Dear CellProfiler Team,
I am trying to use the CellProfiler 2.0 to analyse a section from a whole slide image. As you can see in the attached image DefaultOUT__3.mat (77.9 KB) by zooming in on the objects of interest (purple stained RNA) some of the detail is lost.
Additionally, I also tried to run the attached pipeline DefaultOUT__3.mat (77.9 KB) which is a modified version of one of the pipelines suggested in a previous post ‘Quantifying colours in histology’ in the forum for CellProfiler 1.0.
The issues that I need help with are:
- Is there a way of pre-preparing the image in order to enhance its quality for use with CellProfiler 2.0? Do you have any suggestions for WSI?
- Is it possible to use the pipeline to calculate the ratio of the RNA molecules (purple) to the Nuclei (grayish stained).
Thank you for your help.