…where Sλ is the sample intensity at wavelength λ, Dλ is the dark intensity at wavelength λ, Rλ is the reference
intensity at wavelength λ.

Figure 6-1: Typical absorbance setup. The light source (far right) sends light via an input fiber into a cuvette in a cuvette
holder (bottom center). The light interacts with the sample. The output fiber carries light from the sample to the
spectrometer (top center), which is connected to the PC (far left).

Absorbance is also proportional to the concentration of the substance interacting with the light (this is known as
Beer’s Law). Common absorption applications include the quantification of chemical concentrations in aqueous or
gaseous samples.
Follow the steps below to take an absorbance measurement using OOIBase32:
1. Place OOIBase32 in scope mode by clicking the scope mode icon on the toolbar or selecting Spectrum |
Scope Mode from the menu bar.
2. Ensure that the entire signal is on scale. The intensity of the reference signal should peak at about 3500
counts. If necessary, adjust the integration time until the intensity is approximately 3500 counts.

(Continued)

USB2000 Operating Instructions 24

Sample Experiments

3. Place a sample of the solvent into a cuvette and take a reference spectrum. You must take a reference
spectrum before measuring absorbance.

Note: Do not put the sample itself in the path when taking a reference spectrum, only the solvent.

Click the Store Reference spectrum icon on the toolbar or select Spectrum | Store Reference from the
menu bar to store the reference. This command merely stores a reference spectrum in memory. You
must select File | Save | Reference from the menu bar to permanently save the spectrum to disk.
4. Block the light path to the spectrometer. Then, take a dark spectrum by clicking the Store Dark
Spectrum icon on the toolbar or by selecting Spectrum | Store Dark from the menu bar. This command
merely stores a dark spectrum in memory. You must select File | Save | Dark from the menu to
permanently save the spectrum to disk.
Note: If possible, do not turn off the light source when taking a dark spectrum. If you must turn off your
light source to store a dark spectrum, allow enough time for the lamp to warm up again before
continuing your experiment. After the lamp warms up again, store a new reference (Step 3).
You must take a dark spectrum before measuring absorbance.
5. Put the sample in place and ensure that the light path is clear. Then, take an absorbance measurement
by clicking on the Absorbance Mode icon on the toolbar or selecting Spectrum | Absorbance Mode
from the menu. To permanently save the spectrum to disk, click the Save icon on the toolbar or select
File | Save | Processed from the menu bar.

Note: If you change any sampling variable (integration time, averaging, smoothing, angle, temperature,
fiber size, etc.), you must store a new dark and reference spectrum.

USB2000 Operating Instructions 25

Sample Experiments

Transmission Experiments
Transmission is the percentage of energy passing through a sample relative to the amount that passes through
the reference. Transmission Mode also displays the portion of light reflected from a sample, since transmission
and reflection measurements use the same mathematical calculations. The transmission is expressed as a
percentage (%Tλ) relative to a standard substance (such as air). OOIBase32 calculates %Tλ (or %Rλ) with the
following equation…

Sλ - Dλ
%Tλ = x 100%
Rλ - Dλ

…where Sλ is the sample intensity at wavelength λ, Dλ is the dark intensity at wavelength λ, Rλ is the reference
intensity at wavelength λ.

Figure 6-2: Typical transmission setup. The light source (far right) sends light via the input leg of a transmission probe
into a container (bottom center). The light interacts with the sample. The output leg of the transmission probe carries the
information to the spectrometer (top center), which transmits the information to the PC (far left).

Common transmission applications include measuring light through solutions, optical filters, optical coatings, and
other optical elements (such as lenses and fibers).
Perform the following steps to take a transmission measurement using OOIBase32:
1. Place OOIBase32 in scope mode by clicking the Scope Mode icon on the toolbar or by selecting
Spectrum | Scope Mode from the menu bar.
2. Ensure that the entire signal is on scale. The intensity of the reference signal should peak at about 3500
counts. If necessary, adjust the integration time until the intensity is approximately 3500 counts.

