Integrated Light Microscopy Core

ImageJ / Fiji Help

ImageJ Tutorials Written by Core Staff

ImageJ Basics Tutorial (downloadable .pdf) — Just downloaded ImageJ and wondering what to do next? This is the tutorial for you! It covers basic topics including how to open an image or stack of images, adjusting brightness and contrast, how to make color and multicolor merge images, adding scale bars, and how to make 3D and timelapse movies.

ImageJ Intermediate Class Tutorial (downloadable .pdf) — The companion to our Intermediate ImageJ class. Contains information on image quantification, including object counting, area / length / intensity measurements and use of the Redirect and ROI manager tools.

ImageJ Macro Writing Workshop (downloadable .pdf) — The Power Point from our Macro Writing Workshop. Contains tips for macro writing / troubleshooting illustrated with sample code

Download-able tutorial .pdfs for more advanced ImageJ functions:

Converting Pannoramic Viewer files to open in ImageJ

Opening files with the LOCI Bio-Formats plugin

Making montages

Basic cell counting

Counting objects by template matching

ImageJ can be downloaded from the NIH website
Fiji is maintained at the University of Wisconsin Madison
The Fiji help forum

ImageJ Macros Written by Core Staff

ImageJ is scriptable software! Macros can be used to automate image processing with ImageJ/Fiji.

Macros written by Core staff are currently available in our GitHub repository.

In the spirit of open-source software, these macros are free for anyone to use and modify for their own research, but if you do use or modify the code and re-release it into the wild, please acknowledge the macro writer(s).