Total files = 39 tiff images Sample information
1. A subset of slides were selected at random while ensuring that all the treatment groups were represented
Total tiles = 902 Average number of tiles / image = ~55
3. A subset of tiles (total=80; 5 tiles/sample) were randomly selected to test the pixel classifier trained on series-700 samples. The subset was selected in a way to include tiles having variable proportions of collagen and tissue.
4. Collagen masks exported from QuPath were overlaid on original MT images using CellProfiler - some example overlays below
There is some overcalling in general, but it is avoiding common pitfalls such as incorrectly calling lymphocyte clusters as collagen.