Ellen Zhong

Stop training on nan

2

`cryodrgn train_vae` should break if nan loss is hit instead of silently continuing for the specified number of epochs

Look into GPU implementations

cryodrgn parse_ctf_csparc fails when .cs file is missing image size

1

Sometimes the cryosparc CTF metadata file (.cs) doesn't contain the image size. Add additional arguments to `cryodrgn parse_ctf_csparc` to overwrite these fields. ``` $ cryodrgn parse_ctf_csparc J150/P10_J150_passthrough_particles.cs -o ctf.pkl 2021-04-18...

Correct for higher order optical effects in the CTF in cryoDRGN training. Reference: https://journals.iucr.org/m/issues/2020/02/00/fq5009/ Potential testing datasets: the proteasome (EMPIAR-10185) and aldolase (EMPIAR-10181)

backproject_voxel FSC plot should automatically detect the pixel size

1

I ran `cryodrgn backproject_voxel` on a cryo-ET dataset, and this was the output plot: Command: ``` $ cryodrgn backproject_voxel particles.star --tilt -d 2.93 --poses pose.pkl --ctf ctf.pkl --datadir subtilts/ -o...