AUTOMATED WELL DETECTION THROUGH MATLAB AND COLONIES COUNTING THROUGH
IMAGEJ


1) Set the variable "ImageFolder" in the file "DetectWells.m" to the
   existing folder that contains plate scans (default is
   "./IMAGES"). Run the script.

2) Edit the file "count.ijm" to set the input/output path to the
   folder containing the newly produced images (default is
   "./IMAGES"), and an output path to save the masks computed by
   ImageJ (default is "./OVALS", create it if it does not exist). Run
   the script as an ImageJ macro and save the resulting table from
   ImageJ.

3) In order to map wells to drug IDs, check
   Position_of_drugs_in_well.pdf. The ImageJ macro produces images
   named "Plate#_WellsID.jpg" indicating the position of the well in
   each the plate. The mapping of IDs to drug names is contained in
   the rankedLINCSprofiles_ testedDrugs_cellClusters.xls files
   included in the Zenodo release.
