Sensory coding and the causal impact of mouse cortex in a visual decision

Zatka-Haas, Peter; Steinmetz, Nicholas A.; Carandini, Matteo; Harris, Kenneth D.

doi:10.7554/elife.63163

Cited by 76 publications

(106 citation statements)

References 79 publications

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“…Although differentiation analysis revealed area-specific and layer-specific differences in responses to unscrambled and phase-scrambled stimuli, our ability to decode stimulus category from neural responses was remarkably similar across areas and layers. These findings are consistent with a growing literature that reveals a dissociation between encoding and function ( Erlich et al, 2015 ; Katz et al, 2016 ; Tsunada et al, 2016 ; Liu and Pack, 2017 ; Jin and Glickfeld, 2020 ; Zatka-Haas et al, 2021 ). The contrast between our ND and decoding results highlights an important distinction: decoding reveals information content, but this information is necessarily measured from the extrinsic perspective ( Tononi, 2004 ; Oizumi et al, 2014 ; Tononi et al, 2016 ; Buzsáki, 2019 ).…”

Section: Discussionsupporting

confidence: 92%

Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex

Mayner

Marshall

Billeh

et al. 2022

eNeuro

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Despite significant progress in understanding neural coding, it remains unclear how the coordinated activity of large populations of neurons relates to what an observer actually perceives. Since neurophysiological differences must underlie differences among percepts, differentiation analysis-quantifying distinct patterns of neurophysiological activity-has been proposed as an "inside-out" approach that addresses this question. This methodology contrasts with "outside-in" approaches such as feature tuning and decoding analyses, which are defined in terms of extrinsic experimental variables. Here we used two-photon calcium imaging in mice of both sexes to systematically survey stimulus-evoked neurophysiological differentiation in excitatory neuronal populations in layers 2/3, 4, and 5 across five visual cortical areas (primary, lateromedial, anterolateral, posteromedial, and anteromedial) in response to naturalistic and phase-scrambled movie stimuli. We find that unscrambled stimuli evoke greater neurophysiological differentiation than scrambled stimuli specifically in layers 2/3 of the anterolateral and anteromedial areas, and that this effect is modulated by arousal state and locomotion. By contrast, decoding performance was far above chance and did not vary substantially across areas and layers. Differentiation also differed within the unscrambled stimulus set, suggesting that differentiation analysis may be used to probe the ethological relevance of individual stimuli. Significance statementMuch is known about how neurons encode stimuli in the visual system, yet it remains unclear how their activity generates conscious percepts. Recent studies have linked differentiation of neural activity to subjective ratings of stimulus "meaningfulness" and the presence of consciousness itself. We systematically surveyed different neuronal populations in mouse visual cortex and showed that activity in layers 2/3 of the anterolateral and anteromedial areas is more 3 differentiated in response to naturalistic movie stimuli compared to meaningless phasescrambled stimuli. Contrariwise, decoding performance was high and did not vary substantially across populations. These findings advance our understanding of functional differences among layers and areas and highlight differentiation analysis as a theoretically-motivated approach that can complement analyses that focus on stimulus encoding.

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Section: Discussionsupporting

confidence: 92%

Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex

Mayner

Marshall

Billeh

et al. 2022

eNeuro

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“…The first data are recordings of spontaneous cortical activity of GCaMP6sexpressing mouse pups during their first 8 postnatal days [38]. The second example is a recording of spontaneous cortical activity in a GCaMP6s-expressing adult mouse [35]. In both examples, 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.…”

Section: Introductionmentioning

confidence: 93%

“…Lastly, we analyse the FLOW portraits of spontaneous cortical activity in a head-fixed, behaving adult mouse [35]. To investigate how FLOW portraits align with an animal's behaviour, we analyse infrared videos of spontaneous facial and limb movements alongside cortical calcium activity.…”

Section: Example 3: Cortical Activity During Spontaneous Movementmentioning

confidence: 99%

“…Adult mouse dataset These experimental procedures were conducted at University College London, UK, according to the UK Animals Scientific Procedures Act (1986) and under personal and project licences granted by the Home Office following appropriate ethics review. The dataset and associated procedures were described previously [35]. In brief, the data were from an adult (30 weeks) male mouse expressing GCaMP6s in excitatory neurons (tetO-GCaMP6s; CaMK2a-tTa genotype [11]).…”

Section: Developing Mouse Datasetsmentioning

confidence: 99%

“…Many experiments choose to use genetically encoded calcium indicators from the GCaMP family to image neural calcium dynamics, which is a proxy for electrical neuronal activity [25][26][27][28]; more generally, the visualization methods we discuss here can be applied to any widefield optical imaging experiment, such as imaging with voltage-sensitive dyes [29,30]. 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.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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

Linden

Tabuena

Steinmetz

et al. 2021

J. R. Soc. Interface.

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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.

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Emotion, motivation, decision-making, the orbitofrontal cortex, anterior cingulate cortex, and the amygdala

Rolls

2023

Brain Struct Funct

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The orbitofrontal cortex and amygdala are involved in emotion and in motivation, but the relationship between these functions performed by these brain structures is not clear. To address this, a unified theory of emotion and motivation is described in which motivational states are states in which instrumental goal-directed actions are performed to obtain rewards or avoid punishers, and emotional states are states that are elicited when the reward or punisher is or is not received. This greatly simplifies our understanding of emotion and motivation, for the same set of genes and associated brain systems can define the primary or unlearned rewards and punishers such as sweet taste or pain. Recent evidence on the connectivity of human brain systems involved in emotion and motivation indicates that the orbitofrontal cortex is involved in reward value and experienced emotion with outputs to cortical regions including those involved in language, and is a key brain region involved in depression and the associated changes in motivation. The amygdala has weak effective connectivity back to the cortex in humans, and is implicated in brainstem-mediated responses to stimuli such as freezing and autonomic activity, rather than in declarative emotion. The anterior cingulate cortex is involved in learning actions to obtain rewards, and with the orbitofrontal cortex and ventromedial prefrontal cortex in providing the goals for navigation and in reward-related effects on memory consolidation mediated partly via the cholinergic system.

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Sensory coding and the causal impact of mouse cortex in a visual decision

Cited by 76 publications

References 79 publications

Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex

Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex

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

Emotion, motivation, decision-making, the orbitofrontal cortex, anterior cingulate cortex, and the amygdala

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