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ImageJ is one of the older free, open source image analysis programs. Alone, it's not that powerful; it's real strength is the vast array of plugins for it. It runs on Windows, Mac, and Linux.

FIJI is probably the best distribution of ImageJ for routine data analysis. It comes with a vast array of plugins already installed and ready to use and has an automatic updater so you always have the latest versions of them.

Micro-Manager is a microscope control package that is built on top of ImageJ. It's developed at UCSF and is very powerful; we use it to control the Spinning Disk Confocal in the Nikon Imaging Center.

A tutorial on getting started with micro-manager:

A screen cast tutorial on multi dimensional acquisition using micro-manager:


The following plugins may be of particular interest to our users:

Bioformats- Software tool to open files from a variety of formats. This plugin will allow you to open nd2 files in ImageJ/FIJI.

SIMcheck- Plugin for assessing the quality and reliability of Structured Illumination Microscopy data. This plugin is useful for anyone doing SIM imaging to watch for artifacts and other problems with your data. 

Forums - Community forum for multiple open-source image analysis software packages where you can find answer to common problems and post questions to the community. The forum is very active and you can get help quickly.

Microforum- Community forum based on hardware, acquisition, and specimen-related question.


Kari's 2020 webinar (box link here) has a basic introduction to macros. Below are some Basic Macro's that were written  and last run on in Fiji, ImageJ v 1.53f51, Java 1.81-172 (64-bit).

To open: Download then drag and drop onto ImageJ/Fiji Tool Bar






Batch-imageSeq_CentralSelector Bioformats.ijm

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