Extract Centroids from Multilabel Segmentation

A solution that extracts centroids from a multilabel segmentation using Copick and saves them as candidate picks.

Arguments

--copick_config_path

Path to the Copick configuration JSON file. (default value: PARAMETER_VALUE)

--painting_segmentation_name

Name of the painting segmentation. (default value: PARAMETER_VALUE)

--session_id

Session ID for the segmentation. (default value: PARAMETER_VALUE)

--user_id

User ID for segmentation creation. (default value: PARAMETER_VALUE)

--voxel_spacing

Voxel spacing used to scale pick locations. (default value: PARAMETER_VALUE)

--run_name

Name of the Copick run to process. (default value: PARAMETER_VALUE)

--segmentation_dir

Directory containing the multilabel segmentation. (default value: PARAMETER_VALUE)

--min_particle_size

Minimum size threshold for particles. (default value: 1000)

--max_particle_size

Maximum size threshold for particles. (default value: 50000)

--maxima_filter_size

Size for the maximum detection filter (default 9). (default value: 9)

--segmentation_idx_offset

Offset for segmentation indices (default 0). (default value: 0)

--labels_to_process

Comma-separated list of labels to process. (default value: PARAMETER_VALUE)

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