☆ 4.4 Review

Multiregion neuronal activity: the forest and the trees

NATURE REVIEWS NEUROSCIENCE (2022)

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Article Biochemistry & Molecular Biology

Fluorescence imaging of large-scale neural ensemble dynamics

Tony Hyun Kim et al.

Summary: Recent advances in fluorescence imaging have allowed neuroscientists to observe the dynamics of individual neurons over extended durations. Progress in fluorescent indicators, genetic methods, chronic animal preparations, and microscopes have contributed to the study of brain function and the development of non-human primate models.

CELL (2022)

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Article Biochemistry & Molecular Biology

Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine

Koichiro E. Kishi et al.

Summary: ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, has opened new possibilities in optogenetics with its unique properties. The cryo-EM structure of ChRmine, revealed at 2.0A resolution, uncovers architectural features distinct from other channelrhodopsins and lays the foundation for the creation of new channelrhodopsins for various biological applications.

CELL (2022)

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Article Neurosciences

The importance of accounting for movement when relating neuronal activity to sensory and cognitive processes

Edward Zagha et al.

Summary: Recent studies have found that movement-related activity is present throughout the mouse brain, including early sensory areas. Failing to consider movement when interpreting neuronal function may lead to misattributing activity to other processes. Functional couplings between movement and other activities make it difficult to fully isolate sensory, motor, and cognitive-related activity.

JOURNAL OF NEUROSCIENCE (2022)

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Article Neurosciences

Large-scale neural recordings with single neuron resolution using Neuropixels probes in human cortex

Angelique C. Paulk et al.

Summary: Neuropixels probes allow for simultaneous recordings from more than 200 cortical neurons in human participants during neurosurgical procedures. This technology provides valuable insights into human cognition and pathology.

NATURE NEUROSCIENCE (2022)

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Large-scale neural recordings call for new insights to link brain and behavior

Anne E. Urai et al.

Summary: Neuroscientists have the ability to measure activity from more neurons using emerging tools and technologies, posing challenges to traditional theoretical frameworks and providing new insights. Connecting brain-wide neural recordings to computation and behavior is a current challenge, with the need for new theoretical approaches to understand brain function. Advances in neural recordings and theory development are expected to contribute to a critical improvement in our understanding of the brain.

NATURE NEUROSCIENCE (2022)

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Article Neurosciences

Context-dependent persistency as a coding mechanism for robust and widely distributed value

Ryoma Hattori et al.

Summary: Task-related information is coded with different persistency across the brain. The coding persistency of action history and value in mice varies across areas, learning phases, and task context, with the highest persistency observed in the retrosplenial cortex of expert mice. Persistent coding enables robust signal coding and distribution in neuronal networks.

NEURON (2022)

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Article Biochemistry & Molecular Biology

Large-scale two-photon calcium imaging in freely moving mice

Weijian Zong et al.

Summary: We developed a miniaturized two-photon microscope (MINI2P) that can perform fast and high-resolution calcium imaging of over 1,000 neurons in multiple planes simultaneously. The microscope allows stable imaging without interfering with the behavior of freely moving mice, and its optical system design improves cell yield and enables recording of a large number of neurons.

CELL (2022)

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Article Multidisciplinary Sciences

Emergent reliability in sensory cortical coding and inter-area communication

Sadegh Ebrahimi et al.

Summary: This study investigated the process of neocortical sensory processing during visual discrimination tasks in mice. The results showed that the neocortex had a specific functional connectivity pattern at rest, which rearranged after the onset of sensory stimulus. A short-lived state with increased inter-area sensory data transmission and sensory encoding redundancy was observed, followed by a more stable visual representation that was robust to day-to-day variations in individual cell responses. In addition, a global fluctuation mode conveyed the upcoming response of the mouse to every area examined. These findings suggest that the neocortex supports sensory performance through dynamic changes in connectivity and robust population codes.

NATURE (2022)

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Article Biochemistry & Molecular Biology

Cell-type-specific population dynamics of diverse reward computations

Emily L. Sylwestrak et al.

