Tristan Bepler

icon company MIT icon location Group leader, Simons Machine Learning Center at NYSBC in NYC. We're hiring postdocs and research scientists to advance machine learning for structural biology.

Results 6 issues of Tristan Bepler

topaz extract should have an option to stay away from micrograph edges

Automatically create subdirectories when using 'topaz convert' to box files

enhancement
good first issue

Add warning for when micrograph image names include the file extension

Including the file extension in the micrograph name causes topaz to fail to find micrographs. See for example https://github.com/tbepler/topaz/blob/master/topaz/commands/train_test_split.py#L30 It would be great if topaz could correct these names automatically,...

enhancement
help wanted
good first issue

add option to predict on micrographs in chunks to reduce GPU RAM usage

Applies to "topaz segment" and "topaz extract"

enhancement

Allow 'topaz particle_stack' to accept STAR and CSV input files

enhancement

Topaz training error in multiprocessing data loader

### Discussed in https://github.com/tbepler/topaz/discussions/172 Originally posted by **wuhucryoem** July 24, 2023 When I do a topaz training, it show me there haven't some file or directory, but don't show me...