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.
ndreg is a Python package that performs non-linear affine and deformable image registration.
ndex allows exchange of large image volumes with NeuroData
ndwebtools is a web application that provides NeuroData tools for managing and viewing data on NeuroData's spatial database store.
R. Burns et al. A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data. Nature Methods, 2018.
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.