most of the code that is used for area and depth analysis is in GLM repo, cluster module
selecting number of clusters
I tried doing F-test, jupyter notebook attached. The results of this test were interpretable but the optimal N was slightly off from what we have seen with testing different N. We found that 12 clusters produced consistent interpretable results while F-test suggested 13+ clusters which leads to very small clusters (<10 cells).
Iryna's main priorities:
area and depth analysis for all cre lines
selecting number of clusters
Marina has worked on the tasks below: