This section is an introduction to scientific imaging, including both image acquisition and image analysis, with a focus on ImageJ.
Cooks call them recipes, biologists protocols, and programmers call them HOWTOs. No matter how you refer to them, you’ll find all the topics in the nav-bar at the top of the page!
Like the rest of this wiki, this guide is a community project. Please feel welcome to edit and expand the material here!
If you are new to scientific imaging, please peruse the Principles for a primer!
Installation
Some parts of this guide describe plugins from the Fiji distribution of ImageJ, as well as from the Cookbook update site. Here’s how to set it up:
| 1. | Download and install the Fiji distribution of ImageJ. | |
| 2. | From the Fiji menu, select Help › Update… |  |
| 3. | Click |  |
| 4. | Check the Cookbook update site |  |
| 5. | Click | |
| 6. | Click to download the Cookbook plugins |  |
| 7. | Restart Fiji to complete the plugin installation | |
| 8. | Enjoy your new plugins from the Cookbook menu! |  |
Source
The source code of the Cookbook plugins can be found on GitHub.
Credits
Many of the pages in this section were adapted from the defunct MBF “ImageJ for microscopy” manual, originally created by Tony Collins, which went offline in November 2012.
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 “Ray” Liao (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.
