Generate Synthetic CryoET Data with Polnet

Version

0.1.0

Author

Kyle Harrington and Jonathan Schwartz

License

MIT

Keywords

synthetic data deep learning cryoet tomogram protein structure

Run this script

uv run https://atrium.kyleharrington.com/cryoet/polnet/0.0.1.py

--config_path (str)

--proteins_list (str)

Comma-separated list of protein file paths

--num_tomos_per_snr (int)

Number of tomograms to produce per SNR

Default: 1

--snr (str)

Comma-separated list of SNRs to simulate

Default: 0.5

--tilt_range (str)

Min,Max,Delta for tilt range

Default: -60,60,3

--tomo_shape (str)

Dimensions of tomogram in pixels (X,Y,Z)

Default: 630,630,200

--misalignment (str)

Min,Max,Sigma for tilt misalignments

Default: 1,5,0.5

--voxel_size (float)

Voxel size for simulated tomograms

Default: 10.0

--mb_proteins_list (Optional[str])

Comma-separated list of membrane protein file paths

--membranes_list (Optional[str])

Comma-separated list of membrane file paths