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polnet / generate-copick-project / 0.1.0

Generate a Copick Project with polnet

Generate a Copick Project Composed with polnet simulations.
Tags
copickplanefitting
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)
--num_tomos_per_snr
Number of Tomograms to Produce Per Specified SNR (default value: 1)
--snr
Comma-separated list of SNRs to Apply to Tomograms (default value: 0.5)
--tilt_range
Comma-separated List of Min,Max and Increment for the Tilt Range (default value: -60,60,3)
--tomo_shape
Comma-separated List of Tomogram Dimensions (in Pixels) (default value: 630,630,200)
--misalignment
Comma-separated list Tilt Shift Minimum, Maximum and Sigma Mis-Alignmnets (default value: 1,5,0.5)
--voxel_size
Voxel Size for Simulated Tomograms (default value: 10)
--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: )
--membranes_list
Comma-separated list of membrane file paths (default value: )

Usage instructions

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