This is an archive of the old MediaWiki-based ImageJ wiki. The current website can be found at


Cookbook Topics
Introduction and Installation
Annotating Images
Color Image Processing
Image Intensity Processing
Importing Image Files
Particle Analysis
Saving and Exporting
Stack-slice Manipulations

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!

Installing ImageJ

The Cookbook is based on the Fiji distribution of ImageJ.

Error creating thumbnail: Unable to save thumbnail to destination
~ Download Fiji for your OS ~
Error creating thumbnail: Unable to save thumbnail to destination
Windows (64-bit)
Linux (64-bit)
Other downloads
Windows (32-bit) 32-bit All platforms (no JRE) No JRE Linux (32-bit) 32-bit

Installing the Cookbook plugins

From the Fiji menu, select Help  › Update...
1 Update Fiji.png
Click the Manage update sites button
2 Manage update sites.png
Check the Cookbook update site
3 Enable cookbook.png
Close the Manage update sites dialog
Click Apply changes to download the Cookbook plugins
4 Apply changes.png
Restart Fiji to complete the plugin installation
Enjoy your new plugins from the Cookbook menu!
5 Use the Cookbook.png


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:

The plugins featured in the Cookbook were collated from various sources and have various authors and licenses.