Metadata-Version: 2.1
Name: raw2tmap
Version: 0.1.0
Summary: Convert OME-Zarr files to TMAP format
Home-page: https://github.com/TissUUmaps/raw2tmap
Author: SciLifeLab BioImage Informatics Facility (BIIF)
Author-email: biif@scilifelab.se
License: MIT
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.9
Description-Content-Type: text/markdown
Provides-Extra: dzi
License-File: LICENSE

# raw2tmap

![pypi](https://img.shields.io/pypi/v/raw2tmap?label=pypi&link=https%3A%2F%2Fpypi.org%2Fproject%2Fraw2tmap%2F)
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Convert OME-Zarr files to TMAP format

## Requirements

This software requires [Python](https://www.python.org) 3.9 or later.

## Installation

Use the package manager [pip](https://pip.pypa.io) 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](https://github.com/glencoesoftware/bioformats2raw).

## Support

If you find a bug, please [raise an issue](https://github.com/TissUUmaps/raw2tmap/issues/new).

## Contributing

Pull requests are welcome.

For major changes, please open an issue first to discuss what you would like to change.

## Changelog

[Changelog](https://github.com/TissUUmaps/raw2tmap/blob/main/CHANGELOG.md)

## Authors

[SciLifeLab BioImage Informatics Facility (BIIF)](https://biifsweden.github.io)

## License

[MIT](https://github.com/TissUUmaps/raw2tmap/blob/main/LICENSE)

# Changelog

All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unreleased]

## [0.1.0] - 2023-07-03

Initial release

[unreleased]: https://github.com/TissUUmaps/raw2tmap/compare/v0.1.0...HEAD
[0.1.0]: https://github.com/TissUUmaps/raw2tmap/releases/tag/v0.1.0

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.
