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README.md

Documentation Status Build Status Coverage Status Binder

NAVis is a Python 3 (3.6 or later) library for Neuron Analysis and Visualization with focus on hierarchical tree-like neuron data.

Documentation

NAVis is on ReadTheDocs.

Features

  • fetch data directly from neuprint, insectbraindb or neuromorpho
  • SWC import
  • interactive 2D (matplotlib) and 3D (vispy or plotly) plotting of neurons
  • virtual neuron surgery: cutting, pruning, rerooting
  • implements NBLAST (Costa et al., 2016)
  • clustering (e.g. by connectivity or synapse placement)
  • interface with Blender3D
  • interface with R neuron libraries: e.g. nat, rcatmaid, elmr
  • support for affine, HDF5, CMTK and thin plate spine transforms

Getting started

See the documentation for detailed installation instructions, tutorials and examples. For the impatient:

pip3 install navis

Alternatively click on the launch binder badge above to try out navis hosted by mybinder!

NAVis & friends

NAVis comes with batteries included but is also highly extensible. Some libraries built on top of NAVis:

  • flybrains provides templates and transforms to use with navis
  • pymaid pulls and pushes data to/from CATMAID servers
  • fafbseg contains tools to work with autosegmented data for the FAFB EM dataset

License

This code is under GNU GPL V3

Acknowledgments

NAVis is inspired by and inherits much of its design from the excellent natverse R packages by Greg Jefferis, Alex Bates, James Manton and others.

References

NAVis implements or provides interfaces with algorithms described in:

  1. Comparison of neurons based on morphology: Neuron. 2016 doi: 10.1016/j.neuron.2016.06.012 NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases. Costa M, Manton JD, Ostrovsky AD, Prohaska S, Jefferis GSXE. link
  2. Comparison of neurons based on connectivity: Science. 2012 Jul 27;337(6093):437-44. doi: 10.1126/science.1221762. The connectome of a decision-making neural network. Jarrell TA, Wang Y, Bloniarz AE, Brittin CA, Xu M, Thomson JN, Albertson DG, Hall DH, Emmons SW. link
  3. Comparison of neurons based on synapse distribution: eLife. doi: 10.7554/eLife.16799 Synaptic transmission parallels neuromodulation in a central food-intake circuit. Schlegel P, Texada MJ, Miroschnikow A, Schoofs A, Hückesfeld S, Peters M, … Pankratz MJ. link
  4. Synapse flow centrality and segregation index: eLife. doi: 10.7554/eLife.12059 Quantitative neuroanatomy for connectomics in Drosophila. Schneider-Mizell CM, Gerhard S, Longair M, Kazimiers T, Li, Feng L, Zwart M … Cardona A. link