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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
imaging
cryoet
Python
napari
cellcanvas
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.