Computational toolbox for large scale Calcium Imaging Analysis
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.
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, (11)15:846-847, 2018.
D. G. C. Hildebrand, M. Cicconet, R. M. Torres, W. Choi, T. M. Quan, J. Moon, A. W. Wetzel, A. Scott Champion, B. J. Graham, O. Randlett, G. S. Plummer, R. Portugues, I. H. Bianco, S. Saalfeld, A. D. Baden, K. Lillaney, R. Burns, J. T. Vogelstein, A. F. Schier, W. C. A. Lee, W. K. Jeong, J. W. Lichtman, and F. Engert. Whole-brain serial-section electron microscopy in larval zebrafish. Nature, (7654)545:345-349, 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.