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cellcanvas / generate-pixel-embedding / 0.0.22

Predict Tomogram Segmentations with SwinUNETR

Apply a SwinUNETR model to a mrc or zarr tomogram to produce embeddings, and save them in a Zarr.
Tags
imagingcryoetPython
Citation
CellCanvas team.https://cellcanvas.org
Solution written by
Kyle Harrington
License of solution
MIT
Source Code
View on GitHub

Arguments

--inputfile
Path to the input MRC file or zarr path containing the tomogram (default value: PARAMETER_VALUE)
--outputdirectory
Path for the output directory to save the H5 file (default value: PARAMETER_VALUE)
--checkpointpath
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.