| Name | mrc2omezarr JSON |
| Version |
0.3
JSON |
| download |
| home_page | None |
| Summary | Command line tool to convert MRC-files to OME-Zarr. |
| upload_time | 2024-09-20 13:33:41 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | MIT License Copyright (c) 2024 Utz H. Ermel Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
conversion
cryo-et
cryoet
mrc
ome
tomography
zarr
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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
```bash
git clone https://github.com/uermel/mrc2omezarr.git
cd mrc2omezarr
pip install .
```
## Usage
```bash
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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