Advanced FIJI Workshop

This workshop is designed for users who want to automatically process and quantify images using the open source image analysis program, FIJI (FIJI Is Just ImageJ). It is intended for people who are familiar with the program.

FIJI is an open source image analysis program which builds upon ImageJ as it comes 'batteries included' meaning extra plugins and libraries are included by default for an easy installation. The software works on Windows, Mac & Linux and can be run headless on HPC.

Topics Covered
The intention of this workshop is to introduce users to the automation tools in FIJI including Plugins, Batch Processing and Scripting.

Using Other People's tools for automation
+Installing and Updating Plugins
-Visualisation Plugins: 3D Viewer, Big Data Viewer & Clear Volume
-Segmentation Plugin: StarDist
-Tracking Plugin: TrackMate

Creating your own automation
+Finding commands in FIJI
+Batch Processing
+Scripting

Example exercises in this workshop
In addition to slides and descriptive examples of key concepts the workshop includes worked examples for attendees to gain hands on experience with. This are listed below.

Exercises
Exercise 1: Installing Plugins
Exercise 2: Trying 3D Volume Viewers
Exercise 3: Explore Deep Learning plugin StarDist
Exercise 4: Trackmate worked example
Exercise 5: Batch Processing
Exercise 6: Running a script

Workshop Files
To access the exercise files please click on the following link to OSF. Here you can download the complete folder of data and PDFs of the workshop guides.
https://bit.ly/3xUy4Td

This video was presented by Nicholas Condon at the ACRF Cancer Biology Imaging Facility at the Institute for Molecular Bioscience at The University of Queensland, Brisbane, Australia.

Nicholas Condon is supported by the Chan Zuckerberg Initiative as an Imaging Scientist.

For information about the IMB Microscopy facility visit: https://imb.uq.edu.au/microscopy