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