(Continued)

USB2000 Operating Instructions 26

Sample Experiments

6. Place a sample of the solvent into a cuvette and take a reference spectrum. You must take a reference
spectrum before measuring transmission.

Note: Do not put the sample itself in the path when taking a reference spectrum, only the solvent.

Click the Store Reference spectrum icon on the toolbar or select Spectrum | Store Reference from the
menu bar to store the reference. This command merely stores a reference spectrum in memory. You
must select File | Save | Reference from the menu bar to permanently save the spectrum to disk.
3. Block the light path to the spectrometer. Then, take a dark spectrum by clicking the Store Dark
Spectrum icon on the toolbar or by selecting Spectrum | Store Dark from the menu bar. This command
merely stores a dark spectrum in memory. You must select File | Save | Dark from the menu to
permanently save the spectrum to disk.
Note: If possible, do not turn off the light source when taking a dark spectrum. If you must turn off your
light source to store a dark spectrum, allow enough time for the lamp to warm up again before
continuing your experiment.
You must take a dark spectrum before measuring transmission.
4. Put the sample in place and verify that the light path is clear. Then, take a transmission measurement by
clicking the Transmission Mode icon on the toolbar or selecting Spectrum | Transmission Mode from
the menu bar. To save the spectrum to disk, click the Save icon on the toolbar or select File | Save |
Processed from the menu bar.

Note: If you change any sampling variable (integration time, averaging, smoothing, angle, temperature,
fiber size, etc.), you must store a new dark and reference spectrum.

USB2000 Operating Instructions 27

Sample Experiments

Reflection Experiments
Reflection is the return of radiation by a surface, without a change in wavelength. Reflection can be:
• Specular (the angle of incidence is equal to the angle of reflection)
• Diffuse (the angle of incidence is not equal to the angle of reflection)
Every surface returns both specular and diffuse reflections. Some surfaces may return mostly specular reflection,
while others may return mostly diffuse reflection. Specular reflection increases proportionately with the amount of
gloss on a surface.
Reflection is expressed as a percentage (%Rλ) relative to the reflection from a standard reference substance…

Sλ - Dλ
%Rλ = x 100%
Rλ - Dλ

…where Sλ is the sample intensity at wavelength λ, Dλ is the dark intensity at wavelength λ, Rλ is the reference
intensity at wavelength λ.

Figure 6-3: Typical reflection setup. A light source (far right) sends light via the input leg of a reflection probe onto a
sample (bottom center). A reflection probe holder holds the probe in either a 90 or 45-degree angle from the surface. The
output leg of the reflection probe carries light from the sample to the spectrometer (top center), which is connected to the
PC (far left).

Common reflection applications include measuring the properties of mirrors and coatings. Other applications
include measuring the visual properties of the color in paints, plastics, and food products.

USB2000 Operating Instructions 28

Sample Experiments

Perform the following steps to take reflection measurements using OOIBase32:

