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Illinois IGB

Core Facilities

FIJI and ImageJ

FIJI/ImageJ Training – We offer basic FIJI training with an included toolset for particle/cell counting.  Specific needs for analysis can be discussed prior to the training. While FIJI has a wide range of plugins available, we recommend getting trained on Axiovision, Imaris, and Autoquant for cell counting, 3D reconstruction, and deconvolution respectively.  For training please contact Austin Cyphersmith.

FIJI can be downloaded here.

Below you will find guides and corresponding toolsets designed to make the data analysis process smoother.  If there is a toolset or guide you'd like to see added, please contact Austin Cyphersmith.

Guide Toolset
Particle Analysis Link

To save a toolset, right click and choose "save as"

Copy the txt file to > Macros > Toolsets

Toolsets can be accessed in FIJI from the ">>" icon on the far right of the tool menu.  

They are designed to take you through the analysis one step at a time from left to right.