About
Solution Catalog
Documentation
Tutorial
cellcanvas album catalog
sharing cellcanvas tools
cellcanvas
/
generate-pixel-embedding
/ 0.0.13
Predict Tomogram Segmentations with SwinUNETR
Apply a SwinUNETR model to MRC tomograms to produce embeddings, and save them in a Zarr.
Tags
imaging
cryoet
Python
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 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.