1. Place OOIBase32 is in scope mode by clicking the Scope Mode icon on the toolbar, or by selecting
Spectrum | Scope Mode from the menu bar.
2. Ensure that the entire signal is on scale. The intensity of the reference signal should peak at about 3500
counts.
3. Take a reference spectrum with the WS-1 Diffuse Reflectance Standard or the STAN-SSH High-
reflectivity Reference Standard. You must take a reference spectrum before measuring reflection.
Click the Store Reference spectrum icon on the toolbar or select Spectrum | Store Reference from the
menu bar to store the reference. This command merely stores a reference spectrum in memory. You
must select File | Save | Reference from the menu bar to permanently save the spectrum to disk.
4. Block the light path to the spectrometer. Then, take a dark spectrum by clicking the Store Dark
Spectrum icon on the toolbar or by selecting Spectrum | Store Dark from the menu bar. This command
merely stores a dark spectrum in memory. You must select File | Save | Dark from the menu to
permanently save the spectrum to disk.
Note: If possible, do not turn off the light source when taking a dark spectrum. If you must turn off your
light source to store a dark spectrum, allow enough time for the lamp to warm up again before
continuing your experiment.
You must take a dark spectrum before measuring transmission.
5. Put the sample is in place and ensure that the light path is clear. Then, take a reflection measurement by
clicking on the Transmission Mode icon on the toolbar or selecting Spectrum | Transmission Mode
from the menu bar (since the mathematical calculations used to calculate transmission and reflection are
identical). To save the spectrum to disk, click the Save icon on the toolbar or select File | Save |
Processed from the menu bar.
Note: If you change any sampling variable (integration time, averaging, smoothing, angle, temperature,
fiber size, etc.), you must store a new dark and reference spectrum.

USB2000 Operating Instructions 29

Sample Experiments

Relative Irradiance Experiments

Irradiance is the amount of energy at each wavelength emitted from a radiant sample. In relative terms, it is a
comparison of the fraction of energy the sample emits and the energy the sampling system collects from a lamp
with a blackbody energy distribution (normalized to 1 at the energy maximum). OOIBase32 calculates relative
irradiance with the following equation…

Sλ - Dλ
Iλ = Bλ ( R -D )
λ λ

…where Bλ is the relative energy of the reference (calculated from the color temperature) at wavelength λ, Sλ is
the sample intensity at wavelength λ, Dλ is the dark intensity at wavelength λ, Rλ is the reference intensity at
wavelength λ.

Figure 6-4: Typical Relative Irradiance Setup. A light source with a known color temperature (such as the LS-1or
LS-1-LL - lower right) is used to take a reference spectrum. The light to measure (lower left) is accumulated through a
CC-3 Cosine Corrector (or FOIS integrating sphere) into an input fiber, which carries the light information to the
spectrometer. The spectrometer then transmits the information to the PC, which compares the measured spectra against
the reference spectrum, thus removing wavelength-dependent instrument response from the measurement.

Common applications include characterizing the light output of LEDs, incandescent lamps, and other radiant
energy sources such as sunlight. Relative irradiance measurements also include fluorescence measurements,
which measure the energy given off by materials that have been excited by light at shorter wavelengths.

USB2000 Operating Instructions 30

Sample Experiments

Perform the following steps to take a relative irradiance measurement using OOIBase32:
1. Place OOIBase32 is in scope mode by clicking the Scope Mode icon on the toolbar, or by selecting
Spectrum | Scope Mode from the menu bar.
2. Ensure that the entire signal is on scale. The intensity of the reference signal should peak at about 3500
counts.

Note: The light source must be a blackbody of known color temperature.

3. In the Reference Color Temperature dialog box, enter the color temperature of the light source (in
Kelvin) and click the OK button.
4. Take a reference spectrum using a light source with a black body of a known color temperature, such as
the LS-1.
Click the Store Reference spectrum icon on the toolbar or select Spectrum | Store Reference from the
menu bar to store the reference. This command merely stores a reference spectrum in memory. You
must select File | Save | Reference from the menu bar to permanently save the spectrum to disk.
5. Block the light path to the spectrometer. Then, take a dark spectrum by clicking the Store Dark
Spectrum icon on the toolbar or by selecting Spectrum | Store Dark from the menu bar. This command
merely stores a dark spectrum in memory. You must select File | Save | Dark from the menu to
permanently save the spectrum to disk.
Note: If possible, do not turn off the light source when taking a dark spectrum. If you must turn off your
light source to store a dark spectrum, allow enough time for the lamp to warm up again before
continuing your experiment.
You must take a dark spectrum before measuring relative irradiance.
6. Position the fiber at the light source you wish to measure. Then, choose the Irradiance mode icon on the
toolbar or select Spectrum | Relative Irradiance Mode from the menu bar.
7. Click the Save icon on the toolbar or select File | Save | Processed from the menu bar to save the
spectrum to disk.

