napari-bacseg 1.1.2
Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.
Requires Python: >=3.9

# napari-BacSEG

[![License BSD-3](https://img.shields.io/pypi/l/napari-bacseg.svg?color=green)](https://github.com/piedrro/napari-bacseg/raw/main/LICENSE)
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Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.

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This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.

## Installing BacSeg from PyPi

Create a new conda environment:

    conda create --name napari-bacseg python==3.9
    conda activate napari-bacseg
    conda install -c anaconda git
    conda update --all

Install `napari-bacseg` via [pip]:

    pip install napari-bacseg

Launch Napari:

    napari

Install latest version of 'napri-bacseg' from [pip]:

    pip install napari-bacseg --upgrade

Select **napari-bacseg** from the **Plugins** dropdown menu

## Installing BacSeg From GitHub

    conda create –-name napari-bacseg python==3.9
    conda activate napari-bacseg
    conda install -c anaconda git
    conda update --all

    pip install napari[all]

    pip install git+https://github.com/piedrro/napari-bacseg.git

## Updating BacSeg From Github
Once you have installed the plugin, you can update the plugin by running the following commands:

    pip install git+https://github.com/piedrro/napari-bacseg.git

## GPU Installation
 Once you have installed the plugin, you can install the GPU version of the plugin by running the following commands:

    pip uninstall torch torchvision torchaudio -y
    pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu118

If the latest CUDA versions don't work, try an older version like cuda 11.3:

    pip uninstall torch torchvision torchaudio -y
    pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu113


## 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-bacseg" 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/piedrro/napari-bacseg/issues

[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/