Ellen Zhong
Ellen Zhong
We moved our documentation to gitbook (preference for a WYSIWYG editor): https://ez-lab.gitbook.io/cryodrgn/ @michal-g was going to look into possibly revisiting sphinx docs, but pending that, we should remove the sphinx...
Todo... @michal-g will look into this. Possibly related to some of the broken `cryodrgn_utils` scripts after the ImageSource refactor (version 3.x+)
We recently removed `cryodrgn preprocess` starting in cryodrgn version 3.x, but we still need to clean up some of the deprecated functions and update the documentation. Some of the cleanup...
We should have a tool `cryodrgn_utils write_cs` to streamline re-importing particles to cryoSPARC. If the input to cryoDRGN originated from cryoSPARC, this tool could keep certain (all?) fields like the...
Add a flag to `cryodrgn train_vae` to high-pass filter images to the encoder. Potentially helpful in detecting motions in transmembrane helices.
Add these notes as separate pages in the shinx docs: Re-importing particles to cryoSPARC: https://github.com/zhonge/cryodrgn/issues/150#issuecomment-1465094751 Graph traversal documentation: https://github.com/zhonge/cryodrgn/discussions/83#discussioncomment-1525929
> I've tested the notebooks too and they're working correctly w.r.t the rest of the `config` changes introduced in this PR. However, the notebooks are failing both in the `master`...
We should be able to parse .star files that contain multiple optics groups
Color the kmeans20 samples by the default chimerax map colors   Include visualizations of the PC traversals:    
Figure out how to import results groups in cryoSPARC v4.1 (e.g. to avoid having to re-import particle stacks), perhaps with the new `cryosparc-tools` API. Related to several previous issues.