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Python 3 library for Neuron Analysis and Visualization with focus on hierarchical tree-like neuron data.
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README.md

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

Documentation

NAVis is on ReadTheDocs.

Features

  • interactive 2D (matplotlib) and 3D (vispy or plotly) plotting of neurons
  • virtual neuron surgery: cutting, pruning, rerooting
  • clustering methods (e.g. by connectivity or synapse placement)
  • fetch neurons directly from neuromorpho.org
  • Python bindings for R neuron libraries (e.g. nat, rcatmaid, elmr)
  • interfaces with Blender 3D and Cytoscape

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!

License

This code is under GNU GPL V3

TO-DOs

NAVis is a generalization of pymaid and some of the code is still being refactored. Basic functionality is implemented but there are still some TO-DOs:

  • update example notebooks and docs
  • update Cytoscape interface
  • update Blender interface to Blender 2.8
  • write new tests

Acknowledgments

NAVis is inspired by and inherits much of its design from the excellent nat & friends 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
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