Metadata-Version: 2.1
Name: napari-bacseg
Version: 1.1.0
Summary: Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.
Author-email: Piers Turner <piers.turner@physics.ox.ac.uk>
Project-URL: Homepage, https://github.com/piedrro/napari-bacseg
Project-URL: Bug Tracker, https://github.com/piedrro/napari-bacseg/issues
Classifier: Framework :: napari
Classifier: Environment :: Plugins
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: napari[all] ==0.5.0
Requires-Dist: torch
Requires-Dist: cellpose >=3.0.1
Requires-Dist: opencv-python
Requires-Dist: picassosr ==0.6.5
Requires-Dist: bactfit >=0.1.6
Requires-Dist: numpy
Requires-Dist: pyqt5
Requires-Dist: pyqt6
Requires-Dist: qtpy
Requires-Dist: scipy
Requires-Dist: natsort
Requires-Dist: tqdm
Requires-Dist: imagecodecs
Requires-Dist: tifffile
Requires-Dist: pandas
Requires-Dist: mat4py
Requires-Dist: glob2
Requires-Dist: matplotlib
Requires-Dist: scikit-image
Requires-Dist: roifile
Requires-Dist: openpyxl
Requires-Dist: shapely
Requires-Dist: colicoords
Requires-Dist: psutil
Requires-Dist: xmltodict
Requires-Dist: astropy
Requires-Dist: tiler
Requires-Dist: imageio-ffmpeg
Requires-Dist: aicspylibczi
Requires-Dist: czifile
Requires-Dist: omnipose
Requires-Dist: h5py
Requires-Dist: pyqtgraph
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-BacSEG

[![License BSD-3](https://img.shields.io/pypi/l/napari-bacseg.svg?color=green)](https://github.com/piedrro/napari-bacseg/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/napari-bacseg.svg?color=green)](https://pypi.org/project/napari-bacseg)
[![Python Version](https://img.shields.io/pypi/pyversions/napari-bacseg.svg?color=green)](https://python.org)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-bacseg)](https://napari-hub.org/plugins/napari-bacseg)

Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.

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

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/
