Command line tool to convert MRC-files to OME-Zarr.
Project description
mrc2omezarr
Command line tool for conversion from MRC to multiscale OME-Zarr format.
Default settings produce Zarr-files similar to those on the CZI cryoET data portal:
- Files contain one image
- Scales: 1x, 2x, 4x (original resolution)
- Scale transformations transform to angstrom coordinates
- Chunk size: 256, 256, 256
The original MRC-header is retained as a dictionary in the root .zattrs file.
Input as well as output can be local or remote. For remote files include the protocol in the filename, e.g. s3://bucket/path/to/file.mrc
.
Install
git clone https://github.com/uermel/mrc2omezarr.git
cd mrc2omezarr
pip install .
Usage
Usage: mrc2omezarr [OPTIONS]
Options:
--mrc-path TEXT Path to the MRC file. Include the protocol
if necessary. (e.g. s3://) [required]
--zarr-path TEXT Path to the output Zarr file. Include the
protocol if necessary. (e.g. s3://)
[required]
--permissive / --no-permissive Whether to read the MRC file in permissive
mode. [default: no-permissive]
--overwrite / --no-overwrite Whether to overwrite the output Zarr file.
[default: overwrite]
--scale-factors TEXT Scale factors for multiscale pyramid. Comma-
separated list of integers. [default:
1,2,4]
--voxel-size TEXT Voxel size in Angstroms. Comma-separated
list of floats or single float. If not
provided, it will be read from the MRC
header.
--is-image-stack / --no-is-image-stack
Whether the data is an image stack
(determined from MRC-header by default).
--chunk-size INTEGER Chunk size for the Zarr file. [default:
256]
--filesystem-args TEXT Path to a JSON file containing additional
arguments to pass to the fsspec-filesystem.
--help Show this message and exit.
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