Summary: The integration of computational analysis of cellular activity and modern transcriptomic cell typology is crucial for understanding the cellular-level mechanisms underlying brain function and dysfunction. By applying this approach to the study of the habenula, researchers discovered how reward-predictive cues and reward outcomes are encoded in distinct genetically defined neural populations. They used genetically targeted recordings to train a nonlinear dynamical systems model, which revealed activity dynamics consistent with a line attractor. High-density, cell-type-specific electrophysiological recordings and optogenetic perturbation provided further evidence for this model. Reverse-engineering techniques predicted how Tac1(+) cells integrate reward history, and in vivo experimentation confirmed these predictions. This integrated approach allows for data-driven computational models to generate actionable hypotheses for cell-type-specific investigation in biological systems.

CELL (2022)

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Disentangling the flow of signals between populations of neurons

Evren Gokcen et al.

Summary: By utilizing the dimensionality reduction framework called delayed latents across groups (DLAG), we can unravel the intricate flow of signals between populations of neurons and understand how these signals contribute to cortical computation.

NATURE COMPUTATIONAL SCIENCE (2022)

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Article Biotechnology & Applied Microbiology

Deep brain optogenetics without intracranial surgery

Ritchie Chen et al.

Summary: Achieving precise control over specific neural circuits in the deep brain without surgery is possible using ChRmine, enabling behavioral modulation and optogenetic control of neural activity at unprecedented depths.

NATURE BIOTECHNOLOGY (2021)

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Editorial Material Biochemistry & Molecular Biology

From microbial membrane proteins to the mysteries of emotion

Karl Deisseroth

Summary: Following the 2021 Lasker Basic Medical Research Award, Deisseroth reflects on the international collaboration, basic mechanistic and structural discoveries of light-sensitive microbial proteins, the exploration of brain cell function, and the mysteries of psychiatry.

CELL (2021)

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Article Multidisciplinary Sciences

Striatal activity topographically reflects cortical activity

Andrew J. Peters et al.

Summary: The relationship between cortical and striatal activity is precise, topographic, causal, and invariant to behavior. Striatal activity follows a mediolateral gradient related to different behavioral correlates. This consistent and causal mapping of cortical activity in the striatum is not influenced by task engagement.

NATURE (2021)

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Article Multidisciplinary Sciences

Survey of spiking in the mouse visual system reveals functional hierarchy

Joshua H. Siegle et al.

Summary: The study explores the hierarchical organization of functional connectivity in the mammalian visual system, revealing correlations between neural activity and behavioral choice that increase along the hierarchy. This provides a foundation for understanding coding and signal propagation across hierarchically organized cortical and thalamic visual areas.

NATURE (2021)

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Article Biochemistry & Molecular Biology

State-dependent responses to intracranial brain stimulation in a patient with depression

Katherine W. Scangos et al.

Summary: Deep brain stimulation shows promise in treating severe depression, but questions about anatomical targeting remain. A study implanting intracranial electrodes in a depressed patient found rapid, reproducible emotional responses that were context and state dependent, providing proof of concept for personalized, circuit-specific medicine in psychiatry.

NATURE MEDICINE (2021)

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Article Neurosciences

The sensory representation of causally controlled objects

Kelly B. Clancy et al.

Summary: The intentional control over external objects is influenced by sensory experience. Through a BMI task with mice, it was shown that brain areas can be rapidly reconfigured to exert control over a cursor in a sensory-feedback-dependent manner. The higher visual cortex is more engaged when expert animals control the cursor.

NEURON (2021)

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A multimodal cell census and atlas of the mammalian primary motor cortex

Edward M. Callaway et al.

Summary: This study presents a multimodal cell census and atlas of the mammalian primary motor cortex, integrating various molecular and spatial information to reveal a unified genetic landscape of cortical cell types. The results establish a mechanistic framework of neuronal cell-type organization by linking molecular genetic information with phenotypic properties.

NATURE (2021)

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Article Multidisciplinary Sciences

Genetic dissection of the glutamatergic neuron system in cerebral cortex

Katherine S. Matho et al.

Summary: The study established genetic strategies and tools to dissect and fate-map subpopulations of pyramidal neurons based on their developmental and molecular programs. Through combinatorial strategies, subsets of pyramidal neurons defined by developmental origin, marker expression, anatomical location, and projection targets can be targeted for viral access. These strategies provide an experimental framework for understanding the hierarchical organization and developmental trajectory of subpopulations of pyramidal neurons.

