copick / project_from_dataportal / 0.2.2

Fetch Data from CryoET Data Portal and Integrate with Copick

Fetches tomograms, tilt series, annotations, segmentations, and metadata from cryoet_data_portal and integrates them into the specified Copick project.
Tags
imagingcryoetPython
Citation
Cellcanvas and Copick teamshttps://cellcanvas.org
Solution written by
Kyle Harrington
License of solution
MIT
Source Code

Arguments

--dataset_id
Dataset ID to process. (default value: PARAMETER_VALUE)
--copick_config_path
Path to the Copick configuration file. (default value: PARAMETER_VALUE)
--voxel_spacing
Optional voxel spacing to filter tomograms. (default value: PARAMETER_VALUE)
--overlay_root
Path to the overlay root directory. (default value: PARAMETER_VALUE)
--static_root
Path to the static root directory. (default value: PARAMETER_VALUE)

Usage instructions

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