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Volker Baecker

# segment-embryo

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

3D Segment ascidian embryos using cellpose. The images are first rescaled to be isotropic and then downscaled, before cellpose is used. The resulting labels are upscaled to match the original data.

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

This [napari] plugin was generated with [copier] using the [napari-plugin-template].



## Installation

You can install `segment-embryo` via [pip]:

    pip install segment-embryo




## 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-embryo" 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/

segment-embryo






3D Segment ascidian embryos using cellpose. The images are first rescaled to be isotropic and then downscaled, before cellpose is used. The resulting labels are upscaled to match the original data.

This napari plugin was generated with copier using the napari-plugin-template.

Installation
You can install segment-embryo via pip:
pip install segment-embryo

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-embryo" is free and open source software
Issues
If you encounter any problems, please [file an issue] along with a detailed description.

segment-embryo

3D Segment ascidian embryos using cellpose. The images are first rescaled to be isotropic and then downscaled, before cellpose is used. The resulting labels are upscaled to match the original data.

Embryo Segmentation

3D Segment ascidian embryos using cellpose. The images are first rescaled to be isotropic and then downscaled, before cellpose is used. The resulting labels are upscaled to match the original data.

Installation¶

Contributing¶

License¶

Issues¶