I’m a little confused as to the output of the RelateObjects module.
I am trying to count the mRNA speckles which fall within a nuclei’s area.
I used IdentifySecondaryObject around my DAPI stains allowing a larger range as a cell area, and used this as my parent object.
I used IdentifyPrimaryObject on my mRNA stains and used this as my child object. Next I used RelateObjects in order to find what I am looking for (and I did this for each channel/gene separately).
In the output I receive multiple csv files and although I would expect to find what I am looking for in the relateObjects csv I do not. I see that the relate gives me in the last colomn a list of parent object, though it lists there my child objects as parent; where as I see in the identifyPrimaryObjects csv the last colomn showing the list of the real parent.
I don’t even understand how I see a parent colomn in the identifyPrimaryObjects csv. Can someone please explain this to me?
Furthermore, I can now use a simple python script to count per parent how many children it has, but I thought this module would output that count for me. Where can I see this count? It doesn’t show in the csv files.
Here is my pipeline:
firstTry.cpproj (1.5 MB)
Here are my input images (DAPI + 3 genes):
C1-MAX_WT 5 slc38a1 myoc mfge8 dapi 40x.tif (12.0 MB) C2-MAX_WT 5 slc38a1 myoc mfge8 dapi 40x.tif (12.0 MB) C3-MAX_WT 5 slc38a1 myoc mfge8 dapi 40x.tif (12.0 MB) C4-MAX_WT 5 slc38a1 myoc mfge8 dapi 40x.tif (12.0 MB)
Thanks in advance,