Unable to differentiate between different myofiber types in the image


I am trying to identify the copper, green and black color myofibers from my image using cell profiler, and I tried to use identify modules. However, these modules are not able to identify the different colors correctly. I have attached my pipeline to this post. Any help would be greatly appreciated.

Test1.cpproj (765.2 KB)


Hi there,

Please use module UnmixColors instead of ColorsToGray

In my test, you would need 2 separate UnmixColors,

Hope that helps.



Thank you so much for your help, is there any way where I can identify the black fibers as well?
I have attached another sample image


The black fibers are tricky, if you want to directly extract them out of a color image.

I would suggest to extract first green and red fibers, then simply do a MaskImage operation to get the black fibers, follow this “equation”

original image - green fibers - red fibers = whatever left = mostly black fibers + some peri/endomysium



Thank you for the help! I had one last question, I want to extract the green and copper and black seperately from the image and measure the area, roundness and nuclei in those fibers, I tried using identify primary, secondary and tertiary object modules but it does not identify the fibers correctly. What would you suggest me to do?



I think you may be a bit confused about what primary, secondary etc objects are- hopefully this can help. I’d think all of your objects should be identified as primary objects.



I was able to perform your suggestions for my previous image but it does not work for this following image. Do you have any other suggestion in mind for me to seperate the green and orange and black/darker green fibers?