NATURE (2021)

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Reset of hippocampal-prefrontal circuitry facilitates learning

Alan J. Park et al.

Summary: Novelty helps reset neural circuits in the brain to promote adaptive learning. Exposure to novelty environment reorganizes neural circuits in mice, enhancing learning-related plasticity, and this effect can be mediated by dopamine D1 receptors.

NATURE (2021)

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Online analysis of microendoscopic 1-photon calcium imaging data streams

Johannes Friedrich et al.

Summary: This study introduces two online algorithms for extracting neuronal activity from streaming microendoscopic data, addressing the issues of high memory and computing requirements in previous methods. The algorithms provide fast and scalable analysis of data, enabling real-time processing and new potential for closed-loop experiments in deep brain areas.

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Flexible simultaneous mesoscale two-photon imaging of neural activity at high speeds

Mitchell Clough et al.

Summary: Understanding brain function requires monitoring both local and global brain dynamics, with two-photon imaging presenting trade-offs between imaging area and acquisition speed. The authors introduce Quadroscope, a flexible microscope capable of simultaneously capturing four independently targetable brain regions at video rate across 5 mm field of view, demonstrating the ability to measure calcium activity in the mouse sensorimotor cortex at behaviorally relevant timescales.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Diesel2p mesoscope with dual independent scan engines for flexible capture of dynamics in distributed neural circuitry

Che-Hang Yu et al.

Summary: The Diesel2p system is an open-source system with Dual Independent Enhanced Scan Engines for Large field-of-view Two-Photon imaging, offering subcellular resolution over a large field-of-view. The system demonstrates flexibility and various use cases for calcium imaging of neurons in the living brain.

NATURE COMMUNICATIONS (2021)

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Article Biochemical Research Methods

Through the looking glass: A review of cranial window technology for optical access to the brain

Samuel W. Cramer et al.

Summary: Deciphering neurologic function is a challenging task that involves understanding the neuronal networks and emergent properties. Mechanistic insights into these networks require tools that assess both single neuron activity and mesoscale output simultaneously. The development of cranial window technologies has enabled monitoring neuronal activity from subcellular to mesoscale resolution and future research may focus on evaluating the relative merits of different designs.

JOURNAL OF NEUROSCIENCE METHODS (2021)

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Article Biochemical Research Methods

Miniaturized head-mounted microscope for whole-cortex mesoscale imaging in freely behaving mice

Mathew L. Rynes et al.

Summary: The development of the "mini-mScope" fluorescence microscope allows for whole-cortex imaging in freely behaving mice, enabling the recording of mesoscale calcium activity in various contexts.

NATURE METHODS (2021)

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Article Neurosciences

Multimodal neural recordings with Neuro-FITM uncover diverse patterns of cortical-hippocampal interactions

Xin Liu et al.

Summary: The authors introduced a flexible, insertable, and transparent microelectrode array, Neuro-FITM, for multimodal recordings of cortical and hippocampal activity patterns. They demonstrated that diverse cortical activity patterns accompanied hippocampal sharp-wave ripples, with cortical activation often preceding the ripples. This suggests a selective and diverse interaction between hippocampal and large-scale cortical activity during sharp-wave ripples, underlying various cognitive functions.

NATURE NEUROSCIENCE (2021)

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Article Neurosciences

Mesoscale cortical dynamics reflect the interaction of sensory evidence and temporal expectation during perceptual decision-making

Ivana Orsolic et al.

Summary: The study found that during the decision-making process, sensory evidence activates specific cortical areas, and recruitment of the motor cortex depends on the interaction of sensory evidence and temporal expectation.

NEURON (2021)

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Article Neurosciences

Coordination of escape and spatial navigation circuits orchestrates versatile flight from threats

Weisheng Wang et al.

Summary: This study demonstrates that cholecystokinin-expressing cells in the hypothalamic dorsal premammillary nucleus play a crucial role in controlling context-specific escape behaviors in mice, unlike other nuclei implicated in flight. The dorsal premammillary nucleus is able to influence spatial navigation and escape circuits, leading to versatile flight behaviors.

NEURON (2021)

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Article Multidisciplinary Sciences

Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings

Nicholas A. Steinmetz et al.

