Cell profiler for Masson's trichrome staining


Just recently I started using this software. Thanks for developing the wonderful software.
I am trying to quantify the amount of collagen in the liver section. I have attached my pipeline and few images here. Could you look at my pipeline and kindly give me your suggestion to improve the pipeline for quantification of collagen in the section?


Collagen Analysis.cp (6.54 KB)

Hi Dinesh,

I’m attaching a pipeline which should get you closer to what you want. The basic approach of using UnmixColors is the same as what you were using, with a different choice of stains. The key is that even though you can specify a stain of choice, variations between the idealized case and the reality makes it so that you should simply choose the stain with the color(s) that best resemble the hue in your image, regardless of the stain name.

Rat 123.cp (4.3 KB)

Wow!!! Super fast reply Mark…
I’ll try the pipeline now