README.md.backup

# MIC-MAQ <img src="resources/MIC-MAQ_logo.png" width="100" >

## About 

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

## Install

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](https://github.com/MultimodalImagingCenter/MIC-MAQ/blob/main/documentations/MIC-MAQ_Installation_Guide_v1.1.pdf)


## Usage

run >Plugin>MIC-MAQ>MIC-MAQ

full explanation of the workflow and parameters is available in [MIC-MAQ_Manual.pdf](https://github.com/MultimodalImagingCenter/MIC-MAQ/blob/main/documentations/MIC-MAQ_Manual_v1.2.pdf)

Tutorials are Available on the [youtube channel of the Multimodal Imaging Center](https://www.youtube.com/channel/UCVhGRHCSjIdgD__1yYVIhoA)

[<img src="https://github.com/MultimodalImagingCenter/MIC-MAQ/blob/main/resources/MIC-MAQ_Tutorial_Cell_segmentation.png" width="50%">](https://www.youtube.com/watch?v=vR2kGQ9U5do)

[<img src="https://github.com/MultimodalImagingCenter/MIC-MAQ/blob/main/resources/MIC-MAQ_Tutorial_Cell_segmentation.png" width="50%">](https://www.youtube.com/watch?v=Mei3Y9hJMyE)


## Licensing

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