Go with the FLOW: visualizing spatiotemporal dynamics in optical widefield calcium imaging

Author:

Linden Nathaniel J.12,Tabuena Dennis R.23,Steinmetz Nicholas A.4,Moody William J.2,Brunton Steven L.5ORCID,Brunton Bingni W.2ORCID

Affiliation:

1. Department of Bioengineering, University of Washington, Seattle, WA 98195-0005, USA

2. Department of Biology, University of Washington, Seattle, WA 98195-0005, USA

3. Graduate Program in Neuroscience, University of Washington, Seattle, WA 98195-0005, USA

4. Department of Biological Structure, University of Washington, Seattle, WA 98195-0005, USA

5. Department of Mechanical Engineering, University of Washington, Seattle, WA 98195-0005, USA

Abstract

Widefield calcium imaging has recently emerged as a powerful experimental technique to record coordinated large-scale brain activity. These measurements present a unique opportunity to characterize spatiotemporally coherent structures that underlie neural activity across many regions of the brain. In this work, we leverage analytic techniques from fluid dynamics to develop a visualization framework that highlights features of flow across the cortex, mapping wavefronts that may be correlated with behavioural events. First, we transform the time series of widefield calcium images into time-varying vector fields using optic flow. Next, we extract concise diagrams summarizing the dynamics, which we refer to as FLOW (flow lines in optical widefield imaging) portraits . These FLOW portraits provide an intuitive map of dynamic calcium activity, including regions of initiation and termination, as well as the direction and extent of activity spread. To extract these structures, we use the finite-time Lyapunov exponent technique developed to analyse time-varying manifolds in unsteady fluids. Importantly, our approach captures coherent structures that are poorly represented by traditional modal decomposition techniques. We demonstrate the application of FLOW portraits on three simple synthetic datasets and two widefield calcium imaging datasets, including cortical waves in the developing mouse and spontaneous cortical activity in an adult mouse.

Funder

Army Research Office

marie sklobdowska-curie fellowship

Human Frontier Science Program

Washington Research Foundation

Air Force Office of Scientific Research

Alfred P. Sloan Foundation

Weill Neurohub

National Institutes of Health

Publisher

The Royal Society

Subject

Biomedical Engineering,Biochemistry,Biomaterials,Bioengineering,Biophysics,Biotechnology

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