I am new to CellProfiler. I noticed that when you use a function such as IdentifyPrimaryObject, it will give a cell count (# of Accepted Objects), however when I use other functions, such as EditObjectsManually or MaskObjects, I am not given any cell counts. I was wondering if there is a way to have CellProfiler give a cell count after using these functions.
I have attached my pipeline and a sample image.
This is embryonic mouse cerebellum stained for Sox2 (red), BrdU (green), and EdU (blue). What needs to be accomplished by this pipeline is the following:
Get a cell count of the total number of Sox2+ (red) cells. (This I can do usuing the IdentifyPrimaryObjects module).
Identify the BrdU+/Sox2+ cells (green/red). I read in a previous post that using the MaskObjects module would be good for looking at colocalization, however I need to get a count of the objects produced by this step. (see File “Sox2BrdU Positive Cells” (MaskObjects #9))
Identify the EdU+/BrdU+/Sox2+ cells (blue/green/red). Again, here I use the MaskObjects module to use the objects generated in the above step (BrdU+/Sox2+) as a mask for the EdU+ cells. Here I also need a count. (see File “BrdUEdU Positive Cells” (MaskObjects #12))
pipeline.cpproj (298 KB)