Package: napari-process-points-and-surfaces
napari-process-points-and-surfaces (nppas)Process and analyze surfaces usingvedoinnapari.The nppas gastruloid example is derived fromAV Luque and JV Veenvliet (2023)which is licensedCC-BYand can be downloaded from here:https://zenodo.org/record/7603081UsageYou find menus for surface generation, smoothing and analysis in the menuTools > SurfacesandTools > Points.
For detailed explanation of the underlying algorithms, please refer to thevedodocumentation.For processing meshes in Python scripts, see thedemo notebook.
There you also learn how this screenshot is made:For performing quantitative measurements of surface in Python scripts, see thedemo notebook.
There you also learn how this screenshot is made:Surface measurements and annotationsUsing the menuTools > 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 menuTools > 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 ashsvbefore 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 menuTools > Measurement tables > Surface quality/annotation to table (nppas)For classifying surface vertices using machine learning, please refer to thenapari APOCdocumentation.Measurement visualizationTo visualize measurements on the surface, just double-click on the table column headers.InstallationYou can installnapari-process-points-and-surfacesvia mamba/conda and pip:mamba install vedo vtk libnetcdf=4.7.4 -c conda-forge
pip install napari-process-points-and-surfacesTroubleshooting: Open3d installationSince version 0.4.0,nppasdoes no longer depend onopen3d.
Some deprecated functions still use Open3d though.
Follow the installation instructions in theopen3d documentationto install it and keep using those functions.
Also consider updating code and no longer using these deprecated functions.
Seerelease notesfor details.See alsoThere are other napari plugins with similar / overlapping functionalitymorphometricsnapari-accelerated-pixel-and-object-classificationnapari-pymeshlabnapari-pyclesperanto-assistantnapari-stressAnd there is software for doing similar things:meshlabparaviewContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,
"napari-process-points-and-surfaces" is free and open source softwareAcknowledgementsSome code snippets and example data were taken from thevedoandopen3drepositories and documentation. Seethirdparty licensesfor licensing details.
The Standford Bunny example dataset has been taken fromThe Stanford 3D Scanning Repository.
The nppas gastruloid example is derived fromAV Luque and JV Veenvliet (2023)which is licensedCC-BYand can be downloaded from here:https://zenodo.org/record/7603081IssuesIf you encounter any problems, please create a thread onimage.scalong with a detailed description and tag@haesleinhuepf.