Welcome! This is the landing page for a repository of workshop materials for Fiji workshops run at JAX in the 2nd half of 2024.
Two workshops are planned, an introduction one and a follow-up one that will get into macros and scripting. You can find descriptions and links to the materials below.

Introduction to Fiji Workshop

Fiji is distribution of ImageJ, which has over 25 years of broad usage in scientific image analysis. This two-session introductory workshop to Fiji will start with introducing the basic concepts of image analysis (e.g. pixels, bit-depth) and then it will cover key concepts such as the GUI layout, scale bars, measurements, and stacks. The second session will be focused on more advanced analysis concepts, including segmentation, colocalization, and tracking. Note: this workshop will not delve deeply into macros and scripting, this will be the focus of a follow-up workshop.

Introduction to Fiji Workshop Materials

The above link is to a set of slides and training materials written in HTML/CSS with the Reveal.js framework. This is an updated, Fiji-only, fork of tutorial materials by Erick Martins Ratamero, those in turns were heavily inspired by the original slides from Dave Mason, then at the University of Liverpool Centre for Cell Imaging.

Intermediate Fiji Workshop: Macros and Scripting

Fiji is distribution of ImageJ, which has over 25 years of broad usage in scientific image analysis. This two-session introductory workshop to Fiji will focus on macros and scripting. Note: no prior coding experience is needed.

Intermediate Fiji Workshop: Macros and Scripting Basics

The above link is to a set of slides and training materials covering the basics of ImageJ macros. It is written in HTML/CSS with the Reveal.js framework. This is an updated, Fiji-only, fork of tutorial materials by Erick Martins Ratamero, those in turns were inspired by slides by Philo van Kemenade.

Intermediate Fiji Workshop: Putting together a proper ImageJ macro

The above link is to a set of slides and training materials covering a set of exercises to step-by-step write a proper ImageJ macro and then install it into Fiji. It is written in HTML/CSS with the Reveal.js framework. This is an updated fork of tutorial materials by Erick Martins Ratamero.

Licensing and reuse

The Reveal.js framework is used under the terms of the MIT license.

The slide content and images (see exception below) are provided under a CC-BY license. You may reuse the contents for any purpose in any way you please as long as you attribute the source material.

One of the materials for training is a derivative of the Broad Bioimage Benchmark Collection BBBC008 which is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

Acknowledgements

These materials were originally written/adapted by Erick Martins Ratamero for CAMDU usage at the University of Warwick.
“Introduction to Programming Fiji” slides use material from a set of slides from Philo van Kemenade.