It is a major challenge to understand functional neuronal circuits across the whole brain. Existing methods for observing neuronal activity represent a major bottleneck in addressing biological problems. In our lab, we developed Swept Confocally Aligned Planar Excitation (SCAPE) microscopy, which offers the ability to image a large 3D volume (e.g. 1000x800x250um) at speeds exceeding 10 volumes per second. Used with different genetically encoded fluorescent indicators, SCAPE enables us to observe neuronal activity across the whole brain of different small animal models, or a much larger volume of intact cortex/tissue compared to traditional approaches. The unique single objective design and flexible system layout of SCAPE makes it simple to image different samples without complex sample preparation and restraint. During this thesis work, I collaborated with biology and neuroscience labs to develop and optimize a range of novel in-vivo/in-vitro neuroimaging applications using SCAPE microscopy.

In particular, my research has focused on using SCAPE to image freely crawling Drosophila Melanogaster larvae, intact mouse olfactory epithelium, head fixed behaving adult Drosophila, larval zebrafish brain and beating heart, and the neuronal system of behaving C. elegans, all in collaboration with experts in these models from Columbia University and other research institutions. I also developed and optimized different sample preparations and experimental procedures to take full advantage of the high-speed 3D imaging capabilities and flexibility of SCAPE microscopy. Finally, I optimized computational and image analysis techniques for large scale 5D SCAPE imaging datasets, including 3D cell tracking, large scale 3D data motion correction/registration, and cellular level neuronal activity extraction with different dimensionality reduction methods. The experiments I have performed in different animal models have enriched the long-term development of SCAPE by providing valuable feedback for system improvement and dissemination, and pushing the SCAPE design towards a more interchangeable platform with diverse capabilities suitable for routine uses by our collaborators and the wider neuroscience community.