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======MSCS (Micropatterned Single Cell Sorting)======
**use this plugin to sort micropatterned single cell images from high-throughput experiments.**

======Author======
Jean-Philippe Grossier
jp.grossier at gmail dot com

======Features======
 handle 96well format images
 process multiple experiments/plates
 can sort different micropatterns according to their size

======Description======
this plugin requires at least two image channels to work: one for the micropattern and one to count nuclei (DAPI typically). It handles up to two extra channels for marker of interest

- choose a directory containing either directly the images to analyse (single analysis) or subfolders of different experiments/plates
- choosing "96 well format" allows to sort files according to rows (A-H) and columns (1-12) in the corresponding tab
- choosing "sort files" allows to sort all channel files in a folder using regular expression
- choose the number of extra channel to analyse (in addition to the micropattern and nucleus channel)

- files tab:
enter file extension, basic regular expression to sort files and a name for output extra channel images

- micropattern tab:
  enter a size (diameter in pixel) for each pattern class seperated by a coma: "80, 150" will look for two pattern types of 80 and 150 pixel in diameter.
  enter a tolerance for the pattern size (find pattern with size +/- size*tolerance) 
  enter a minimum area in squared pixel and maximum intensity

- nucleus tab
 set the following parameters to isolate and count nuclei:
  minimum mean intensity, 
  maximum intensity,
  minimum and maximum area (squared pixel),
  minimum circularity (0<circ.<1) of an expected single nuclei
  choose a radius for the tophat filter (juste above the expected nucleus radius)

- 96 screen format
  enter a regular expression to sort files according to the 96 well format
  first group () contains rows (usually LETTER)
  second group () contains columns (usually numbers)
  third group () contains fields (usually numbers)
  
======Installation======
Download {{:plugin:analysis:micropatterned_single_cell_sorting_mscs:mscs_0.3.jar|}} file, save it to the plugin folder of ImageJ and use the "MSCS" in the Plugins menu.

======Download======
{{:plugin:analysis:micropatterned_single_cell_sorting_mscs:mscs_0.3.jar|}}
======Licence======

======Changelog======
13/04/19: version 0.3 (beta) change minor bugs
======Known Bugs======