Metadata-Version: 2.1
Name: napari-easy-augment-batch-dl
Version: 0.0.3
Summary: A plugin to perform unet based deep learning with a small number of labels and augmentation
Author: Brian Northan
Author-email: bnorthan@gmail.com
License: 
        Copyright (c) 2024, Brian Northan
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this
          list of conditions and the following disclaimer.
        
        * Redistributions in binary form must reproduce the above copyright notice,
          this list of conditions and the following disclaimer in the documentation
          and/or other materials provided with the distribution.
        
        * Neither the name of copyright holder nor the names of its
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        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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Project-URL: Bug Tracker, https://github.com/bnorthan/napari-easy-augment-batch-dl/issues
Project-URL: Documentation, https://github.com/bnorthan/napari-easy-augment-batch-dl#README.md
Project-URL: Source Code, https://github.com/bnorthan/napari-easy-augment-batch-dl
Project-URL: User Support, https://github.com/bnorthan/napari-easy-augment-batch-dl/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD 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 :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: magicgui
Requires-Dist: qtpy
Requires-Dist: scikit-image
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-easy-augment-batch-dl

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A plugin to perform unet based deep learning with a small number of labels and augmentation

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

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

<!--
Don't miss the full getting started guide to set up your new package:
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and review the napari docs for plugin developers:
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## Installation

To install latest development version :

    pip install git+https://github.com/bnorthan/napari-easy-augment-batch-dl.git

You will also need to install the latest development version of tnia-python:

    pip install git+https://github.com/True-North-Intelligent-Algorithms/tnia-python.git

You will need to install napari and for augmentation you will need albumentations library.  Also explicitly install numpy 1.26.  (We have not tested with numpy 2.0 so it is a good idea to explicitly install numpy 1.26 to avoid another dependency installing numpy 2.x)

```
    pip install numpy==1.26
    pip install napari[all]
    pip install albumentations
    pip install matplotlib
```

You will also need one or more of stardist, cellpose, segment-everything or Yolo

### Stardist

#### Windows

```
    conda install -c conda-forge cudatoolkit=11.2 cudnn=8.1.0
    pip install "tensorflow<2.11"
    pip install stardist==0.8.5
    pip install gputools
    pip install edt
```

#### Linux

```
    pip install tensorflow[and-cuda]
    pip install stardist
    pip install gputools
    pip install edt
```

### Pytorch (for unet segmentation)

```
    pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu118
    pip install pytorch-lightning
    pip install monai
    pip install scipy
    pip install tifffile
```

### Cellpose

```
    pip install cellpose
```

### SAM (Segment Anything)

```
    pip install segment-everything
```

###

(more details to come on installing dependencies)


(Coming soon) You can install `napari-easy-augment-batch-dl` via [pip]:

    pip install napari-easy-augment-batch-dl



## 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-easy-augment-batch-dl" 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/bnorthan/napari-easy-augment-batch-dl/issues

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