we underplay how good the encoded / generated cells look
Details
It is a HUGE WIN that the model is learning appropriate organelle distributions. This is underplayed in the text to a point well beyond modesty or even diffidence, just mentioned offhand in lines 127-128 about how the images “appear”, without even any comment about whether the appearance matches with what is known to be correct for those structures. It is TOTALLY AWESOME that the model learned to put the tight junctions at the appropriate apical location! Remember that this was a big part of the motivation to undertake the full-on 3D retraining of the model in January. I think that another panel should be added to the figure to emphasize this point. I suggest asking Thao to draw a “typical” interphase iPS cell with a bunch of the organelles labeled, and show LARGER IMAGES for a single cell (close to the middle of the distribution) with the “most likely” reconstructions for a bunch of structures where there is a simple rule that can be articulated. For example, mitochondria should be distributed throughout the cytoplasm, but are never found inside the nucleus. The nuclear lamina forms a closed shell around the DNA. The tight junction is at the apical side and around the cell periphery. The nucleolus (both fibrillarin and nucleophosmin) form blobs that are always inside of the nucleus, never outside. Paxillin is always at the basal surface.
Issue summary
we underplay how good the encoded / generated cells look
Details
TODO