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