Imaging volumetric dynamics at high speed in mouse and zebrafish brain with confocal light field microscopy

Abstract

Neural network performs complex computations through coordinating collective neural dynamics that are fast and in three-dimensions. Meanwhile, its proper function relies on its 3D supporting environment, including the highly dynamic vascular system that drives energy and material flow.Better understanding of these processes requires methods to capture fast volumetric dynamics in thick tissue. This becomes challenging due to the trade-off between speed and optical sectioning capability in conventional imaging techniques. Here we present a new imaging method, confocal light field microscopy, to enable fast volumetric imaging deep into brain. We demonstrated the power of this method by recording whole brain calcium transients in freely swimming larval zebrafish and observed behaviorally correlated activities on single neurons during its prey capture. Furthermore, we captured neural activities and circulating blood cells over a volume ⌀ 800 μm x 150 μm at 70 Hz and up to 600 μm deep in the mice brain.

DiLFM: an artifact-suppressed and noise-robust light-field microscopy through dictionary learning

“…S12 ). Compared to other LFM techniques which require scanning 33 or multiview imaging 22 , DiLFM gives an efficient performance-improving solution without any hardware modifications.

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Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light-fields

“…Methods to improve signal extraction in scattering tissue have been demonstrated by computationally extracting fluorescence sources without reconstruction, 15,20,22,[38][39][40] although reconstruction-less signal extraction cannot resolve the propagation of calcium signals throughout spatially extended structures such as dendrites. Combining the principles of confocal microscopy with LFM, 41 selective-volume illumination, 19,42,43 These results demonstrate the capabilities and limitations of two light-field reconstruction algorithms for high SNR calcium fluorescence imaging. The trade-offs described above highlight the importance of adapting the volume reconstruction strategy to the scientific goals and requirements of future neurophysiology experiments.…”

Optimizing Calcium Detection Methods in Animal Systems: A Sandbox for Synthetic Biology

“…Cardenas-Diaz et al were able to characterize candidate genes in vitro in the human EndoC-βH1 cell line by generating a dual reporter to express both an insulin-luciferase fusion protein and a GCaMP6s variant [112]. The slow kinetics, wide dynamic range, and high baseline brightness of GCaMP6s was suitable for studying Ca 2+ flux in β cells with fluorescence microscopy or pan-neuronal expression in mice and zebrafish [86,113]. [98].…”