A joint project between NeuroData and Florian Engert's lab. This project aims to create and host an open-source atlas of the zebrafish brain, as well as generate a realistic multiscale circuit model of the larval zebrafish brain. The model will span spatial ranges from the nanoscale at the synaptic level, to local microcircuits, to inter-area connectivity. The ultimate goal will be to infer algorithms defining behavior from behavioral assays.



Computational toolbox for large scale Calcium Imaging Analysis


Performs non-linear affine and deformable image registration.


The deployment of tools which support the Open Connectome Project


D. G. C. Hildebrand et al. Whole-brain serial-section electron microscopy in larval zebrafish. Nature, 2017.

O. Randlett et al. Whole-brain activity mapping onto a zebrafish brain atlas. Nature Methods, 2015.

People on project

Ben Falk
Joshua Vogelstein
Florian Engert
Owen Randlett
Onyeka Nnaemeka


Sensorimotor processing, decision making, and internal states: towards a realistic multiscale circuit model of the larval zebrafish brain