Convert a mrc to omezarr using mrc2omezarr.
Tags
imagingcryoet
Citation
Utz Ermel.https://github.com/uermel/mrc2omezarr
Solution written by
Kyle Harrington
License of solution
MIT
Source Code
Arguments
--mrc_path
Path to the MRC file. Include the protocol if necessary (e.g., s3://). (default value: PARAMETER_VALUE)
--zarr_path
Path to the output Zarr file. Include the protocol if necessary (e.g., s3://). (default value: PARAMETER_VALUE)
--permissive
Whether to read the MRC file in permissive mode. (default value: PARAMETER_VALUE)
--overwrite
Whether to overwrite the output Zarr file. (default value: PARAMETER_VALUE)
--scale_factors
Scale factors for multiscale pyramid. Comma-separated list of integers. (default value: PARAMETER_VALUE)
--voxel_size
Voxel size in Angstroms. Comma-separated list of floats or a single float. If not provided, it will be read from the MRC header. (default value: PARAMETER_VALUE)
--is_image_stack
Whether the data is an image stack (determined from MRC-header by default). (default value: PARAMETER_VALUE)
--chunk_size
Chunk size for the Zarr file. (default value: PARAMETER_VALUE)
--filesystem_args
Path to a JSON file containing additional arguments to pass to the fsspec-filesystem. (default value: PARAMETER_VALUE)
--pyramid_method
Method to downscale the data. Options: local_mean, downsample. (default value: PARAMETER_VALUE)