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Introduction To ImageJ - 4 - 23

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11 views

Introduction To ImageJ - 4 - 23

Uploaded by

Gustavo Rosero
Copyright
© © All Rights Reserved
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
You are on page 1/ 29

OUTLINE

● WHAT IS IMAGEJ?
○ UNDERSTANDING THE IMAGEJ/FIJI
FAMILY
● WHAT CAN IMAGEJ/FIJI DO?
○ PLUGINS: BIOVOXXEL, STARDIST ETC…
○ SCRIPTING AND AUTOMATION
● IMAGEJ ON OTHER PLATFORMS
○ PYIMAGEJ
○ KNIME
● LEARNING MORE ABOUT IMAGEJ/FIJI
○ ONLINE RESOURCES
● ADDITIONAL RESOURCES
WHAT IS IMAGEJ?

● PRIMARILY* A DESKTOP APPLICATION FOR SCIENTIFIC IMAGE ANALYSIS


● OPEN SOURCE WITH STRONG COMMUNITY SUPPORT
● WRITTEN IN JAVA, ENABLING IMAGEJ TO RUN IN DIVERSE COMPUTING
ENVIRONMENTS
● REUSABLE SET OF LIBRARIES AND SHARED FRAMEWORK FOR IMAGE ANALYSIS
● MULTIPLE “FLAVORS” OF IMAGEJ:

* ImageJ2’s headless feature allows ImageJ2 to run on distributed computing networks


WHAT IS IMAGEJ?

● STABLE VERSION OF THE ORIGINAL IMAGEJ (1.X)


HAS BEEN MAINTAINED SINCE 1997.
● IMAGEJ2 IS A MODERNIZATION AND RE-
ARCHITECTING OF THE ORIGINAL IMAGEJ (1.X)
Wayne Rasband
● THE IMAGEJ LEGACY LAYER MAINTAINS
BACKWARDS COMPATIBILITY BETWEEN IMAGEJ2
AND IMAGEJ (1.X)
● FIJI IS A “BATTERIES INCLUDED” DISTRIBUTION OF
IMAGEJ2
THE MAIN WINDOW

Menu

Tools

Status
Search

● Tip: click on the status bar


● Tip: right / double-click on Tools

Getting Started page of the ImageJ wiki


CTRL + L: SEARCH BAR

Edit ▶ Options ▶ Search Bar... ▶ Pressing L focuses the search bar


STAYING UP-TO-DATE

Updater page of the ImageJ wiki


STAYING UP-TO-DATE

Not this one!

Updater page of the ImageJ wiki


STAYING UP-TO-DATE

Following an Update Site


OPENING DATA…
Drag and Drop
File ▶ Open…

File
▶ Import
▶ Bio-Formats

Importing Image Files page of the ImageJ wiki


WHAT CAN FIJI DO?
Stitching
Segmentation

Big Data
Tracking
Search on imagej.net to learn more about
your topic
Original ImageJ documentation at imagej.org

● Original ImageJ user guide


● Extensive documentation on
commands and macros
● Tutorials, examples, image
processing guides
Learn and teach others on the image.sc forum

https://forum.image.sc/
ImageJ and more on the forum!

● There is more than


just ImageJ help on
the forum!

● Have a basic image


processing question?
Ask the forum!
Introduction to the ImageJ/Fiji
Ecosystem
● Background on ImageJ/Fiji
● Where to learn more about Fiji
● Other resources
Other online resources
● Learn more about ImageJ and image processing
○ https://bioimagebook.github.io/index.html
● Advanced tutorials
○ https://github.com/imagej/tutorials
● Find more presentations at:
○ https://imagej.net/events/presentations
Digital Image Basics with ImageJ/Fiji
● Digital images
● Image dimensions
● Image bit depth
Generating scientific digital images

Output
● Usually 8-bit, 12-bit, 16-bit
gray scale images.
● Can be n-dimensional (i.e.
“XYCTZ”).
● Images are usually .TIFF
format or proprietary
format (e.g. .nd2).
An example image dataset

Channel: 1

Channel: 2

Channel: 3

Available at:
media.imagej.net/workshops/data/3d/hela_infected_timeseries.tif
A closer look: Digital images are arrays of values

250x250 50x50 10x10


Digital Image Basics with ImageJ/Fiji
● Digital images
● Image dimensions
● Image bit depth
Scientific images can be n-dimensional

Info bar

● Channel
○ 3 channels (currently set to 1)
● Time
○ 15 time points (currently set to 14)
● Size (microns & pixels)
○ 250x250 pixels or 81.25x81.25 um
● Bit depth
○ 16-bit
● File size
○ 5.4 MB
2-dimensional datasets

Examples:
- Single channel images
- Slices*

* Slices can also be n-dimensional


3-dimensional datasets

Examples:
- Movies
- Z-stacks
- Multi-channel images
- Slices*

* Slices can also be n-dimensional


5-dimensional datasets

Examples:
- Multi-channel 3D
movies
- Slices*

* Slices can also be n-dimensional


Digital Image Basics with ImageJ/Fiji
● Digital images
● Image dimensions
● Image bit depth
Scientific images are typically n-dimensional

Info bar

● Channel
○ 3 channels (currently set to 1)
● Time
○ 15 time points (currently set to 14)
● Size (microns & pixels)
○ 250x250 pixels or 81.25x81.25 um
● Bit depth
○ 16-bit
● File size
○ 5.4 MB
What is image bit depth?

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