Measuring aSMA and Collagen1 in Cell Profiler 3.1.9


I’m Pratap, Bioinformatician. I’m new to Image analysis field and running Cell Profiler 3.1.9. My aim is to quantify aSMA and Collagen 1 for various drug treatments.

Here I have attached two groups in the cell profiler project. One is 10 ng TGF-b1 treated and the other one is Pirf31 treated. There are four channels: Nucleus, cytoplasm, aSMA and Collagen1.

I have played with various parameters and deployed the following pipeline which gave good segmentation. I’m not sure what I got was the most optimal segmentation results or not? Can anyone suggest me, whether my segmentation is good or not on my aSMA and Collagen1 Channels.

Apart from that, I’m having a doubt that, how “Measure Image intensity module” will be helpful in my case? Image intensity module would be helpful in my case, if I select the option “Measure the intensity only from areas enclosed by objects: YES” for aSMA and Collagen channels . Please let me know, whether my understanding is right or wrong.

Best Regards,
10ng_TGF-b1_R1-1_aSMA.tif (2.2 MB) 10ng_TGF-b1_R1-1_collagen1.tif (2.2 MB) 10ng_TGF-b1_R1-1_cytoplasm.tif (2.2 MB) 10ng_TGF-b1_R1-1_nucleus.tif (2.2 MB) Pirf_31_5ng_TGF-b1_R4-9_aSMA.tif (2.2 MB) Pirf_31_5ng_TGF-b1_R4-9_collagen1.tif (2.2 MB) Pirf_31_5ng_TGF-b1_R4-9_cytoplasm.tif (2.2 MB) Pirf_31_5ng_TGF-b1_R4-9_nucleus.tif (2.2 MB)


Output_Collagen1_10ng_TGF-b1 Output_Cytoplasm_10ng_TGF-b1 Output_Nuclues_10ng_TGF-b1 Test_Screen4.cpproj (219.5 KB)

Hi Pratap,
Segmentations look fine to me. Your pipeline seems to be working well. Why you want to measure only “Measure Image intensity module” for comparing between conditions. As you are detecting several objects (cells) in each image, adding more measurements like MeasureObjectSizeShape, MeasureObjectIntensity, MeasureObjectIntensityDistributions etc gives you more flexibility to do the analysis later on and will be helpful in revealing patterns.