Generate an embedding with TomoTwin for a crop of a mrc
TomoTwin on an example from the czii cryoet dataportal.
Tags
templatejavaimagej2scijava
Citation
Rice, G., Wagner, T., Stabrin, M. et al. TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining. Nat Methods (2023). https://doi.org/10.1038/s41592-023-01878-z.https://tomotwin-cryoet.readthedocs.io/en/stable/index.html
Solution written by
Kyle Harrington
License of solution
MIT
Arguments
--mrcfile
Path to the MRC file (default value: PARAMETER_VALUE)
--embeddingfile
Path for the output embedding file (default value: PARAMETER_VALUE)
--use_median_mask
Use median mask for filtering (default value: 0)
--x_start
Crop start on the X axis (default value: PARAMETER_VALUE)
--x_end
Crop end on the X axis (default value: PARAMETER_VALUE)
--y_start
Crop start on the Y axis (default value: PARAMETER_VALUE)
--y_end
Crop end on the Y axis (default value: PARAMETER_VALUE)
--z_start
Crop start on the Z axis (default value: PARAMETER_VALUE)
--z_end
Crop end on the Z axis (default value: PARAMETER_VALUE)
Usage instructions
Please follow this link for details on how to install and run this solution.
