I’m a very new CellProfiler user and have spent some time reading through the manual and trying to decode existing pipelines that our lab has used, and have a basic grasp on some settings and logic behind them but am a little lost on others.
I am trying to create a pipeline that achieves the same measurement information as described in this paper: http://jms.org.br/PDF/v22n2a06.pdf
where they used SigmaScan to analyze collagen content and fiber color, as well as spatial distribution of fibers in polarized light images of picrosirius red stained histological sections. This and other papers describe hue definition ranges for red, orange, yellow, and green collagen fibers in their methods and I’m a little confused as to how I can define these for my images using CellProfiler.
I’ve tried building a pipeline where I used custom definitions for my stain under “UnmixColors”, and used little snippets of a picture (where by eye I isolated a portion of collagen fibers that were strictly red, strictly orange, etc.) to use as my “reference photos” for the estimation. However, this (probably incorrect) method clearly grabs most of the photo using these parameters instead of just selecting the portions that each color is supposed to refer to, as evidenced when I step through test mode.
I think my biggest hurdle is trying to figure out how to ID just the color portions that I want. Any help would be greatly appreciated!
First attempt at pipeline: PicroSiriusRed_polarized_pipeline.cppipe (20.6 KB)