Note: If you change any sampling variable (integration time, averaging, smoothing, angle, temperature,
fiber size, etc.), you must store a new dark and reference spectrum.

USB2000 Operating Instructions 31

Sample Experiments

Time Acquisition Experiments

OOIBase32 allows you to perform time acquisition experiments. Time acquisition experiments track processes,
perform kinetic analyses, and monitor spectral events all as a function of time. You can collect, as a function of
time, spectral data from up to six single wavelengths (designated as Channels A through F) and up to two
mathematical combinations of these wavelengths (designated as Combinations 1 and 2). Additionally, you can
acquire data in any mode (transmission, absorbance, etc.).
For more details about this and other OOIBase32 functions, refer to the OOIBase32 Spectrometer Operating
Software Manual.
Follow the steps below to perform a time series experiment in OOIBase32:
1. Enter scope mode and store a reference spectra and dark spectra.
2. Choose the measurement mode (absorbance, transmission, etc.) and select Time Acquisition |
Configure | Configure Time Channels from the menu bar to access the Time Acquisition Channel
Configuration screen.
Proceed to the Configuring the Time Acquisition Channel Configuration Screen section below.

Configuring the Time Acquisition Channel Configuration Screen

1. Perform the following steps on the Time Acquisition Channel Configuration screen:
a. Select Enabled to set the time acquisition calculation for the wavelength. The time acquisition
process will not calculate data if you do not select this option for at least
b. Select Plotted to see a real-time graph of the acquired data in a spectral window.
c. Select a Spectrometer Channel for the time acquisition process
d. Specify the analysis wavelength in the Wavelength (nm) box.
e. Specify the number of pixels around the analysis wavelength to average in the Bandwidth
(pixels) box.
f. Select a multiplicative factor to apply to the data before plotting or storing. Then, select an
additive constant or offset to apply to the data. OOIBase32 applies the additive constant or offset
after applying the factor but before plotting or storing data.

The equation for the Factor and Offset functions is:

Results = (Factor * Data) + Offset
2. Configure a time acquisition process for the second single wavelength (if desired). Select the Channel B
page and repeat Steps 1-3 for Channel B.

To configure a time acquisition process for the third, fourth, fifth, and sixth single wavelengths, select the
Channel C, Channel D, Channel E, and Channel F pages, respectively, and set the necessary
parameters.

(Continued)

USB2000 Operating Instructions 32

Sample Experiments

3. Configure a time acquisition process for a combination of two time channels (if desired) by selecting
Combination 1.

Perform the steps below to configure a combination:

g. Select Enabled to set the time acquisition calculation for the wavelength.
h. Enable Plotted to see a real-time graph of the acquired data in a spectral window.
i. Specify Time Channel A through F for the First Channel.
j. Select the mathematical operation to produce the data for Combination 1.
k. Specify Time Channel A through F for the Second Channel.
l. Select a multiplicative factor to apply to the data before plotting or storing. Then, select an
additive constant or offset to apply to the data. OOIBase32 applies the additive constant or offset
after applying the factor but before plotting or storing data.

The equation for the Factor and Offset functions is:

Results = (Factor * Data) + Offset
4. Configure a time acquisition process for the Combination 2 page, if desired. This page is virtually identical
to the Combination 1 page, with the exception that you can choose Combination 1 for the first or second
channel in Combination 2.
5. Click the Apply button to apply the changes, and then click the OK button to close the Time Acquisition
Channel Configuration screen.
Proceed to the Configuring the Configure Acquisition Screen section below.

