I’m having problems with setting a workable pipeline with CP.
The aims seems pretty straightforward though. I want to be able to count the total cell number (using DAPI) and then characterize the percent of stained cells with one or more different antidodies.
I have a few questions:
- I have .tif files with 4 channel (DAPI, 488, 560 and 641). Can I upload this to CP and ask him to split channel? I only found this function with the colortogray function (but only as RGB files).
- I started with the pipeline from CP website (percentpositive) which seemed to do what I want to do. I tried to twick it a bit to work, but it doesn’t. The software doesn’t distinguish well enough my primaryobject as being the DAPI nuclei. I tried a lot of different things but can’t make it work
- For some of my staining, I seem to have a “high” background but we are still able to see positive cells. I was wondering what parameter I can change so CP can distinguish between the background and a real staining?
Is it possible to adapt that parameter for different staining (which would have different background level)…
Thank you for your help!
PercentPositive.cppipe (20.5 KB)
DIFF8A_d5_GFP_Sox2_Olig2_1_MMStack_Pos0.ome-1.tif.zip (9.8 MB)