AboutSolution CatalogDocumentationTutorial
cellcanvas album catalog
sharing cellcanvas tools
copick / generate-cellcanvas-features / 0.0.12

Batch Process Zarr Files for Pixel Embedding

Automatically process all Zarr files within a specified directory structure using a SwinUNETR model.
Tags
imagingcryoetPythonnaparicellcanvas
Citation
CellCanvas and Copick teams.https://cellcanvas.org
Solution written by
Kyle Harrington
License of solution
MIT
Source Code
View on GitHub

Arguments

--copick_directory
Path to the copick directory containing the Zarr files to process. (default value: PARAMETER_VALUE)
--checkpoint_path
Path to the checkpoint file of the trained SwinUNETR model. (default value: PARAMETER_VALUE)

Usage instructions

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