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copick
/
get-median-embeddings
/ 0.0.5
Analyze Median Embeddings for Each Object Type Across Multiple Runs
Generates a file containing the median embeddings for each object type based on the picks in multiple runs, filtered by user IDs if provided.
Tags
imaging
cryoet
Python
napari
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 run names to process. (default value: PARAMETER_VALUE)
--feature_types
Comma-separated list of feature types to extract embeddings for. (default value: PARAMETER_VALUE)
--voxel_spacing
Voxel spacing used to scale pick locations. (default value: PARAMETER_VALUE)
--tomo_type
Tomogram type to use for each tomogram, e.g. denoised. (default value: PARAMETER_VALUE)
--radius
Radius for calculating median embeddings. (default value: PARAMETER_VALUE)
--user_ids
Comma-separated list of user IDs to filter picks by. If not provided, all picks will be processed. (default value: PARAMETER_VALUE)
--output_path
Path for the output file. (default value: PARAMETER_VALUE)
Usage instructions
Please follow
this link
for details on how to install and run this solution.