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Neuron Analysis and Visualization#

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


Features - Quickstart - Installation

Features#

  • Polgyglot


    Support for all kinds of neuron types: skeletons, meshes, dotprops and images.

  • Exploration


    Designed to let you explore your data interactively from Jupyter notebooks, terminal or via scripts.

  • Analysis


    Calculate Strahler indices, cable length, volume, tortuosity, NBLAST and many other morphometrics.

  • Visualization


    Generate beautiful, publication-ready 2D (matplotlib) and 3D (octarine, vispy or plotly) figures.

  • Processing


    Smoothing, resampling, skeletonization, meshing and more!

  • Fast


    Uses compiled Rust code under-the-hood and out-of-the-box support for multiprocessing.

  • Clustering


    Cluster your neurons by e.g. morphology using NBLAST.

  • Transforms


    Fully featured transform system to move neurons between brain spaces. We support CMTK, Elastix, landmark-based transforms and more!

  • Import/Export


    Read and write from/to SWC, NRRD, Neuroglancer's precomputed format, OBJ, STL and more!

  • Connected


    Load neurons straight from Allen's MICrONS datasets, neuromorpho, neuPrint or any NeuroGlancer source.

  • Interfaces


    Load neurons into Blender 3D, simulate neurons and networks using NEURON, or use the R natverse library via rpy2.

  • Extensible


    Write your own library built on top of NAVis functions. See our ecosystem for examples.

Check out the Tutorials and API reference to see what you can do with NAVis.

Need help? Use discussions on Github to ask questions!

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