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polnet / generate-tomogram / 0.1.18

Generate a tomogram with polnet

Generate tomograms with polnet, and save them in a Zarr.
Tags
imagingcryoetPython
Citation
Martinez-Sanchez A.*, Jasnin M., Phelippeau H. and Lamm L. Simulating the cellular context in synthetic datasets for cryo-electron tomography, bioRxiv.https://github.com/anmartinezs/polnet
Solution written by
Jonathan Schwartz and Kyle Harrington
License of solution
MIT
Source Code
View on GitHub

Arguments

--copick_config_path
Path to the Copick configuration file (default value: PARAMETER_VALUE)
--run_name
Name of the run for organizing outputs (default value: PARAMETER_VALUE)
--proteins_list
Comma-separated list of protein file paths (default value: PARAMETER_VALUE)
--mb_proteins_list
Comma-separated list of membrane protein file paths (default value: PARAMETER_VALUE)
--membranes_list
Comma-separated list of membrane file paths (default value: PARAMETER_VALUE)
--user_id
User ID for Copick (default value: PARAMETER_VALUE)
--session_id
Session ID for Copick (default value: PARAMETER_VALUE)
--segmentation_name
Name for the segmentation in Copick (default value: PARAMETER_VALUE)
--tomo_type
Type of tomogram for naming in Copick (default value: PARAMETER_VALUE)
--return_protein_labels_only
Return only the labels for proteins (true/false) (default value: 1)

Usage instructions

Please follow this link for details on how to install and run this solution.