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Identification of cellular-activity dynamics across large tissue volumes in the mammalian brain

Logan Grosenick, Michael Broxton, Christina K. Kim, Conor Liston, Ben Poole, Samuel Yang, Aaron Andalman, Edward Scharff, Noy Cohen, Ofer Yizhar, Charu Ramakrishnan, Surya Ganguli, Patrick Suppes, Marc Levoy, Karl Deisseroth
doi: https://doi.org/10.1101/132688
Logan Grosenick
1Department of Bioengineering, Stanford University, Stanford, CA USA
2Center for Mind, Brain, and Computation, Stanford University, Stanford, CA USA
3Neuroscience Program, Stanford University, Stanford, CA USA
4CNC Program, Stanford University, Stanford, CA USA
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Michael Broxton
5Department of Computer Science, Stanford University, Stanford, CA USA
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Christina K. Kim
1Department of Bioengineering, Stanford University, Stanford, CA USA
3Neuroscience Program, Stanford University, Stanford, CA USA
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Conor Liston
1Department of Bioengineering, Stanford University, Stanford, CA USA
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Ben Poole
5Department of Computer Science, Stanford University, Stanford, CA USA
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Samuel Yang
6Department of Electrical Engineering, Stanford University, Stanford, CA USA
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Aaron Andalman
1Department of Bioengineering, Stanford University, Stanford, CA USA
4CNC Program, Stanford University, Stanford, CA USA
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Edward Scharff
4CNC Program, Stanford University, Stanford, CA USA
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Noy Cohen
6Department of Electrical Engineering, Stanford University, Stanford, CA USA
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Ofer Yizhar
1Department of Bioengineering, Stanford University, Stanford, CA USA
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Charu Ramakrishnan
1Department of Bioengineering, Stanford University, Stanford, CA USA
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Surya Ganguli
10Department of Applied Physics, Stanford University, Stanford, CA USA
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Patrick Suppes
9Department of Philosophy, Stanford University, Stanford, CA USA
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Marc Levoy
5Department of Computer Science, Stanford University, Stanford, CA USA
6Department of Electrical Engineering, Stanford University, Stanford, CA USA
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Karl Deisseroth
1Department of Bioengineering, Stanford University, Stanford, CA USA
4CNC Program, Stanford University, Stanford, CA USA
7Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA USA
11Howard Hughes Medical Institute, Stanford University, Stanford, CA USA
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  • For correspondence: deissero@stanford.edu
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Abstract

Tracking the coordinated activity of cellular events through volumes of intact tissue is a major challenge in biology that has inspired significant technological innovation. Yet scanless measurement of the high-speed activity of individual neurons across three dimensions in scattering mammalian tissue remains an open problem. Here we develop and validate a computational imaging approach (SWIFT) that integrates high-dimensional, structured statistics with light field microscopy to allow the synchronous acquisition of single-neuron resolution activity throughout intact tissue volumes as fast as a camera can capture images (currently up to 100 Hz at full camera resolution), attaining rates needed to keep pace with emerging fast calcium and voltage sensors. We demonstrate that this large field-of-view, single-snapshot volume acquisition method—which requires only a simple and inexpensive modification to a standard fluorescence microscope—enables scanless capture of coordinated activity patterns throughout mammalian neural volumes. Further, the volumetric nature of SWIFT also allows fast in vivo imaging, motion correction, and cell identification throughout curved subcortical structures like the dorsal hippocampus, where cellular-resolution dynamics spanning hippocampal subfields can be simultaneously observed during a virtual context learning task in a behaving animal. SWIFT’s ability to rapidly and easily record from volumes of many cells across layers opens the door to widespread identification of dynamical motifs and timing dependencies among coordinated cell assemblies during adaptive, modulated, or maladaptive physiological processes in neural systems.

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Posted May 01, 2017.
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Identification of cellular-activity dynamics across large tissue volumes in the mammalian brain
Logan Grosenick, Michael Broxton, Christina K. Kim, Conor Liston, Ben Poole, Samuel Yang, Aaron Andalman, Edward Scharff, Noy Cohen, Ofer Yizhar, Charu Ramakrishnan, Surya Ganguli, Patrick Suppes, Marc Levoy, Karl Deisseroth
bioRxiv 132688; doi: https://doi.org/10.1101/132688
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Identification of cellular-activity dynamics across large tissue volumes in the mammalian brain
Logan Grosenick, Michael Broxton, Christina K. Kim, Conor Liston, Ben Poole, Samuel Yang, Aaron Andalman, Edward Scharff, Noy Cohen, Ofer Yizhar, Charu Ramakrishnan, Surya Ganguli, Patrick Suppes, Marc Levoy, Karl Deisseroth
bioRxiv 132688; doi: https://doi.org/10.1101/132688

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