Summary: The research introduces the Neuropixels 2.0 probe and newly designed analysis algorithms, enabling high-quality recordings for long time scales in small mammals. Automatic post hoc correction for brain movements allows recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior.

SCIENCE (2021)

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Article Cell Biology

High-fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in vivo

Michael E. Xie et al.

Summary: This study presents an improved signal extraction pipeline that can resolve supra- and subthreshold voltages of neurons in vivo. The method incorporates biophysical and optical constraints, and has been validated with experimental and simulated datasets to demonstrate its effectiveness. Applications to various brain regions and different genetically encoded voltage indicators have been shown.

CELL REPORTS (2021)

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Article Biochemical Research Methods

Neural anatomy and optical microscopy (NAOMi) simulation for evaluating calcium imaging methods

Alexander Song et al.

Summary: This study introduces a new framework NAOMi for evaluating two-photon microscopy methods via computational simulation, providing a powerful tool for neural imaging research. Results show that modern segmentation algorithms perform well in extracting neural signals but may have a higher false positive rate. Comparison of optical setups reveals different designs have varying strengths in image quality and spatial sampling.

JOURNAL OF NEUROSCIENCE METHODS (2021)

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Article Multidisciplinary Sciences

Representational drift in primary olfactory cortex

Carl E. Schoonover et al.

Summary: The study found that although activity in the primary olfactory cortex could discriminate between odorants at any time, the odor-evoked responses drifted over days to weeks. Daily exposure to the same odorant slowed the rate of drift, but when exposure was halted the rate increased again. This instability may be related to the unstructured connectivity of the piriform cortex.

NATURE (2021)

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Article Biochemical Research Methods

High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy

Jeffrey Demas et al.

Summary: Two-photon microscopy has enabled high-resolution imaging of neuroactivity within scattering brain tissue, but there are still tradeoffs between speed and spatiotemporal sampling. Light beads microscopy (LBM) introduces a scalable and spatiotemporally optimal acquisition approach for recording neuroactivity at different scales, offering opportunities for discovering neurocomputations in the mammalian brain.

NATURE METHODS (2021)

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Article Neurosciences

A database and deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging

Peter Rupprecht et al.

Summary: Researchers developed an algorithm for spike inference (CASCADE) based on supervised deep networks, utilizing a large ground truth database to infer absolute spike rates and outperforming existing model-based algorithms. CASCADE optimizes performance for unseen data by resampling ground truth data, matching the respective sampling rate and noise level, without the need for user adjustment of any parameters.

NATURE NEUROSCIENCE (2021)

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Article Biochemical Research Methods

Chronic, cortex-wide imaging of specific cell populations during behavior

Joao Couto et al.

Summary: Measurements of neuronal activity across different brain areas are crucial for understanding the neural correlates of cognitive and motor processes. Wide-field imaging of genetically encoded indicators is a high-throughput, cost-effective, and flexible approach that allows high temporal resolution measurements of specific cell populations and a cortex-wide field of view.

NATURE PROTOCOLS (2021)

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Article Neurosciences

A cerebellar-thalamocortical pathway drives behavioral context-dependent movement initiation

Joshua Dacre et al.

Summary: The study showed how an auditory go cue transforms thalamocortical activity patterns and affects movement initiation, demonstrating the role of the cerebellar-thalamocortical pathway in context-dependent movement initiation.

NEURON (2021)

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Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology

Joshua H. Siegle et al.

Summary: This study compared evoked responses in the visual cortex of awake mice using extracellular electrophysiology and two-photon calcium imaging, finding more responsive neurons in electrophysiology and higher stimulus selectivity in calcium imaging, partially reconciled by applying a spikes-to-calcium forward model.

ELIFE (2021)

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Proceedings Paper Acoustics

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Erdem Varol et al.

Summary: Neuropixels probes provide high temporal and single-cell spatial resolution for studying neuronal voltage signals, but probe shifting during in vivo recordings can lead to inaccuracies in voltage readings and neural activity estimates. A new decentralized registration method is introduced to improve accuracy over previous template-based approaches.

2021 IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH AND SIGNAL PROCESSING (ICASSP 2021) (2021)

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Modeling behaviorally relevant neural dynamics enabled by preferential subspace identification

Omid G. Sani et al.

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