Ellen Zhong

As a follow up, it may be important to change any dynamic masking parameters so that the mask used in the C1 refinement includes the asymmetric/heterogeneous regions. Otherwise, the effect...

Hi Doonam, I will look into this. I suspect that there is a pose whose rotation falls exactly on the axis, which then causes something to get rounded to beyond...

Can you tell us your commands? Unless your dataset is all in a single continuous .mrcs file, the input to `cryodrgn backproject_voxel`, `cryodrgn train_vae`, etc. should be the `.star` or...

Were you able to get it to work using `--datadir`? IIRC, the behavior should be to append the relative path in the .star file to the provided `--datadir`, and if...

Thank you for the detailed writeup @cbeck22. Sean, this should also be possible. If I remember correctly, there is an "Export" button on the outputs tab of a cryoSPARC job....

Hi Alana, it looks like there are probably some NaNs in the latent embeddings z.pkl. You can run analyze on an earlier epoch. We have recently updated the code to...

Thank you for providing the example file. I was able to load the .cs file in Python after adding `allow_pickle=True`: ``` csfile = np.load('J156_split_0_exported.cs', allow_pickle=True) ``` Is this still a...

Thank you for the detailed post! Please file an issue on the tomodrgn github repo. I believe they adapted our backproject_voxel script, but I can't speak to what changes they...

Gotcha, we can certainly prioritize this feature. It might be super helpful to get some example files, and we can reach out to you if needed!

Interesting! Do the volumes from the different regions reflect the pose heterogeneity e.g. I think it would look similar to preferred orientation artifacts? How good do you think the input...