Configuring the Time Acquisition Configuration Screen

1. Select Time Acquisition | Configure | Configure Acquisition from the menu bar to open the Time
Acquisition Configuration screen.
2. Enable Stream Data to Disk to save time acquisition data.
3. Enter a value in the Write Data to Disk Every X Acquisitions box to set the frequency for data saves.
OOIBase32 saves data more frequently if the number is smaller, or less frequently if the number is larger.
Entering a large number enhances the performance of the time acquisition process.
Note: At specified time intervals, OOIBase32 stores data into time acquisition channels or combination
channels. OOIBase32 can plot the data in a spectral window, or stream the data to disk, or both.
OOIBase32 can display up to 2048 acquisitions in a spectral window. If OOIBase32 collects more
than 2048 acquisitions, it only displays the last 2048. To store more than 2048 acquisitions, you
must stream the data to disk.

Writing data to the disk is a slow process (relative to the speed of some spectral acquisitions) and
causes a decrease in system performance. However, writing data to disk more frequently gives a
larger margin of safety.
4. Enable Show Values in Status Bar to see the time acquisition values in the status bar. These values
replace the cursor values.
5. Name the Stream Filename for the time acquisition process. Clicking on the ellipsis to the right of this
box opens a file save dialog box, allowing you to navigate to a designated folder.
(Continued)

USB2000 Operating Instructions 33

Sample Experiments

6. Enable Save Every Acquisition to store data for every spectral acquisition during a time acquisition
process (optional).
Note: OOIBase32 has options to either store data for each acquisition, or to collect data only after a
specified delay. Several factors affect the minimum time acquisition frequency, including
integration time, number of spectrometer channels, samples averaged, and computer speed. If
you instruct OOIBase32 to store data every 100 milliseconds, the delay between data
acquisitions will be 100 milliseconds or more, depending on your experimental configuration.
OOIBase32 spends a large amount of time calculating, rendering, and displaying the spectra in a
spectral window. You can suspend the graph display, which greatly improves the performance of
OOIBase32.
7. Enter an Initial Delay to set the delay preceding the time acquisition process. Keep in mind that the delay
countdown does not begin until you start the time acquisition process. Be sure to select Hours, Minutes,
Seconds, or Milliseconds immediately to the right of the initial delay entry.
8. Enter a value to set the Frequency of the data collected in a time acquisition process. OOIBase32
stamps data from a time acquisition with a time accurate to one millisecond. Be sure to select Hours,
Minutes, Seconds, or Milliseconds immediately to the right of the frequency entry. You can enable the
Save Every Acquisition box to store the acquisitions that occur at this frequency. See Step 6 for more
information.
9. Enter a value to set the Duration for the entire time acquisition process. Be sure to select Hours, Minutes,
Seconds, or Milliseconds to the right of the duration entry. Click the OK button to close the Time
Acquisition Configuration dialog box. Then, enable Continue Until Manually Stopped, which instructs
OOIBase32 to store data until you manually stop the acquisition process (optional).

USB2000 Operating Instructions 34

Appendix A

Appendix A: Calibrating the Wavelength of the

USB2000
This Appendix describes how to calibrate the wavelength of your spectrometer. Though each spectrometer is
calibrated before it leaves Ocean Optics, the wavelength for all spectrometers will drift slightly as a function of
time and environmental conditions. Ocean Optics recommends periodically recalibrating the USB2000.

About Wavelength Calibration

You are going to be solving the following equation, which shows that the relationship between pixel number and
wavelength is a third-order polynomial…

λp = I + C1 p + C2 p2 + C3 p3

...where λ is the wavelength of pixel p, I is the wavelength of pixel 0, C1 is the first coefficient (nm/pixel), C2 is the
2 3
second coefficient (nm/pixel ), and C3 is the third coefficient (nm/pixel ). You will be calculating the value for I and
the three Cs.

Calibrating the Spectrometer

Preparing for Calibration

To re-calibrate the wavelength of your spectrometer, you will need the following:
• A light source capable of producing spectral lines
Note: Ocean Optics’ HG-1 Mercury-Argon lamp is ideal for recalibration. If you do not have an HG-1, you
will need a light source that produces several (at least 4-6) spectral lines in the wavelength region of
your spectrometer.

