MIC-MAQ for Microscopy Images of Cells - Multi Analyses and Quantifications is an ImageJ/Fiji Plugin for automatic segmentation of nuclei and/or cells for quantifications in other channels including foci detection

• MIC-MAQ automatically segments cells and/or nuclei on 2D microscopy images
• The plugin takes Z-stack but works only on 2D projection
• It provides intensity based and/or morphological measurements in nuclei and/or cells in multi channels experiment
• The plugin can propose the foci/spots detection

First install Cellpose

installation instruction can be found at https://github.com/MouseLand/cellpose#installation

Then install and configure Cellpose wrapper for Fiji

installation instruction can be found at https://github.com/BIOP/ijl-utilities-wrappers#ib-fiji---cellpose-wrapper

Finally install MIC-MAQ plugin The best is to use the updater in Fiji:

menu >Help>Update...

click the button "Manage update sites"

select MIC-MAQ

if it is not available directly you can add it (button add update site) with the folowing URL https://sites.imagej.net/MIC-MAQ/

more complete information to install MIC-MAQ is available in the MIC-MAQ_Installation_Guide.pdf

run >Plugin>MIC-MAQ>MIC-MAQ

full explanation of the workflow and parameters is available in MIC-MAQ_Manual.pdf

Tutorials are Available on the youtube channel of the Multimodal Imaging Center

MIC-MAQ plugin is licensed under the GNU GPL v2 License