ImageJ / Fiji Help
UChicago ImageJ Class Tutorials
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
Tutorial .pdfs for More Advanced ImageJ Functions
Converting Pannoramic Viewer files to open in ImageJ
Opening files with the LOCI Bio-Formats plugin
Counting objects by template matching
ImageJ/Fiji 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).
Installing ImageJ or Fiji on Your Own Computer
ImageJ can be downloaded from the NIH website: https://imagej.nih.gov/ij/
Fiji is maintained at the University of Wisconsin Madison: https://fiji.sc/
Note: It is possible to install multiple versions of ImageJ and/or Fiji on the same computer
The Fiji help forum: https://forum.image.sc/tags/fiji