Integrated Light Microscopy Core

ImageJ / Fiji Help

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).

ImageJ Tutorials Written by Core Staff

Core staff have written a number of tutorials for ImageJ / Fiji use, including guides to go along with our popular ImageJ classes.

Next ImageJ / Fiji classes

March 13, 2020 – In light of the University’s cancellation of in-person classes, we are not planning in-person ImageJ classes for Spring Quarter 2020.  

You can use the ImageJ tutorial .pdfs further down this page and send questions via email to Christine.  We are working on an on-line / webinar format for future ImageJ classes.  Thank you for your patience. 

ImageJ / Fiji Classes

Our ImageJ classes and workshops are FREE to anyone interested in image processing with ImageJ. Off-campus visitors are welcome.

ImageJ Basics will show you how to get from raw data to a multi-panel, multi-color paper or talk figure. Topics include: opening images from proprietary file types (such as Leica .lif and .lei, SlideBook .sld), creating multi-color images, adding scale bars, working with hyperstacks, and installing and using plugins and macros.

Intermediate ImageJ builds on the Basics class, covering basic image quantification. Topics include particle counting, intensity analysis, using the ROI manager and basic colocalization with the JACoP plugin.

For Basics and Intermediate classes, a laptop pre-loaded with ImageJ or Fiji is welcome but NOT required.

Macro Workshops are for people already doing figure creation and / or image analysis with ImageJ. We will cover macro writing basics and then participants will get a chance to write their own macro (on their own laptop) with help. For Macro Workshops, a laptop with ImageJ or Fiji installed and a few “test” images of the kind you want to process are encouraged. No prior computer programming experience is necessary.

Summer Session Combines ImageJ Basics and Intermediate ImageJ into one class, so you only need to attend one session!

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