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.
Highlights
Coordinated organization of neural activity among brain regions is believed to serve many crucial roles, including performing specific computations in the cortex [1,2,3] and supporting brain development [4,5,6]; further, its disruption may lead to neurological disease [7,8,9]
We develop a visualization framework to capture the spatiotemporal dynamics of neural activity by extracting field lines in optical widefield imaging, which we call FLOW portraits
The resulting visualization depicts the average approximate finitetime Lyapunov exponent (FTLE) ridges in a recording window to summarize the time-invariant patterns of activity. We refer to this visualization as FLOW portraits because it is designed for compressible vector fields typical of widefield imaging of calcium activity
Summary
Coordinated organization of neural activity among brain regions is believed to serve many crucial roles, including performing specific computations in the cortex [1,2,3] and supporting brain development [4,5,6]; further, its disruption may lead to neurological disease [7,8,9]. Cortical activity has been measured using widefield calcium imaging in a variety of experiments, notably to study perceptual decision making [1,3,31,32,33,34,35], to extract cortical functional connectivity [8,36,37], to characterize cortical activity that organizes brain development [38] and to study the effects of disease in the cortex [7,8,9] In all of these data, it is typical to observe multiple regions activating transiently or in regular succession, with distinct initiation sites and wave-like flows across the fields of view. We demonstrate that FLOW portraits extract meaningful and interpretable outlines of the dominant patterns in the cortical activity that contribute to our understanding of the animals’ developmental and behavioural states
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