Connectivity Explorer

A free, browser-based interactive 3D viewer for cortical neuron connectivity - no installation or login required. Pick a source neuron, sample its synaptic targets, and explore their skeletons and synapse locations in real time, then continue your analysis directly in Neuroglancer.

Data is from the MICrONS cortical column dataset (v1718): ~1,300 neurons and ~146K intrinsic synapses. Faint gray skeletons in the background are neurons from the 1 mm³ volume outside the column, shown for spatial context.

Demo.mp4

Getting Started

git clone https://github.com/deangeckt/connectivity_explorer.git
cd connectivity_explorer
npm install
npm start

The app will open at http://localhost:3000.

Local Development

npm start      # development server with hot reload
npm run build  # production bundle

Citation

If you use Connectivity Explorer in your work, please cite:

@software{geckt2026neurons,
  author  = {Geckt, Dean},
  title   = {Connectivity Explorer: Interactive 3D Browser for Cortical Neuron Connectivity},
  year    = {2026},
  url     = {https://github.com/deangeckt/connectivity_explorer}
}

Acknowledgments

• Data provided by the MICrONS Project - a large-scale electron-microscopy reconstruction of a cortical column from mouse visual cortex.

• This is a fork of my previous open-source online-tool: the SWC Editor, turned, with the help of Claude to this Explorer.