Metadata-Version: 2.1
Name: napari-blender
Version: 1.0.1
Summary: A plug-in to help visualize and analyze organoid segmentation using Blender
Author-email: "Krijn H. van der Steen" <k.h.vandersteen@gmail.com>
License: 
        Mozilla Public License Version 2.0
Project-URL: Bug Tracker, https://github.com/Living-Technologies/napari-blender/issues
Project-URL: Documentation, https://living-technologies.github.io/napari-blender/index.html
Project-URL: Source Code, https://github.com/Living-Technologies/napari-blender
Project-URL: User Support, https://github.com/Living-Technologies/napari-blender/issues
Classifier: Development Status :: 3 - Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: magicgui
Requires-Dist: qtpy
Requires-Dist: scikit-image
Requires-Dist: napari-video
Requires-Dist: tifffile
Requires-Dist: bpy >=4.0.0
Requires-Dist: trimesh
Requires-Dist: opencv-python
Requires-Dist: scipy
Requires-Dist: pathlib
Requires-Dist: mathutils
Requires-Dist: pandas

# napari-blender

napari-blender is a plugin for napari that allows you to render 3D scenes using Blender.

This is a system that combines optical validation of model predictions by having different 3D visualizations and quantitative evaluation. Utilizing Blender’s rendering capabilities for deepening the understanding of nuclei segmentation for users with different levels of expertise. Examples are time-lapse animations (aimed to be generated from label data), opaque ground truth visualizations with solid prediction objects to compare prediction quality optically and 3D images where nuclei are coloured according to their prediction quality. To facilitate meaningful quantitative evaluation, different metrics are calculated for these predictions and displayed within the animation, such as the Jaccard index, Intersection over Union and the F1-score. The emphasis in this system is on operating it with limited technical knowledge, allowing for bridging between researchers and developers; but includes metrics that allow for a deeper understanding of performance for expert users.

Documentation can be found at https://living-technologies.github.io/napari-blender/
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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:
https://github.com/napari/cookiecutter-napari-plugin#getting-started

and review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
-->

## Installation

The installation of `napari-blender` is made easier by the inclusion of a virtual environment containing specified versions of each library. These versions should be followed, since dependencies could otherwise break the build. 

Download the [environment.yml], and navigate to the directory of the file. Install by:

    conda env create -f environment.yml
    conda activate napari-blender-env

Now you can install the plug-in using:

    pip install napari-blender

Note:

In Windows, an error might occur in the installation of the `mathutils` package, stating 'Microsoft Visual C++ 14.0 or greater is required'. A fix can be found on[StackOverflow].


To install latest development version :

    pip install git+https://github.com/Living-Technologies/napari-blender.git

## License

Distributed under the terms of the [Mozilla Public License 2.0] license,
"napari-blender" 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
[environment.yml]: https://github.com/Living-Technologies/napari-blender/blob/main/environment.yml
[StackOverflow]: https://stackoverflow.com/questions/64261546/how-to-solve-error-microsoft-visual-c-14-0-or-greater-is-required-when-inst
[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/Living-Technologies/napari-blender/issues

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