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.
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
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