napari-process-points-and-surfaces

Process and analyze surfaces using open3d and vedo in napari

    Workflow step:
    ClusteringDistribution-based clustering
    VisualizationImage visualisationSurface rendering
    Image annotationSparse image annotationLandmark assignment
    Image SegmentationCell segmentation

View project data

License PyPI Python Version tests codecov Development Status napari hub

Process and analyze surfaces using open3d and vedo in napari.

Usage

You find a couple of surface generation, smoothing and analysis functions in the menu Tools > Surfaces and Tools > Points. For detailed explanation of the underlying algorithms, please refer to the open3d documentation. Some code snippets and the knot example data have been taken from the open3d project which is MIT licensed and from the vedo documentation which is MIT licensed. The Standford Bunny example dataset has been taken from the The Stanford 3D Scanning Repository.

For processing meshes in Python scripts, see the demo notebook. There you also learn how this screenshot is made:

img.png

For performing quantitative measurements of meshes in Python scripts, see the demo notebook. There you also learn how this screenshot is made:

img.png

Installation

You can install napari-process-points-and-surfaces via pip:

pip install napari-process-points-and-surfaces

See also

There are other napari plugins with similar / overlapping functionality

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-process-points-and-surfaces" is free and open source software

Issues

If you encounter any problems, please create a thread on image.sc along with a detailed description and tag @haesleinhuepf.

Version:

  • 0.3.1

Release date:

  • 17 June 2022

First released:

  • 05 February 2022

License:

  • BSD-3-Clause

Supported data:

  • Information not submitted

GitHub activity:

  • Stars: 5
  • Forks: 1
  • Issues + PRs: 5

Python versions supported:

Operating system:

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • numpy
  • napari
  • napari-tools-menu (>=0.1.14)
  • napari-time-slicer (>=0.4.5)
  • napari-workflows (>=0.2.3)
  • open3d
  • ipyvtklink
  • vedo

Sign up to receive updates