napari-blender 1.0.1

A plug-in to help visualize and analyze organoid segmentation using Blender

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/

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

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 onStackOverflow.

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.