copick / binary-to-multilabel-segmentation / 0.0.2

Create Multilabel Segmentation from Individual Segmentations

Creates a multilabel segmentation by combining individual segmentations for all pickable objects, including particles, in a Copick project. Can process a single run or all runs in the project.

Arguments

--copick_config_path

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

--voxel_spacing

Voxel spacing to use for the segmentation. (default value: PARAMETER_VALUE)

--input_user_id

User ID for input segmentations. (default value: PARAMETER_VALUE)

--input_session_id

Session ID for input segmentations. (default value: PARAMETER_VALUE)

--run_name

Name of the run to process. If not provided, all runs will be processed. (default value: PARAMETER_VALUE)

--output_user_id

User ID for the output multilabel segmentation. (default value: PARAMETER_VALUE)

--multilabel_name

Name for the new multilabel segmentation. (default value: PARAMETER_VALUE)

Usage instructions

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