Qupath Multiplex Analysis

Scripts that allow to automatize  a multiplex analysis in qupath. The input is a multi channel image with one channel containing a staining of cell nuclei and the other channels containing markers for a specific molecule. The goal is to obtain a count of positive cells for the markers in the different channels and for the combinations of positive markers. The workflow also adds the total numbers of positive cells for each marker to the results table (cells positive for multiple markers are not counted positive for the individual markers in the original qupath result).