I am trying to count 3 different types of neurons in z-stacks projection. I was able to develop a pipeline but I still do not have a final file with information I can understand (Ex: #of neurons per color, #ofneurons that co-localize 2 color or maybe 3, etc etc). My goal is simple I only need to have the total number of objects in each color image and how many overlap between: greenxred, redxblue, bluexgreen and, if possible greenxredxblue. Could someone please take a look in my pipeline and provide me some guidance? In addition, although I was able to extract one spreadsheet I can not really understand what is there.
Not sure how to share my pipeline and images here. So here is the link to a message I sent before: http://forum.cellprofiler.org/t/counting-3-types-of-neurons-in-a-z-stack-confocal-projection/4954
Thank you so much!