Question about the strategic of percent colonisation



I’m new to CellProfiler and need some help.
I am working to count the number of arbuscules( like the dark parts in the picture )
in root samples for a study calculating the percent colonisation of roots. I want to identify and count the number of arbuscules, I tried DLpipe that identifying the stained parts or particles, but it worked not well. It is hard to distinguish the dark parts from other parts of the picture. The pipeline I tried is below. Can you tell me how can I do it with CellProfiler?

Many thanks in advance,

DLpipe.cppipe (13.0 KB)



I notice that you used ColorToGray,in which you extracted “Blue” channel. I suggest to use “UnmixColors” instead, in which you set the name of stain as “Hematoxylin” or any blue dyes.

Then in your IdentifyPrimaryObject:

  • Set object size: 20-300
  • Set Threshold strategy: Global, Otsu, Three classes with middle intensity class set to “Background”

Hope that helps.


Hi Minh,

Thanks a lot for your advice. I tried the settings you suggested, but I found that the result cannot be exported

I tried to change the output file location but it doesn’t work. How should I solve this problem? Additional, if I want to open the spreadsheet exported in Excel, what format should I choose?

Many thanks,


Hi there,

I suspect you are running in test mode until this module right? Please note that in test mode, “ExportToSpreadSheet” and ExportToDatabase will not work. You’ve got to run the real analysis for the result.

For your question related to Excel, “ExportToSpreadsheet” as you’ve set right now will be alright.



Hi Minh,

Thank you so much for your help!

I got my data, but it seemed not accurate as I expected. In the image I inputted for analysis there were 28 cells and 12 of them contains arbuscules, while in the spreadsheet I got it listed over 100 cells. I wonder if the varied sizes of cells influence the result, or can I calculate the percentage of stained area in the image? It can be found that the percent staining of the image can also reflect the arbuscular colonisation of roots.

Many thanks!



It should be noted that we did not identify any cells here ! We only identified the arbuscules, or to be more precise, we only identified the objects with blue signals.

Yes, you’d better add the module “MeasureAreaOccupied”, where you will have the percentage of stained area in the image.