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copick
/
project_from_dataportal
/ 0.0.1
Convert MRCs from a data portal dataset to zarr and Generate cellcanvas Pixel Embeddings
Processes MRC files to ZARR and generates embeddings for tomography data.
Tags
imaging
cryoet
Python
Citation
Cellcanvas and copick teams
https://cellcanvas.org
Solution written by
Kyle Harrington
License of solution
MIT
Source Code
View on GitHub
Arguments
--dataset_id
Dataset ID to process. (default value: PARAMETER_VALUE)
--num_runs
Number of runs to process from the dataset. (default value: PARAMETER_VALUE)
--region_exclude
Tuple defining regions to exclude in the format (x_start, x_end, y_start, y_end, z_start, z_end). (default value: PARAMETER_VALUE)
--checkpoint_path
Path to the checkpoint file of the trained model. (default value: PARAMETER_VALUE)
--copick_root_directory
Root directory of the copick project where outputs should be saved. (default value: PARAMETER_VALUE)
Usage instructions
Please follow
this link
for details on how to install and run this solution.