Hi Colocalization expert,
I’ve written a little script in Python to do some colocalization analysis measuring the Pearson and Spearman coefficient.
Unfortunately the datasets I am working with doesn’t have a separate channel to create the ROI and I’m afraid that using automatic threshold on one channel will bias the result. My questions are:
- Is it better in that case to use a fix threshold?
- Or alternatively, since for every images, there is only one cell in the middle of the field of view, I can create a bounding box area around the threshold cells.
My problems with the second solution is that it includes a lot of the background which “artificially” increase the coefficient.