• A USB2000 spectrometer
• An optical fiber (for spectrometers without a built-in slit, a 50-µm fiber works best)
• A spreadsheet program (Excel or Quattro Pro, for example) or a calculator that performs third-order linear
regressions

Note: If you are using Microsoft Excel, choose Tools | Add-Ins and check AnalysisToolPak and
AnalysisTookPak-VBA.

USB2000 Operating Instructions 35

Appendix A

Calibrating the Wavelength of the Spectrometer

Perform the steps below to calibrate the wavelength of the spectrometer:
1. Place OOIBase32 into Scope Mode and take a spectrum of your light source. Adjust the integration time
(or the A/D conversion frequency) until there are several peaks on the screen that are not off-scale.
2. Move the cursor to one of the peaks and position the cursor so that it is at the point of maximum intensity.
3. Record the pixel number that is displayed in the status bar or legend (located beneath the graph). Repeat
this step for all of the peaks in your spectrum.
4. Use the spreadsheet program or calculator to create a table like the one shown below. In the first column,
place the exact or true wavelength of the spectral lines that you used.
In the second column of this worksheet, place the observed pixel number. In the third column, calculate
the pixel number squared, and in the fourth column, calculate the pixel number cubed.

Independent Values Computed

Dependent from the Regression
Variable Variables Output

Predicted
True Wavelength (nm) Pixel # Pixel # 2 Pixel # 3 Difference
Wavelength
253.65 175 30625 5359375 253.56 0.09
296.73 296 87616 25934336 296.72 0.01
302.15 312 97344 30371328 302.40 -0.25
313.16 342 116964 40001688 313.02 0.13
334.15 402 161604 64964808 334.19 -0.05
365.02 490 240100 117649000 365.05 -0.04
404.66 604 364816 220348864 404.67 -0.01
407.78 613 375769 230346397 407.78 0.00
435.84 694 481636 334255384 435.65 0.19
546.07 1022 1044484 1067462648 546.13 -0.06
576.96 1116 1245456 1389928896 577.05 -0.09
579.07 1122 1258884 1412467848 579.01 0.06
696.54 1491 2223081 3314613771 696.70 -0.15
706.72 1523 2319529 3532642667 706.62 0.10
727.29 1590 2528100 4019679000 727.24 0.06
738.40 1627 2647129 4306878883 738.53 -0.13
751.47 1669 2785561 4649101309 751.27 0.19

(Continued)

USB2000 Operating Instructions 36

Appendix A

5. Use the spreadsheet or calculator to calculate the wavelength calibration coefficients. In the spreadsheet
program, find the functions to perform linear regressions.
• If using Quattro Pro, look under Tools | Advanced Math
• If using Excel, look under Analysis ToolPak
6. Select the true wavelength as the dependent variable (Y). Select the pixel number, pixel number squared,
and the pixel number cubed as the independent variables (X). After executing the regression, you will
obtain an output similar to the one shown below.
Regression Statistics
Multiple R 0.999999831
R Square 0.999999663
Adjusted R Square 0.999999607
Standard Error 0.125540214
Observations 22

Intercept

Coefficients Standard Error

Intercept 190.473993 0.369047536 First coefficient
X Variable 1 0.36263983 0.001684745
X Variable 2 -1.174416E-05 8.35279E-07
X Variable 3 -2.523787E-09 2.656608E-10 Second coefficient

Third coefficient

The figure above notes the numbers of importance.

7. Record the Intercept, as well as the First, Second, and Third Coefficients. Additionally, look at the value
for R squared. It should be very close to 1. If not, you have most likely assigned one of your wavelengths
incorrectly.
Keep these values at hand.

