Convert OME-Zarr files to TMAP format
Project description
raw2tmap
Convert OME-Zarr files to TMAP format
Requirements
This software requires Python 3.9 or later.
Installation
Use the package manager pip to install raw2tmap:
pip install raw2tmap
To enable the --dzi
option, install with the dzi
extra (requires libvips):
pip install "raw2tmap[dzi]"
Usage
To convert an OME-Zarr file to TMAP format:
❯ raw2tmap --help
Usage: raw2tmap [OPTIONS] RAW_FILE TMAP_FILE
Convert OME-Zarr files to TMAP format.
Options:
-t, --time INTEGER RANGE Time index. [x>=0]
-c, --channel INTEGER / TEXT Channel index or name.
-z, --depth INTEGER RANGE Depth (z) index. [x>=0]
--layers DIRECTORY Path to layer images, relative to TMAP_FILE.
Defaults to '.{TMAP_FILE}/layers'.
--compression Compression algorithm. [default: none]
--tilesize INTEGER RANGE Tile size in pixels. [default: 256; x>0]
--format [0.1|0.2|0.3|0.4] OME-Zarr format version. [default: 0.4]
--dzi Write DZI file (requires pyvips).
-q, --quiet Quiet mode (hide progress bar).
--version Show the version and exit.
--help Show this message and exit.
Example:
raw2tmap -t 0 -z 0 https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0052A/5514375.zarr 5514375.tmap
OME-Zarr files can for example be created using bioformats2raw.
Support
If you find a bug, please raise an issue.
Contributing
Pull requests are welcome.
For major changes, please open an issue first to discuss what you would like to change.
Changelog
Authors
SciLifeLab BioImage Informatics Facility (BIIF)
License
Changelog
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
Unreleased
0.1.0 - 2023-07-03
Initial release
MIT License
Copyright (c) 2023 SciLifeLab BioImage Informatics Facility
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.
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