Metadata-Version: 2.2
Name: napari-file2folder
Version: 0.0.3
Summary: Save multidimensional file as folder of tifs
Author: Jules Vanaret
Author-email: jules.vanaret@univ-amu.fr
License: 
        The MIT License (MIT)
        
        Copyright (c) 2024 Jules Vanaret
        
        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.
        
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: qtpy
Requires-Dist: magicgui
Requires-Dist: tifffile
Requires-Dist: bioio
Requires-Dist: bioio-ome-tiff
Requires-Dist: bioio-ome-zarr
Requires-Dist: bioio-nd2
Requires-Dist: bioio-czi
Provides-Extra: testing
Requires-Dist: tox; extra == "testing"
Requires-Dist: pytest; extra == "testing"
Requires-Dist: pytest-cov; extra == "testing"
Requires-Dist: pytest-qt; extra == "testing"
Requires-Dist: napari; extra == "testing"
Requires-Dist: pyqt5; extra == "testing"

# napari-file2folder

[![License MIT](https://img.shields.io/pypi/l/napari-file2folder.svg?color=green)](https://github.com/GuignardLab/napari-file2folder/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/napari-file2folder.svg?color=green)](https://pypi.org/project/napari-file2folder)
[![Python Version](https://img.shields.io/pypi/pyversions/napari-file2folder.svg?color=green)](https://python.org)
[![tests](https://github.com/jules-vanaret/napari-file2folder/workflows/tests/badge.svg)](https://github.com/jules-vanaret/napari-file2folder/actions)
[![codecov](https://codecov.io/gh/jules-vanaret/napari-file2folder/branch/main/graph/badge.svg)](https://codecov.io/gh/jules-vanaret/napari-file2folder)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-file2folder)](https://napari-hub.org/plugins/napari-file2folder)

<img src="https://github.com/GuignardLab/tapenade/blob/main/imgs/tapenade3.png" width="100">

A plugin to inspect bioimages (e.g. .tif, .czi, .nd2, .lsm...) and save them as individual .tif files in a folder.

`napari-file2folder` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.

If you use this plugin for your research, please [cite us](https://github.com/GuignardLab/tapenade/blob/main/README.md#how-to-cite).

## Overview

<img src="imgs/napari-file2folder-demo.gif"/>

This plugin allows you to inspect (possibly large) bioimages by displaying their shape (number of elements in each dimension), and allowing you to save each element along a chosen dimension as a separate .tif file in a folder. This is useful when you have a large movie or stack of images and you want to save each frame or slice as a separate file. Optionally, the plugin allows the user to visualize the middle element of a given dimension to help the user decide which dimension to save as separate files.

The plugin currently supports the following file formats:
- .tif
- .ome.tiff
- .zarr
- .ome.zarr
- .nd2
- .lsm
- .czi

This plugin leverages [tifffile], [bioio], and [zarr] to circumvent loading the entire images in memory, which allows inspection of very large images.

> [!CAUTION]
> When inspecting the middle element of a dimension, or when saving one element of a dimension as a separate file, the plugin loads the element in memory, which means that at least this lone element must fit in memory.

## Installation

The plugin obviously requires [napari] to run. If you don't have it yet, follow the instructions [here](https://napari.org/stable/tutorials/fundamentals/installation.html).

The simplest way to install `napari-file2folder` is via the [napari] plugin manager. Open Napari, go to `Plugins > Install/Uninstall Packages...` and search for `napari-file2folder`. Click on the install button and you are ready to go!

You can install `napari-file2folder` via [pip]:

    pip install napari-file2folder




## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

## License

Distributed under the terms of the [MIT] license,
"napari-file2folder" is free and open source software

## Issues

If you encounter any problems, please [file an issue] along with a detailed description.

----------------------------------

This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.

<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started

and review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
-->

[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin

[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
[tifffile]: https://github.com/cgohlke/tifffile
[bioio]: https://github.com/bioio-devs/bioio
[zarr]: https://github.com/zarr-developers/zarr-python
