Object Counts


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:

  1. Get a cell count of the total number of Sox2+ (red) cells. (This I can do usuing the IdentifyPrimaryObjects module).

  2. 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))

  3. 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)

I just realized I forgot to add a sample image to the original post, so I have attached one here.

Also, I was able to get an object count by adding in a ClassifyObjects module after each MaskObjects module. However, if there is another way to do this, I would love to hear it.

pipeline.cpproj (301 KB)

I notice that your pipeline did not include an ExportToSpreadsheet module. If you add this module and have it output the per-image csv (which it will with the default settings), the per-image counts of all the objects obtained are included.

Great! Thank you!

Hi Mbray,
I use the same of her Pipeline but not using Classifyobject. I have primary object (cells), and other primary object (spots released in the cytoplasm of the activated cells. Then I maskObjects for cells that contains spots inside cytoplasm (activatedCells). finally on the output file I got the number of total cells (from primary object #1) and the number of masked cells that contain the second primary object. Is it ok that these masked cells are activated one without doing classifying object.

Cells_ActivatedCells_Specks_05042016.cppipe (15.4 KB)Ahmed