Open andmccall opened 2 years ago
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/coloc-2-threshold-varies-widely-across-timepoints/69429/7
I should probably mention too that I have a functioning costes randomizer class that only randomizes within the defined region, and that you could probably integrate with Coloc2. I'm not the best programmer, so it probably needs some polishing:
Thanks @andmccall, I appreciate it! I will try to come around to this issue when I can, but my queue is rather absurdly long. Previous developers of Coloc 2 including @tomka and @etadobson are not on the project anymore, so it will fall to me, unless someone in the community is able to file a PR to fix this issue in the meantime.
Randomization occurs over the bounding box of the ROI regardless of which selection method is used (normal ROI, mask, or ROI manager). This can have a significant difference on the results, leading to more false positives. Can be tested using the plugin itself by checking the "Display Shuffled images" button.
Also, I noticed that Coloc2 applies a smoothing function to the randomized data. In my testing on my plugin I noticed that smoothing also leads to more false positives. Might be worth looking into.