This book is an analysis-oriented introduction and user guide to ImageJ. It is inspired by the defunct MBF “ImageJ for microscopy” manual which went offline in November 2012, and it describes many of the same plugins from that distribution.
Cooks call them recipes, biologists protocols, and programmers call them HOWTOs. No matter how you refer to them, you’ll find the book topics in the sidebar to the right!
Like the rest of this wiki, this Cookbook is a community project. Please feel welcome to edit and expand the material here! <div class="toc"></div>
The Cookbook is based on the Fiji distribution of ImageJ. TODO downloadfiji:
Installing the Cookbook plugins
From the Fiji menu, select Help › Update...
Click the Manage update sites button
Check the Cookbook update site
Close the Manage update sites dialog
Click Apply changes to download the Cookbook plugins
Restart Fiji to complete the plugin installation
Enjoy your new plugins from the Cookbook menu!
The source code is on GitHub .
The Cookbook pages themselves were adapted from the defunct MBF “ImageJ for microscopy” manual, originally created by Tony Collins.
The Cookbook technical writer team includes:
- Curtis Rueden (technical oversight and maintenance)
- Aparna Pal (January 2014 - May 2015)
- Johannes Schindelin (June 2013 - November 2014)
- Katie Hildebrand (June 2013 - December 2013)
- Amanda MacAllister (June 2013 - December 2013)
- Ruizhi (November 2013 - December 2013)
- Gabby Campagnola (June 2013 - August 2013)
The plugins featured in the Cookbook were collated from various sources and have various authors and licenses.