pytorch_integrated_cell

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Results: Content related to Fig. 5

1

## Issue summary Lots of stuff ## Details > It might be worth considering including some images for the Golgi in brefeldin-treated cells as well as for microtubules in taxol-treated...

donovanr

Results: Figure 2

1

## Issue summary Clean up figure and move to white-background cell images ## Details > Get rid of the black boxes with white Xs; lack of data is better conveyed...

donovanr

Results: Figure 1

1

## Issue summary minor aesthetics but otherwise figure 1 is fine ## Details > Figure 1 is fine. I don’t love the red boxes around “Reference structure variation” and “Image...

donovanr

## Issue summary as beta changes, plot KL vs sorted(dims) and show what happens (maybe more peaked?) ## Details Another feature of the reconstruction vs. compactness trade-off explored by tuning...

donovanr

Code: Error during 'pip install'

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## Issue summary During the 'pip install -e' step, the following error was encountered: ``` Collecting lkaccess (from pytorch-integrated-cell==0.1) ERROR: Could not find a version that satisfies the requirement lkaccess...

Calebium

## Issue summary orthogonal latent space ==> reproducible training? ## Details > If it is really true that the latent space dimensions also end up tending towards being orthogonal to...

donovanr

## Issue summary talk up coupling summary stats ## Details > The contingency results summarized in part B are really great, again the specific couplings observed are a HUGE WIN...

donovanr

## 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...

donovanr

## Issue summary color-code by mito annotations ## Details > What is there is fine. I think it would be nice to color-code the mitotic cells by the four annotated...

donovanr

## Issue summary hard truncation of latent space and look at reconstructions ## Details > Again by analogy with PCA, it should be possible to truncate the latent space (force...

donovanr