The goal of this project is to develop a software system that allows neuroscientists to test virtual connectivity and activity models in order to understand neural mechanisms underlying stimuli-induced behavior of the zebrafish. The envisioned system lets the user define a neural network and simulation parameters, run the actual simulation and visually inspect and analyze the results, all in an integrated way. This will lead to short model - simulate - inspect cycles, which will allow the user to effectively judge how adjustments at any stage affect the simulation output. Ultimately, this makes it possible to rapidly verify or discard hypothesized circuit and/or activity models.

Related research topics include:
• multi-scale visualization,
• quantitative analysis,
• coupling with an external neural network simulator, and
• visual and quantitative comparison between measured and simulated data.


  • The current stable software version can be downloaded as a Windows executable file from this link.
  • Developers can download the latest version of the source code here.

3D Data

Zebrafish brain regions, created within the Harvard ZBrain project and converted by us to 3D meshes, can be downloaded here.

Additional Material

Below is a short video of the current system showing the anatomically correct zebrafish brain regions in 3D. Please set the quality to 1080p and watch in fullscreen mode: