I am trying to create a pipeline I can use to count the total number of staining and non-staining nuclei so I can find the percent of cells which are marked with my immunostain (MIB1 or KI-67). This is a task I do routinely manually and using an automated process would be advantageous. I have attached two example images. The example images are representative of what I do routinely. The cells which are marked/stain positively are the dark brown cells in the attached images. The nonreactive cells are those which are pale blue. I have also attached my attempt at creating a pipeline, but I know that this is above my head. I get a whole lot of errors along the way. Does the program have to crop my images? Can I not use any image size? I do appreciate your help with this.
PercentPositive.cp (16 KB)