About
Solution Catalog
Documentation
Tutorial
cellcanvas album catalog
sharing cellcanvas tools
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
imaging
cryoet
Python
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.