Description
Issue summary
top-2 dim latent space plots colored by mito annotation
Details
I strongly suggest that we include the plot Rory made showing the distribution of the four labeled mitotic phases vs interphase in the top two dimensions of the latent space as a new part A. This is a very, very important sanity check showing that the model is “learning” appropriate variations within the data for subpopulations of cells that we know for sure have distinct shapes and internal organizations. Another very useful sanity check would be to show a few key structures in the top two dimensions of their target structure (conditional) latent space zt, also color-coded by mitotic phase. Specifically, for the microtubule zt the metaphase cells should look very “uncommon” but clustered, just as they do for the reference shape plot, but for organelles that are more uniformly distributed through the cytoplasm (mitochondria, peroxisomes, lysosomes) their distributions in the metaphase cells should more closely follow the underlying distribution for all cells (contingent on reference shape). Again it might be useful to get some drawings from Thao to indicate what is expected here.
TODO
- code
- manuscript text
- figure