Process and analyze surfaces using open3d and vedo in napari
You find menus for surface generation, smoothing and analysis in the menu
Tools > Surfaces and
Tools > Points.
For detailed explanation of the underlying algorithms, please refer to the vedo documentation.
For processing meshes in Python scripts, see the demo notebook. There you also learn how this screenshot is made:
For performing quantitative measurements of surface in Python scripts, see the demo notebook. There you also learn how this screenshot is made:
Surface measurements and annotations
Using the menu
Tools > Measurement tables > Surface quality table (vedo, nppas) you can derive quantiative measurements of
the vertices in a given surface layer.
To differentiate regions when analyzing those measurements it is recommended to use the menu
Tools > Surfaces > Annotate surface manually (nppas)
after measurements have been made. This tool allows you to draw annotation label values on the surface.
It is recommended to do activate a colorful colormap such as
hsv before starting to draw annotations.
Furthermore, set the maximum of the contrast limit range to the number of regions you want to annotate + 1.
Annotations can be drawn as freehand lines and circles.
After measurements and annotations were done, you can save the annotation in the same measurement table using the menu
Tools > Measurement tables > Surface quality/annotation to table (nppas)
For classifying surface vertices using machine learning, please refer to the napari APOC documentation.
To visualize measurements on the surface, just double-click on the table column headers.
You can install
napari-process-points-and-surfaces via mamba/conda and pip:
mamba install vedo vtk libnetcdf=4.7.4 -c conda-forge
pip install napari-process-points-and-surfaces
Troubleshooting: Open3d installation
Since version 0.4.0,
nppas does no longer depend on open3d.
Some deprecated functions still use Open3d though.
Follow the installation instructions in the open3d documentation to install it and keep using those functions.
Also consider updating code and no longer using these deprecated functions.
See release notes for details.
There are other napari plugins with similar / overlapping functionality
And there is software for doing similar things:
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.
Distributed under the terms of the BSD-3 license, "napari-process-points-and-surfaces" is free and open source software
Some code snippets and example data were taken from the vedo and open3d repositories and documentation. See thirdparty licenses for licensing details. The Standford Bunny example dataset has been taken from The Stanford 3D Scanning Repository. The nppas gastruloid example is derived from AV Luque and JV Veenvliet (2023) which is licensed CC-BY and can be downloaded from here: https://zenodo.org/record/7603081
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