Scalable volumetric imaging for ultrahigh-speed brain mapping at synaptic resolution

Abstract

The speed of high-resolution optical imaging has been a rate-limiting factor for meso-scale mapping of brain structures and functional circuits, which is of fundamental importance for neuroscience research. Here, we describe a new microscopy method of Volumetric Imaging with Synchronized on-the-fly-scan and Readout (VISoR) for high-throughput, high-quality brain mapping. Combining synchronized scanning beam illumination and oblique imaging over cleared tissue sections in smooth motion, the VISoR system effectively eliminates motion blur to obtain undistorted images. By continuously imaging moving samples without stopping, the system achieves high-speed 3D image acquisition of an entire mouse brain within 1.5 hours, at a resolution capable of visualizing synaptic spines. A pipeline is developed for sample preparation, imaging, 3D image reconstruction and quantification. Our approach is compatible with immunofluorescence methods, enabling flexible cell-type specific brain mapping and is readily scalable for large biological samples such as primate brains. Using this system, we examined behaviorally relevant whole-brain neuronal activation in 16 c-Fos-shEGFP mice under resting or forced swimming conditions. Our results indicate the involvement of multiple subcortical areas in stress response. Intriguingly, neuronal activation in these areas exhibits striking individual variability among different animals, suggesting the necessity of sufficient cohort size for such studies.

The nonhuman primate neuroimaging and neuroanatomy project

“…This will demand alignment fidelity of ~50 μ m or better throughout the brain. This may be attainable using promising approaches such as the VISoR method ( Wang et al, 2019 ) that may facilitate high-throughput, high-resolution optical imaging of thick tissue slabs that can be accurately aligned across slabs and repeatedly stained using multiple immunohistochemical markers (e.g., parvalbumin, somatostatin and neurofilament protein SMI-32).…”

Miniature Fluorescence Microscopy for Imaging Brain Activity in Freely-Behaving Animals

“…On a related but different front, we are building up the Nanjing Brain Observatory (NBO) which provides the capability of imaging of brain activities at high throughput. With the generous support of Nanjing Jiangbei New Area government, the NBO is now equipped with more than ten setups of mTPMs of different types, alongside ultrasensitive structured illumination microscope [42] and Volumetric Imaging with Synchronized on-the-fly-scan and Readout (VISoR) [43]. A dozen or so early-bird projects are ongoing through collaborations with experts in cortical working memory, sleep, autism, depression, neural pharmacology, and neuronal regeneration.…”

Cross-Modality Coherent Registration of Whole Mouse Brains

“…Recent advances in high-resolution light microscopy [1][2][3][4][5][6] , tissue clearing 7-13 , sparse labeling techniques 2,14-17 and full morphology neuron tracing methods [18][19][20][21] now make it feasible to map the mammalian whole-brain at single cell resolution [22][23][24] . Large international efforts such as the BRAIN Initiative Cell Census Network (BICCN) 25 , MouseLight project 19 , Allen Mouse Brain Connectivity Atlas 26 and Mouse Connectome project [27][28][29] , are engaged in cell typing, mapping long-range axonal projection and microcircuit connection analyses.…”