https://github.com/hereariim/napari-conidie

https://github.com/hereariim/napari-conidie

Last synced: about 1 year ago
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• Host: GitHub
• URL: https://github.com/hereariim/napari-conidie
• Owner: hereariim
• License: bsd-3-clause
• Created: 2022-10-06T12:13:01.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2024-05-01T19:01:36.000Z (about 2 years ago)
• Last Synced: 2024-08-09T17:13:18.179Z (almost 2 years ago)
• Language: Python
• Size: 24.3 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# napari-conidie

[![License BSD-3](https://img.shields.io/pypi/l/napari-conidie.svg?color=green)](https://github.com/hereariim/napari-conidie/raw/main/LICENSE)

[![PyPI](https://img.shields.io/pypi/v/napari-conidie.svg?color=green)](https://pypi.org/project/napari-conidie)

[![Python Version](https://img.shields.io/pypi/pyversions/napari-conidie.svg?color=green)](https://python.org)

[![tests](https://github.com/hereariim/napari-conidie/workflows/tests/badge.svg)](https://github.com/hereariim/napari-conidie/actions)

[![codecov](https://codecov.io/gh/hereariim/napari-conidie/branch/main/graph/badge.svg)](https://codecov.io/gh/hereariim/napari-conidie)

[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-conidie)](https://napari-hub.org/plugins/napari-conidie)

A segmentation tool to get conidie and hyphe

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

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

This plugin is a use case for obtaining conidia and hyphae surface from images. This plugin is a private tool dedicated exclusively to the work of the QUASAV team.

## Installation

This private tool cannot be found in the built-in napari. The installation therefore follows two steps:

1 - Install latest development version :

    git clone https://github.com/hereariim/napari-conidie.git

## Getting started

As prerequisite, user must have installed ilastik in its computer.

Before using the plugin, you must have two data:

- The ilastik model

- The compressed file contained your images structured as followed :

```

└── Compressed file

    ├── Folder1

    │   ├── img0_1.jpg

    │   ├── img0_2.jpg

    │   ...

    │   └── img0_n.jpg

    │ 

    ├── Folder2

    │   ├── img1_1.jpg

    │   ├── img1_2.jpg

    │   ...

    │   └── img1_n.jpg

    ...

    │

    └──  Foldern

        ├── imgn_1.jpg

        ├── imgn_2.jpg

        ...

        └── imgn_n.jpg

```

## Plugin

![here](https://github.com/hereariim/napari-conidie/assets/93375163/07cf6bc3-3d55-4ae1-94ac-8e8b33193963)

## 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 [BSD-3] license,

"napari-conidie" is free and open source software

## Issues

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

[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

[file an issue]: https://github.com/hereariim/napari-conidie/issues

[napari]: https://github.com/napari/napari

[tox]: https://tox.readthedocs.io/en/latest/

[pip]: https://pypi.org/project/pip/

[PyPI]: https://pypi.org/