Where atlas, connectome, physiology, and simulation converge into an interactive exploration tool. The visualisation portal is the feedback loop that closes the scientific cycle: build a model, render it, inspect it, find the gaps, refine.

Lesson 04 — Visualization

3D rendering and interactive exploration with navis and plotly:

  • Neuron point clouds — scatter plots of cell body positions, coloured by type
  • Connection matrices — heatmaps of neuropil-to-neuropil connectivity
  • 3D neuropil meshes — surface renderings of the 78 brain regions
  • Interactive HTML exports — explorable in any browser

Lesson 12 — The Digital Twin Portal

The portal philosophy: a model’s limitations are as informative as its successes. The portal exposes:

  • Parameter inspection — every synapse weight, every time constant, traceable to its source
  • Simulation playback — raster plots, firing rate dynamics, population synchrony
  • What-if experiments — perturb a parameter, re-simulate, compare
  • Known gaps — explicitly marking where the model is uncertain or incomplete

Source files: