Quantify the dense red color automatically

Hello, i attached an image, i need to quantify the dense red fibers on it
please help me if you can


Hi,

Please first read this.
What do you want to quantify? Intensity? Length? Total length in image, or individual segment lengths? # of junctions?
You must be very specific for us to help!

Well, I went ahead anyway and created a pipeline for you. See if it works. It was more complicated than I initially thought, mostly because of the circular boundary, and that the red channel wasn’t as specific as I’d hoped in order to segment.

These are the basic steps:

  • It uses ColorToGray -> Gray to define the Well (circular region, which we want to exclude)
  • UnmixColors. Choose the right “stain” to deconvolve the colors properly. I guessed and Eosin seems to work ok.
  • Identify the Well
  • Crop it out
  • Enhance the filaments with a tophat filter (“Speckles”) of 20 pixels width
  • Segment (Identify) the filaments
  • Reassign Object numbers. Not sure if you need this, but it creates a single filament object in the circular area. Otherwise you may have many independent objects.
  • Measure stuff and Export

Hope this helps!
David
pipeline.cp (9.13 KB)