Zebrafish Dynamics Platform

An interactive static website for visualizing zebrafish whole-brain neural circuit inference and structure-function fusion dynamics results.

The site contains two main analysis modules:

• Neural Functional Circuit Inference Visualizes inferred directed neural networks in 3D anatomical space from zebrafish calcium imaging data.
• Structure-Function Fusion: Dynamics Inference Presents governing dynamical equations discovered from inferred network structure using both Symbolic Regression and Network-SINDy.

Website

Once GitHub Pages is enabled, the site can be accessed at:

• https://yiting-sun.github.io/zebrafish-dynamics-platform/

Features

• Interactive 3D rendering of inferred neural circuits
• Edge-weight filtering for circuit visualization
• XYZ axis widget and coordinate scale panel
• Dynamics inference comparison across:
  • gaussian_te
  • joint_granger
  • dbn_refine
• Support for two subgraph scales:
  • N = 200
  • N = 500
• Two dynamics inference methods:
  • Symbolic Regression
  • Network-SINDy

Repository Structure

zebrafish-dynamics-platform/
├── index.html
├── README.md
├── .nojekyll
└── data/
    ├── positions.json
    ├── edges_gaussian_te.json
    ├── edges_joint_granger.json
    ├── edges_dbn_refine.json
    ├── network_dynamics_sindy.json
    └── Network_dynamics_sindy.md

Local Preview

Run a local static server from the repository root:

cd zebrafish-dynamics-platform
python3 -m http.server 8000

Then open:

• http://localhost:8000

Do not open index.html directly with file:// when testing data-dependent visualization, because local browser security policies may block fetch() requests to the JSON files.

Methods Included in the Site

Circuit Inference

• Gaussian TE
• Joint Granger
• DBN Refine

Dynamics Inference

• Symbolic Regression Equation discovery from graph-informed neuronal activity features
• Network-SINDy Sparse network dynamics identification with explicit self-dynamics and coupling terms

Technical Notes

• Frontend is implemented as a single static index.html
• 3D rendering uses Three.js
• Equation rendering uses KaTeX
• Styling uses Tailwind CSS via CDN

License

No license has been added yet. If this repository is intended for public academic reuse, a license should be chosen explicitly.