Closed fursham-h closed 2 years ago
I still wish to speed this part up. @Marcel-Salier do you know the idea behind grouping the cells by ICC intensities?
The thing with the ICC channels is that they change quite e bit from one staining to other and we decided to clasified them in 5 stars instead and then take the population as + as we wish (let's say above 3, 4, etc) depending of what we consider biologically reasonable. I remember we agreed to use k-means to cluster but not in this complicated manner we have to definitely review that.
Yeah I totally understand the reason for clustering.
We should simplify this, let me rest something out and we can discuss.
Closing this issue since it is resolved
I noticed that cells are now grouped for each marker using kmeans clustering. If I understand the function correctly, it:
The workflow above feels complicated. I can understand why clustering was done on all pixels (including background) rather than the avg_intensity, but does it significantly give better clusters? Also, are kmeans cluster number based on pixel intensity?