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Logan Grosenick
Stanford University

Acquisition, creation, & analysis of 4D light fields with applications to calcium imaging & optogenetics

Wednesday 23rd of May 2012 at 12:00pm
560 Evans

In Light Field Microscopy (LFM), images can be computationally refocused after they are captured [1]. This permits acquiring focal stacks and reconstructing volumes from a single camera frame. In Light Field Illumination (LFI), the same ideas can be used to create an illumination system that can deliver focused light to any position in a volume without moving optics, and these two devices (LFM/LFI) can be used together in the same system [2]. So far, these imaging and illumination systems have largely been used independently in proof-of-concept experiments [1,2]. In this talk I will discuss applications of a combined scanless volumetric imaging and volumetric illumination system applied to 4D calcium imaging and photostimulation of neurons in vivo and in vitro. The volumes resulting from these methods are large (>500,000 voxels per time point), collected at 10-100 frames per second, and highly correlated in space and time. Analyzing such data has required the development and application of machine learning methods appropriate to large, sparse, nonnegative data, as well as the estimation of neural graphical models from calcium transients. This talk will cover the reconstruction and creation of volumes in a microscope using Light Fields [1,2], and the current state-of-the-art for analyzing these large volumes in the context of calcium imaging and optogenetics. [1] M. Levoy, R. Ng, A. Adams, M. Footer, and M. Horowitz. Light Field Microscopy. ACM Transactions on Graphics 25(3), Proceedings of SIGGRAPH 2006. [2] M. Levoy, Z. Zhang, and I. McDowall. Recording and controlling the 4D light field in a microscope. Journal of Microscopy, Volume 235, Part 2, 2009, pp. 144-162. Cover article. BIO: Logan received bachelors degrees with honors in Biology and Psychology from Stanford, and a Masters in Statistics from Stanford. He is a Ph.D. candidate in the Neurosciences Program working in the labs of Karl Deisseroth and Patrick Suppes, and a trainee at the Stanford Center for Mind, Brain, and Computation. He is interested in developing and applying novel computational imaging and machine learning techniques in order to observe, control, and understand neuronal circuit dynamics.


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