USB2000 Operating Instructions 37

Appendix A

Saving the New Calibration Coefficients: USB Mode

Ocean Optics programs wavelength calibration coefficients unique to each USB2000 onto an EEPROM memory
chip in the USB2000.
You can overwrite old calibration coefficients on the EEPROM if you are using the USB2000 via the USB port. If
you are using the USB2000 via the serial port, consult the Saving the New Calibration Coefficients: Serial Mode
section later in this Appendix.

To Save Wavelength Calibration Coefficients Using the USB Mode

1. Ensure that the USB2000 is connected to the PC and that you have closed all other applications.
2. Point your browser to http://www.oceanoptics.com/technical/softwaredownloads.asp and scroll down to
Microcode. Click on the USB EEPROM Programmer selection.
3. Save the setup file to your computer.
4. Run the Setup.exe file to install the software. The Welcome screen appears.
5. Click the Next button. The Destination Location screen appears.
6. Accept the default installation location, or click the Browse button to specify a directory. Then, click the
Next button. The Program Manager Group screen appears.
7. Click the Next button. The Start Installation screen appears.
8. Click the Next button to begin the installation. Once the installation finishes, the Installation Complete
screen appears.
9. Click the Finish button and reboot the computer when prompted.
10. Navigate to the USB EEPROM Programmer from the Start menu and run the software.
11. Click on the appropriate USB2000 device displayed in the left pane of the USB Programmer screen.
12. Double-click on each of the calibration coefficients displayed in the right pane of the USB Programmer
screen and enter the new values acquired in Steps 5 and 6 of the Calibrating the Wavelength of the
Spectrometer section in this Appendix.
13. Repeat Step 12 for all of the new values.
14. Click on the Save All Values button to save the information, and then Exit the USB Programmer
software.
The new wavelength calibration coefficients are now loaded onto the EEPROM memory chip on the USB2000.

USB2000 Operating Instructions 38

Appendix A

Saving the New Calibration Coefficients: Serial Mode

If you are connecting the USB2000 Spectrometer to the serial port of the PC, you need to save the new
wavelength calibration coefficients to the .SPEC file that OOIBase32 accesses when opened.
Note: You cannot save the calibration coefficients to the EEPROM memory chip on the USB2000 when using the
serial mode.

To Save Wavelength Calibration Coefficients Using the Serial Mode

1. Open the OOIBase32 application.
2. Select Spectrometer | Configure from the OOIBase32 menu bar. The Configure Spectrometer screen
appears.
3. Select the Wavelength Calibration tab to update the wavelength coefficients within OOIBase32.
4. Enter in the new values acquired from Steps 5 and 6 of the Calibrating the Wavelength of the
Spectrometer section in this Appendix.
5. Click the OK button to save the information in OOIBase32.

USB2000 Operating Instructions 39

Appendix B

Appendix B: USB2000-FLG Spectrometer

The USB2000-FLG Spectrometer is preconfigured for use with fluorescence applications from 380-1050 nm. It
contains proprietary Silver AgPlus Mirrors which provide an increase in sensitivity of 10-35% over the standard
USB2000 Spectrometer.
The USB2000-FLG contains custom firmware that allows you to program a variable between a Single Strobe
signal and the commencement of an acquisition. You can enable this mode entirely through software configuration,
and you can easily control the mode via the OOIBase32 interface.

About the USB2000-FLG

On the USB2000-FLG, Ocean Optics has altered the functionality of the External Hardware Trigger function and
reprogrammed the Single Strobe signal function. These alterations of the USB2000 enable you to operate in the
Variable Delay Mode without the presence of an external trigger signal. The USB2000-FLG will simulate the signal
to trigger the appropriate circuitry in the spectrometer.
The table below summarizes the capacity of the USB2000-FLG in Variable Delay Mode:
Parameter Value in Normal Acquisition Mode Value in Variable Delay Mode
Integration time User controlled 5 ms fixed
Strobe delay 0 µs 2 – 511 µs + 3 µs
Jitter < 25 ns < 25 ns

