Whole-brain functional imaging at cellular resolution using light-sheet microscopy

Abstract

Brain function relies on communication between large populations of neurons across multiple brain areas, a full understanding of which would require knowledge of the time-varying activity of all neurons in the central nervous system. Here we use light-sheet microscopy to record activity, reported through the genetically encoded calcium indicator GCaMP5G, from the entire volume of the brain of the larval zebrafish in vivo at 0.8 Hz, capturing more than 80% of all neurons at single-cell resolution. Demonstrating how this technique can be used to reveal functionally defined circuits across the brain, we identify two populations of neurons with correlated activity patterns. One circuit consists of hindbrain neurons functionally coupled to spinal cord neuropil. The other consists of an anatomically symmetric population in the anterior hindbrain, with activity in the left and right halves oscillating in antiphase, on a timescale of 20 s, and coupled to equally slow oscillations in the inferior olive.

Sensory determinants of behavioral dynamics in Drosophila thermotaxis

“…The Drosophila larva is likely to be the next animal, after C. elegans, that offers a complete wiring diagram of an entire nervous system with synaptic resolution (41). Advances in optical neurophysiology may soon make it possible to record the activities of large ensembles of neurons in the Drosophila larva, as has recently been accomplished in C. elegans and zebrafish larva (42)(43)(44)(45).…”

Connectome Networks: From Cells to Systems

“…Empirical methods for extracting brain network data from structural or functional measurements are continually evolving and represent an area of rapid neurotechnological innovation. Current approaches include the reconstruction of single-cell neuronal morphology and connectivity using electron or light microscopy (e.g., Helmstaedter et al 2013), novel labeling and tract tracing approaches (e.g., Oh et al 2014), large-scale optical recordings (e.g., Ahrens et al 2013), and refinements of noninvasive imaging techniques (e.g., Van Essen et al 2012). …”

Unleashing Optics and Optoacoustics for Developmental Biology

“…By scanning the beam and focusing the sample using a tunable lens, Fahrbach et al [40] were able to image several full 3D stacks of a beating zebrafish heart per second ( Figure 2F,G). Another relevant example of fast scanning in vivo is the approach used in [57] where the authors achieve whole-brain functional imaging in zebrafish ( Figure 2C-E) where the neuronal activity within the brain can be resolved with cellular resolution.…”

“…As examples of specimens being imaged with high quality using light sheet microscopy, we should point out invertebrates such as D. melanogaster [48], C. elegans [58], and T. castaneum [59], and vertebrates such as zebrafish [47,60] (for very useful information regarding zebrafish preparation for laser sheet imaging see [61]). Of particular importance is the work by Ichikawa et al where light sheet microscopy was applied to a developing mouse embryo, given the complexity of keeping a mouse embryo under controlled CO 2 and temperature conditions [62].…”