Rename channels


#1

Hi guys,

I am currently helping someone who has a whole pipeline already made but want to adapt it using the LoadData module and have the images in OMERO.

The main issue is that the different pipelines had names for the different channels different to the one in OMERO eg ‘Nuclei’ instead of ‘DAPI’ etc… I was wondering if there was a way to change these names in CellProfiler or if I should then change the names in all the already established pipelines and modules ?

I thought about using the color2gray or gray2color but I’m not sure this would be the way to go since the LoadData module already separates the different channels.

I hope this is clear enough otherwise I’ll add screenshots… :slight_smile:

Thanks for the help !


#2

Hi-
I’m not super familiar with the OMERO integration wrt LoadData beyond what’s listed here, but my understanding is that it shouldn’t matter what the name in OMERO is, as long as the column headings match the CP names (such as URL_CPChannelName) you should be fine. Please do let me know if that’s not the case!


#3

Hi @bcimini

Thanks for your answer ! :slight_smile:

We have created a Python script in OMERO to get the CSV needed to use the LoadData module. This CSV gives the column heads using the OMERO channels. This is why I’m looking for a way to rename the channels in CellProfiler otherwise I’d have to change every CP pipelines I have. I was wondering if there was a way to avoid that.


#4

Unfortunately no- I think essentially you have 4 options at this juncture-

  • Update the Python script and give it the mappings- ie tell it that if it finds something in OMERO it calls “Nuclei”, call it “DNA” instead in the CSV columns
  • Add a couple modules at the beginning of each pipeline that are essentially just for doing this transformation- you could do a GrayToColor followed by a ColorToGray as you suggested, or use ImageMath with the “Nothing” option (one for each channel you need to change the names of)
  • Open your CSV in a text editor (or Excel) and do a find and replace- find “DNA” and change it to “Nuclei”
  • Open your pipeline file in a text editor and do a find and replace- find “Nuclei” and change it to “DNA”.

#5

That could indeed work, didn’t think of that possible bypass ! :slight_smile:

The find and replace in either the CSV or the pipeline could also work indeed ! I’ll test that !

Thanks for your help :slight_smile: