Daniel Asarnow

MATLAB parpool size

1

I am having trouble finding where the pool size is specified for various steps. I see `matlab_workers` for DynamoTemplateMatching (=1), and the general `jobs_per_node` (=1) and `gpus_per_node` (=2). Running GCTFCtfphaseflipCTFCorrection...

Adding pyem to conda-forge

13

@conda-forge/help-python Hello! I believe my recipe is ready, hopefully I have understood the documentation. The package contains a library and utility functions for image processing in biological electron microscopy, mostly...

Difficulty generalizing with train3d

1

Hi Tristan, I've been experimenting with train3d in the dev branch. I have been using cryoCARE or topaz denoised tomograms with ~4000 manually annotated particles (from 5 tomograms), and I'm...

I'm seeing this error with topaz 0.3.7, but topaz 0.2.5 works fine with the same command. Is it because the model was trained with the older version? The command was...

Specifying conda channels for matching / CUDA torch versions

6

I'm creating environments for several different versions of topaz (including 0.3.7) and I've noticed that with a command like: `mamba create -n topaz python=3.11 topaz fsspec pytorch-cuda=11.8 -c tbepler -c...

Too many open files during fitting

3

I was running fit-model on 18 tomograms using the config.yaml attached below and got this error for "too many open files" (~~`ulimit` is actually unlimited already~~). Have you seen this...