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.

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)

Please follow this link for details on how to install and run this solution.