======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