3D nuclei number counting module in cellprofiler 3.0


Hello. Please understand that I lack English speaking skills.
I am using cellprofiler 3 and want to get the number of nuclei, cell, etc. from 3D Tiff image. The module that classifies and identifies in 2D is IdentifyPrimaryObject and knows that it is Watershed in 3D. The Watershed module does not know the number of nuclei or cells. None of the modules that support 3D images or objects can know the number. What is the module for counting the number of cells in a 3D image?
Does not it support it? It is urgent.


Hi @chl8725, please take a look at the CellProfiler tutorial for segmenting nuclei in 3D. This is a great resource for getting started and includes a pipeline you can modify to your needs. Thanks!


I’ve already tested this example. By the way, cell segmentation is done but not counting. So I could not know the number of cells. Is there any module that can know the number of 3D cells?


After completing the 3d tutorial, CellProfiler will export several CSV files with data characterizing the nuclei in the monolayer. In particular, if you are interested in nuclei count, this number can be found in the 3d_monolayer_Image.csv file that is created after running the pipeline.

I’ve attached a copy of the expected CSV. The column Count_Nuclei has the number of nuclei in the test image. 3d_monolayer_Image.csv (4.7 KB)


I really appreciate your reply. My sample did not consist of three samples in the example and did not go to the last step. I tried to reconstruct the pipeline in this example, and the results are out. But I’m not sure if it’s accurate. Are you sure the number of cells in the result is correct?