Metadata-Version: 2.4
Name: napari-SAMV2
Version: 0.0.7
Summary: Napari plugin for segment anything version 2 model from meta. Plugin primarily useful for segmenting 3d volumetric data or 3d time series data. 
Author: Krishnan Venkataraman
Author-email: krishvraman95@gmail.com
License: 
        Copyright (c) 2024, Krishnan Venkataraman
        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
          contributors may be used to endorse or promote products derived from
          this software without specific prior written permission.
        
        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/Krishvraman/napari-SAMV2/issues
Project-URL: Documentation, https://github.com/Krishvraman/napari-SAMV2#README.md
Project-URL: Source Code, https://github.com/Krishvraman/napari-SAMV2
Project-URL: User Support, https://github.com/Krishvraman/napari-SAMV2/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
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"
Requires-Dist: numpy; extra == "testing"
Dynamic: license-file

# napari-SAMV2

Napari plugin to use segment anything version 2.1 models from Meta.

Plugin made for segmenting 3d volumetric data or 3d time series data.

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

## Installation

The plugin requires the following pre-requisite to be installed :

1. Python and pytorch versions

python>=3.10,torch>=2.5.1 and torchvision>=0.20.1 required

To install pytorch with your respective OS please visit - https://pytorch.org/get-started/locally/

2. SAM v2 installation from meta

Please refer https://github.com/facebookresearch/sam2

3. Install napari

python -m pip install "napari[all]"

Following is a sample conda environment installation with the above pre-req 

    conda create -n samv2_env python=3.10
    conda activate samv2_env
    pip3 install torch torchvision

    git clone https://github.com/facebookresearch/sam2.git && cd sam2
    pip install -e .

    python -m pip install "napari[all]"

    pip install napari-SAMV2


## Usage

Middle mouse click - positive point or keyboard shortcut "a"

Ctrl + Middle mouse click - negative point or keyboard shortcut "n"

Time Series Segmentation :

![samv2_time_series_demo](https://github.com/user-attachments/assets/078ca2bb-3016-4257-ac7c-c3cde8f9d125)



Volume Segmentation :

![samv2_volume_segmentation](https://github.com/user-attachments/assets/af05fcc4-a60d-44e8-ae05-70764d96e828)



Reference :

Example Data in the demo videos are from,

Cell tracking challenge - https://celltrackingchallenge.net/ 

and

FlyEM project - https://www.janelia.org/project-team/flyem/hemibrain


## License

Distributed under the terms of the [BSD-3] license,
"napari-SAMV2" 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/Krishvraman/napari-SAMV2/issues

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