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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#

  • Polyglot

    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, plotly or k3d) figures.

  • Processing

    Smoothing, pruning, 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 morphology using the various NBLAST variants.

  • 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, the H01 dataset or any NeuroGlancer source.

  • Interfaces

    Load neurons into Blender 3D or simulate neurons and networks using NEURON.

  • ML-ready

    Various utilities to support machine learning: sampling, normalization, augmentation and more.

  • 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