Counting Positive labelled Cells

Dear all,

I am struggeling with the following problem: I simply want to identify cells by DAPI (Blue channel) + Phalloidin (red Channel) Staining and count them. Additionally I’d like to count those of the identified cells labelled with a green fluorescence staining (green channel).

Here is my pipeline so far Pipeline 03122020.cpproj (706.0 KB).

Here are my images (3 channels + overlay). 12_CH1.TIF (4.0 MB) 12_CH2.TIF (4.0 MB) 12_CH3.TIF (4.0 MB) 12_CH4.TIF (4.0 MB)

Can anyone help me to improve my pipeline to get a percentage of positive green cells in ratio to all cells?

Thanks a lot

Hi @Flo,

I’ve tweaked your pipeline settings and modules to help you get what you’re looking for. I added a FilterObjects module to produce a subset of Green-positive cells based on intensity readings, which seems to work. To get a percentage you might want to add a CalculateMath module to compare the number of objects from FilterObjects to the total count, but you might want to choose a more stringent positivity threshold in FilterObjects first.

Pipeline HEV IFT_03122020_R1.cppipe (14.3 KB)

I should note that this pipeline will need the v4.0.7 update to work properly.

Hope that helps!