Metadata-Version: 2.1
Name: segment-any-confocal-images
Version: 0.0.8
Summary: Segment Any Confocal Images is a flexible and high-performance plugin designed for segmentation of confocal microscopy data. It supports both 2D and 3D image stacks, enabling users to identify and extract cellular or subcellular structures with minimal manual effort.
Author: Huibao Feng
Author-email: fenghuibao@gmail.com
License: <<<<<<< HEAD
        MIT License
        
        Copyright (c) 2025 fenghuibao
        =======
        
        The MIT License (MIT)
        
        Copyright (c) 2025 Huibao Feng
        >>>>>>> 8d6afec (initial commit)
        
        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:
        
        <<<<<<< HEAD
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        =======
        The above copyright notice and this permission notice shall be included in
        all copies or substantial portions of the Software.
        >>>>>>> 8d6afec (initial commit)
        
        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,
        <<<<<<< HEAD
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
        =======
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
        THE SOFTWARE.
        >>>>>>> 8d6afec (initial commit)
        
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 :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: openpyxl
Requires-Dist: magicgui
Requires-Dist: qtpy
Requires-Dist: scikit-image
Provides-Extra: all
Requires-Dist: napari[all] ; extra == 'all'

# segment-any-confocal-images

[![License MIT](https://img.shields.io/pypi/l/segment-any-confocal-images.svg?color=green)](https://github.com/fenghuibao/segment-any-confocal-images/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/segment-any-confocal-images.svg?color=green)](https://pypi.org/project/segment-any-confocal-images)
[![Python Version](https://img.shields.io/pypi/pyversions/segment-any-confocal-images.svg?color=green)](https://python.org)
[![tests](https://github.com/fenghuibao/segment-any-confocal-images/workflows/tests/badge.svg)](https://github.com/fenghuibao/segment-any-confocal-images/actions)
[![codecov](https://codecov.io/gh/fenghuibao/segment-any-confocal-images/branch/main/graph/badge.svg)](https://codecov.io/gh/fenghuibao/segment-any-confocal-images)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/segment-any-confocal-images)](https://napari-hub.org/plugins/segment-any-confocal-images)
[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)

Segment Any Confocal Images is a flexible and high-performance plugin designed for segmentation of confocal microscopy data. It supports both 2D and 3D image stacks, enabling users to identify and extract cellular or subcellular structures with minimal manual effort.

## Supported inputs

The widget currently supports standard image formats only:

- `*.tif`, `*.tiff`
- `*.png`
- `*.jpg`, `*.jpeg`

Microscope-specific container formats such as `czi`, `nd2`, `lif`, and `lsm` are not loaded by the widget anymore.

Loaded images are normalized into the widget's internal `TCZYX` layout:

- 2D grayscale images become `1 x 1 x 1 x Y x X`
- grayscale stacks become `1 x 1 x Z x Y x X`
- RGB/RGBA images become `1 x 3 x 1 x Y x X`
- RGB/RGBA stacks become `1 x 3 x Z x Y x X`

Physical pixel size metadata is no longer auto-imported from source files. Standard images default to pixel size `1.0`.

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

This [napari] plugin was generated with [copier] using the [napari-plugin-template] (None).

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

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

## Installation

You can install `segment-any-confocal-images` via [pip]:

```
pip install segment-any-confocal-images
```

If napari is not already installed, you can install `segment-any-confocal-images` with napari and Qt via:

```
pip install "segment-any-confocal-images[all]"
```

Core runtime dependencies include `numpy`, `qtpy`, `magicgui`, `superqt`, and `scikit-image`.

## 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,
"segment-any-confocal-images" 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
[copier]: https://copier.readthedocs.io/en/stable/
[@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
[napari-plugin-template]: https://github.com/napari/napari-plugin-template

[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
