I wasn’t sure whether to post this under this thread or else the TMA cell data extraction thread for IF. I have tried some basic scripting using Github sample scripts (Making Measurements in QuPath · GitHub) and have not had luck yet.
I’m new to image analysis and have tried to average one of the detection measurement features in QuPath and then run batch processing for the whole cohort.
My goal is to get the mean, median, and standard deviation for detection measurement features for just three channels:Fcein, Cy3 and Cy5) so that I may compare protein abundance across each case as shown in the snip above. That way I won’t be exporting over 100 columns of information from QuPath.
What would be the best way to go about this? Would I need a script similar to Melvin’s? (Extract cell detection data from segmented areas/annotations in TMA (IF Images) - Qupath - #5 by melvingelbard)