Zebromes

About

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.

Data

Tools

Computational toolbox for large scale Calcium Imaging Analysis

CalmAn

Performs non-linear affine and deformable image registration.

reg

The deployment of tools which support the Open Connectome Project

Publications

J. T. Vogelstein, E. Perlman, B. Falk, A. Baden, W. Gray Roncal, V. Chandrashekhar, F. Collman, S. Seshamani, J. L. Patsolic, K. Lillaney, M. Kazhdan, R. Hider, D. Pryor, J. Matelsky, T. Gion, P. Manavalan, B. Wester, M. Chevillet, E. T. Trautman, K. Khairy, E. Bridgeford, D. M. Kleissas, D. J. Tward, A. K. Crow, B. Hsueh, M. A. Wright, M. I. Miller, S. J. Smith, R. J. Vogelstein, K. Deisseroth, and R. Burns. A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data. Nature Methods, 2018.

D. G. C. Hildebrand, M. Cicconet, R. M. Torres, W. Choi, T. M. Quan, J. Moon, A. W. Wetzel, A. S. Champion, B. J. Graham, O. Randlett, and Others. Whole-brain serial-section electron microscopy in larval zebrafish. Nature, 2017.

O. Randlett, C. L. Wee, E. A. Naumann, O. Nnaemeka, D. Schoppik, J. E. Fitzgerald, R. Portugues, A. M. Lacoste, C. Riegler, F. Engert, and A. F. Schier. 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

Funding

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