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copick / export-to-hdf / 0.0.3

Export Copick Runs to HDF5

A solution that exports multiple Copick runs' tomograms and picks into an HDF5 file.
Tags
imagingcryoetPython
Solution written by
Kyle Harrington
License of solution
MIT
Source Code
View on GitHub

Arguments

--copick_config_path
Path to the Copick configuration JSON file. (default value: PARAMETER_VALUE)
--run_names
Comma-separated list of Copick run names to process. (default value: PARAMETER_VALUE)
--output_hdf_path
Path to the output HDF5 file. (default value: PARAMETER_VALUE)
--voxel_spacing
Voxel spacing used to scale tomogram and pick locations. (default value: PARAMETER_VALUE)
--tomo_type
Type of tomogram to export (e.g., denoised). (default value: PARAMETER_VALUE)
--user_id
Filter picks by user ID. (default value: PARAMETER_VALUE)
--session_id
Filter picks by session ID. (default value: PARAMETER_VALUE)

Usage instructions

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