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.
Work with all kinds of data: skeletons, meshes, dotprops, images.
Run Strahler analysis, cable length, volume, tortuosity and more.
Generate beautiful scientific 2D (matplotlib) and 3D (vispy or plotly) figures.
Smoothing, resampling, skeletonization, meshing and more!
Scalable thanks to out-of-the-box support for multiprocessing.
Cluster your neurons by morphology.
Fully featured transform system to move neurons between brain spaces.
Read and write from/to SWC, NRRD, Neuroglancer’s precomputed format, OBJ, STL and more!
Download neurons straight from Allen’s MICrONS datasets, neuromorpho or neuPrint.
Load neurons into Blender 3D, simulate neurons and networks using NEURON, or use the R natverse library.
Designed to work in Jupyter notebooks, from terminal or as a script.