Repositories list

• navis

  Public
  Python library for analysis of neuroanatomical data.

  visualizationpythonblender+ 17neurosciencetransformsegmentationneuronsswcvolumesskeletons+ 10

  Python

  •

  GNU General Public License v3.0

  •35•107•32•14•Updated Jan 30, 2026Jan 30, 2026

• navis-flybrains

  Public
  Transforms for navis that enable mapping between different Drosophila template brains.

  templatesdrosophilavnc+ 6mirroringbrainregistrationsnavistransformsbridging

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •3•16•5•2•Updated Jan 28, 2026Jan 28, 2026

• fafbseg-py

  Public
  Tools to work with the FlyWire connectome. Fully interoperable with navis.

  googleannotationcave+ 8segmentationbrainflyconnectomenavissynapsesflywire+ 1

  Python

  •

  GNU General Public License v3.0

  •8•19•5•2•Updated Jan 28, 2026Jan 28, 2026

• octarine-navis-plugin

  Public
  Octarine plugin to visualize navis objects

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 13, 2026Jan 13, 2026

• navis-mousebrains

  Public
  Template brains and transforms for mouse brains

  Python

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Jan 4, 2026Jan 4, 2026

• skeletor

  Public
  Extraction of 3D skeletons from meshes.

  pythonskeletonmesh+ 9neuronsvolumesconnectomicsmeshes3dskeletonizationteasar+ 2

  Python

  •

  GNU General Public License v3.0

  •29•250•31•1•Updated Dec 2, 2025Dec 2, 2025

• sparse-cubes

  Public
  Marching cubes for sparse matrices

  voxelcubesmesh+ 4sparsemeshingneuronsmarching

  Python

  •

  GNU General Public License v3.0

  •1•23•1•0•Updated Nov 5, 2025Nov 5, 2025

• pymaid

  Public
  Python library to interface with CATMAID servers. Fully interoperable with navis.

  pythonblender3dneuron+ 3anatomycatmaidnblast

  Python

  •

  GNU General Public License v3.0

  •11•23•36•3•Updated Mar 19, 2025Mar 19, 2025

• neuropython2024

  Public
  Documentation and Material for the 2024 NeuroPython Workshop

  Jupyter Notebook

  •1•1•0•0•Updated Sep 24, 2024Sep 24, 2024

• fastcore

  Public
  [WIP] Fast core functions for navis re-implemented in Cython.

  similarityconnectivityvertex+ 1connectome

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •2•1•3•1•Updated Sep 16, 2024Sep 16, 2024

• .github

  Public
  0•1•0•0•Updated Apr 6, 2023Apr 6, 2023

• connectomes

  Public
  [WIP] Unified interface to various backends used for hosting connectomes in the cloud.

  Python

  •

  GNU General Public License v3.0

  •1•6•3•3•Updated Oct 7, 2022Oct 7, 2022

• navis-pipelines

  Public
  Run navis pipelines described by YAML files.

  GNU General Public License v3.0

  •0•1•0•0•Updated Sep 2, 2022Sep 2, 2022

• navis-nblast-gpu

  Public
  NBLAST running on the GPU using PyTorch [WIP]

  Python

  •

  GNU General Public License v3.0

  •0•3•0•0•Updated Jul 31, 2022Jul 31, 2022

• navis-nblast-large

  Public
  Implementation of NBLAST for large datasets

  neuronslarge-scalenblast

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 23, 2022May 23, 2022

• pymaid_template

  Public
  A starter kit for people using python-catmaid for neuronal analysis

  Python

  •

  The Unlicense

  •0•0•0•0•Updated Feb 21, 2022Feb 21, 2022

• navis-nsim

  Public
  Interface between navis and the NEURON simulator

  GNU General Public License v3.0

  •0•0•0•0•Updated Sep 20, 2021Sep 20, 2021