About
Solution Catalog
Documentation
Tutorial
cellcanvas album catalog
sharing cellcanvas tools
cellcanvas
/
segment-tomogram-binary
/ 0.1.1
Predict Binary Segmentations Using Models
A solution that predicts binary segmentations for each label using models created by an optimization solution, and saves them separately.
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)
--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)
--tomo_type
Type of tomogram to use, e.g., denoised. (default value: PARAMETER_VALUE)
--feature_names
Comma-separated list of feature names to use, e.g., cellcanvas01,cellcanvas02. (default value: PARAMETER_VALUE)
--model_dir
Directory containing the trained models. (default value: PARAMETER_VALUE)
--segmentation_name
Name of the output segmentation. (default value: PARAMETER_VALUE)
Usage instructions
Please follow
this link
for details on how to install and run this solution.