Using the USB2000-FLG

1. Install the OOIBase32 software on your PC.
Note: Ensure that you have installed the OOIBase32 software prior to connecting the USB2000-FLG
Spectrometer to your PC.
2. Connect the USB2000-FLG Spectrometer to the USB port of your PC.
3. Start OOIBase32 and ensure that the spectrometer is acquiring spectra.
4. Verify that the driver version is 4.0.4.9 or later. Open the Help | About option in OOIBase32 to obtain this
information. If the driver meets this requirement, proceed to Step 6. Otherwise, proceed to Step 5.
5. Overwrite (if necessary) the outdated version of the driver with the one included with the USB2000-FLG.
Open Windows Explorer, browse to the OOIBase32 directory (C:\Program Files\Ocean Optics\OOIBase32
is the default installation location) and overwrite the existing ooidrv32.dll with the new file.
6. Enter the desired delay value in the Flash Delay Control Box (See Figure B-1 on the following page).

Note: This value is entered in microseconds (µs), even though the label shows milliseconds (msec).

7. Enter Variable Delay Mode by placing the USB2000-FLG in External Hardware Trigger mode. In
OOIBase32, select Spectrum | Configure Data Acquisition | External Trigger, and then select the
Hardware Trigger option. You do not need to apply a trigger signal.
(Continued)

USB2000 Operating Instructions 40

Appendix B

8. Enable Single Strobe output by checking the Strobe Enable check box (See Figure B-1 on the following
page).

The strobe signal is a rising edge trigger signal that is TTL High for the entire delay period. See Figure B-2
for a timing diagram.
The USB2000-FLG is now configured for operation in Variable Delay Mode.

Figure B-1: The Acquisition Parameters Toolbar.

Note the location of the Flash Delay (entered in µs) and Strobe/Lamp Enable options.

Figure B-2: Timing Diagram for Variable Delay Mode

USB2000 Operating Instructions 41

Index

A M
Accessories, 14, 15 memory chip, 1
A/D Converters, 16 Mirror, 6
Direct-attach, 15
Integrated Sampling Systems, 17 O
Optical Fiber Assemblies, 18
Probes, 18 OOIBase32, 12
Sampling, 17 Optical Fiber Assemblies, 18
Adobe Acrobat Reader, 4 Overview, 1
AgPlus Mirrors, 41
P
C Packing List, 3
Calibrating, 36 Passwords, 4
CCD Detector, 6 Pin Definitions, 10
Compatibility, 9 Pinout, 9
Compatible Products, 15 Power, 7
Configure Hardware, 12
R
D range, 7
Data transfer rate, 7 resolution, 7
Default Spectrometer Configuration File, 12
Detector Collection Lens, 6 S
Device Drivers, 16
Slit, 6
Dimensions, 7
SMA Connector, 6
Dynamic range, 7
Software, 16
Software and Resources Library CD, 4
E Specifications, 5
EEPROM, 1 Detector, 7
Experiments, 23 Spectrometer, 7
Absorbance, 25 Spectroscopic Accessories, 14
Reflection, 29
Relative Irradiance, 31 T
Time Acquisition, 33
Time Acquisition, 33
Transmission, 27
Timing Diagram, 42
Troubleshooting, 19
F
Filter, 6 U
Focal length, 7
Upgrades, 4
Focusing Mirror, 6
USB2000-FLG, 41
USB-ADP-H, 3
G USB-ADP-PC, 3
Grating, 6 USB-CBL-1, 3

I V

Installed Filter, 6 Variable Delay Mode, 41

Installing, 11
W
L Wavelength Calibration, 36
L2 Detector Collection Lens, 6 Wavelength Calibration Data File, 3
Lens, 6 Wavelength Calibration Data Sheet, 3
Weight, 7

USB2000 Operating Instructions 42