NAVis - Neuron Analysis and Visualization

NAVis is a Python library for analysis and visualization of neuron morphology. It stands on the shoulders of the excellent natverse for R.

For a brief introduction to the library, please see Quickstart. Visit the installation page to learn how to install the package. You can browse the example gallery and API reference to see what you can do with navis.

NAVis is designed to be highly extensible. Make sure to check out the other libraries in the navis ecosystem.

NAVis is licensed under the GNU GPL v3+ license. The source code is hosted at Github. Feedback, feature requests, bug reports and general questions are very welcome and best placed in a Github issue.

Features

• works in Jupyter notebooks, from terminal or as script

• supports various neuron types: skeletons, meshes, dotprops, voxels

• process neurons: smoothing, resampling, skeletonization, meshing, …

• virtual neuron surgery: cutting, stitching, pruning, rerooting, …

• morphometrics: Strahler analysis, cable length, volume, tortuosity, …

• cluster by morphology (e.g. NBLAST, persistence, form factor) or connectivity

• 2D (matplotlib) and 3D (vispy & plotly) plotting

• transform neurons between template brains

• Python bindings for R natverse library

• load neurons directly from the Allen’s MICrONS datasets, neuromorpho or neuPrint

• simulate neurons and networks using NEURON

• interface with Blender 3D

• import-export from/to SWC, NRRD, Neuroglancer’s precomputed format and more

• scalable thanks to out-of-the-box support for multiprocessing

• highly extensible - see the ecosystem