Microvessel analysis/quantification

Hello,
my name is Philipp Mayer, I am a resident at the University Hospital of Heidelberg, Germany. For research purposes we want to quantify/analyse microvessels in a certain subset of tumors. I tried to use the Microvessel Analysis Algorithm in Aperio ImageScope for this, but I am not pleased with the results. Is it possible to do this with CellProfiler? I haven’t found any topics about this in the search results of this forum. I have attached a cut-out of an immunohistochemistry for microvessels similar to one of our tumors.

Thank you very much for your help!

Philipp Mayer


Hello Philipp,

Sorry for the delay. We would need some more guidance on what exactly you want to quantify. But in any case, I took a stab at a pipeline though note that I am not a pathologist, nor am I even sure what the microvessels are in this image! Is the red/brown color you are interested in? I glanced at Aperio’s manual and I think the attached pipeline might help.

Also, what exactly is the Aperio software not quantifying to your liking?

Best,
David
microvessel_pipeline.cp (5.67 KB)

P.S. A few more thoughts:

  • Try and avoid jpg images as they are (usually) “lossy”. Use lossless formats like PNG, TIF instead.
  • The color deconvolution in histological images is done with the “UnmixColors” module in CP, but I just guessed at a few, so you might need to change the choices I made depending on your stains.
  • The segmentation is doen in IdentifyPrimaryObjects and the settings depend a lot on what you want to quantify, so please let us know how this example is doing
  • There are lots of other measurements you can make, either on an object basis, or just a whole image. Add other Measurement modules as you see fit.