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Scientific Imaging Tutorials

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 HelpUpdate… 1-update-fiji
3. Click the Manage update sites button 2-manage-update-sites
4. Check the Cookbook update site 3-enable-cookbook
5. Close the Manage update sites dialog  
6. Click Apply changes to download the Cookbook plugins 4-apply-changes
7. Restart Fiji to complete the plugin installation  
8. Enjoy your new plugins from the Cookbook menu! 5-use-the-cookbook

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:

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