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.

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)

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