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Stringer C, Pachitariu M. Analysis methods for large-scale neuronal recordings. Science 2024; 386:eadp7429. [PMID: 39509504 DOI: 10.1126/science.adp7429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 09/27/2024] [Indexed: 11/15/2024]
Abstract
Simultaneous recordings from hundreds or thousands of neurons are becoming routine because of innovations in instrumentation, molecular tools, and data processing software. Such recordings can be analyzed with data science methods, but it is not immediately clear what methods to use or how to adapt them for neuroscience applications. We review, categorize, and illustrate diverse analysis methods for neural population recordings and describe how these methods have been used to make progress on longstanding questions in neuroscience. We review a variety of approaches, ranging from the mathematically simple to the complex, from exploratory to hypothesis-driven, and from recently developed to more established methods. We also illustrate some of the common statistical pitfalls in analyzing large-scale neural data.
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Affiliation(s)
- Carsen Stringer
- Howard Hughes Medical Institute (HHMI) Janelia Research Campus, Ashburn, VA, USA
| | - Marius Pachitariu
- Howard Hughes Medical Institute (HHMI) Janelia Research Campus, Ashburn, VA, USA
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2
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Fan S, Dal Monte O, Nair AR, Fagan NA, Chang SWC. Closed-loop microstimulations of the orbitofrontal cortex during real-life gaze interaction enhance dynamic social attention. Neuron 2024; 112:2631-2644.e6. [PMID: 38823391 PMCID: PMC11309918 DOI: 10.1016/j.neuron.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/11/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024]
Abstract
Neurons from multiple prefrontal areas encode several key variables of social gaze interaction. To explore the causal roles of the primate prefrontal cortex in real-life gaze interaction, we applied weak closed-loop microstimulations that were precisely triggered by specific social gaze events. Microstimulations of the orbitofrontal cortex, but not the dorsomedial prefrontal cortex or the anterior cingulate cortex, enhanced momentary dynamic social attention in the spatial dimension by decreasing the distance of fixations relative to a partner's eyes and in the temporal dimension by reducing the inter-looking interval and the latency to reciprocate the other's directed gaze. By contrast, on a longer timescale, microstimulations of the dorsomedial prefrontal cortex modulated inter-individual gaze dynamics relative to one's own gaze positions. These findings demonstrate that multiple regions in the primate prefrontal cortex may serve as functionally accessible nodes in controlling different aspects of dynamic social attention and suggest their potential for a therapeutic brain interface.
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Affiliation(s)
- Siqi Fan
- Department of Psychology, Yale University, New Haven, CT 06520, USA; The Laboratory of Neural Systems, The Rockefeller University, New York, NY 10065, USA
| | - Olga Dal Monte
- Department of Psychology, Yale University, New Haven, CT 06520, USA; Department of Psychology, University of Turin, 10124 Torino, Italy
| | - Amrita R Nair
- Department of Psychology, Yale University, New Haven, CT 06520, USA
| | - Nicholas A Fagan
- Department of Psychology, Yale University, New Haven, CT 06520, USA
| | - Steve W C Chang
- Department of Psychology, Yale University, New Haven, CT 06520, USA; Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA.
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3
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Handa T, Fukai T, Kurikawa T. Single-Trial Representations of Decision-Related Variables by Decomposed Frontal Corticostriatal Ensemble Activity. eNeuro 2024; 11:ENEURO.0172-24.2024. [PMID: 39054055 DOI: 10.1523/eneuro.0172-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/06/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024] Open
Abstract
The frontal cortex-striatum circuit plays a pivotal role in adaptive goal-directed behaviors. However, it remains unclear how decision-related signals are mediated through cross-regional transmission between the medial frontal cortex and the striatum by neuronal ensembles in making decision based on outcomes of past action. Here, we analyzed neuronal ensemble activity obtained through simultaneous multiunit recordings in the secondary motor cortex (M2) and dorsal striatum (DS) in rats performing an outcome-based left-or-right choice task. By adopting tensor component analysis (TCA), a single-trial-based unsupervised dimensionality reduction approach, for concatenated ensembles of M2 and DS neurons, we identified distinct three spatiotemporal neural dynamics (TCA components) at the single-trial level specific to task-relevant variables. Choice-position-selective neural dynamics reflected the positions chosen and was correlated with the trial-to-trial fluctuation of behavioral variables. Intriguingly, choice-pattern-selective neural dynamics distinguished whether the incoming choice was a repetition or a switch from the previous choice before a response choice. Other neural dynamics was selective to outcome and increased within-trial activity following response. Our results demonstrate how the concatenated ensembles of M2 and DS process distinct features of decision-related signals at various points in time. Thereby, the M2 and DS collaboratively monitor action outcomes and determine the subsequent choice, whether to repeat or switch, for action selection.
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Affiliation(s)
- Takashi Handa
- Department of Neurobiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8553, Japan
- Laboratory for Neural Coding and Brain Computing, RIKEN Center for Brain Science, Saitama 351-0198, Japan
| | - Tomoki Fukai
- Laboratory for Neural Coding and Brain Computing, RIKEN Center for Brain Science, Saitama 351-0198, Japan
- Neural Coding and Brain Computing Unit, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan
| | - Tomoki Kurikawa
- Laboratory for Neural Coding and Brain Computing, RIKEN Center for Brain Science, Saitama 351-0198, Japan
- Department of Complex and Intelligent Systems, Future University of Hakodate, Hokkaido 041-8655, Japan
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Ferro D, Cash-Padgett T, Wang MZ, Hayden BY, Moreno-Bote R. Gaze-centered gating, reactivation, and reevaluation of economic value in orbitofrontal cortex. Nat Commun 2024; 15:6163. [PMID: 39039055 PMCID: PMC11263430 DOI: 10.1038/s41467-024-50214-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/03/2024] [Indexed: 07/24/2024] Open
Abstract
During economic choice, options are often considered in alternation, until commitment. Nonetheless, neuroeconomics typically ignores the dynamic aspects of deliberation. We trained two male macaques to perform a value-based decision-making task in which two risky offers were presented in sequence at the opposite sides of the visual field, each followed by a delay epoch where offers were invisible. Surprisingly, during the two delays, subjects tend to look at empty locations where the offers had previously appeared, with longer fixations increasing the probability of choosing the associated offer. Spiking activity in orbitofrontal cortex reflects the value of the gazed offer, or of the offer associated with the gazed empty spatial location, even if it is not the most recent. This reactivation reflects a reevaluation process, as fluctuations in neural spiking correlate with upcoming choice. Our results suggest that look-at-nothing gazing triggers the reactivation of a previously seen offer for further evaluation.
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Affiliation(s)
- Demetrio Ferro
- Center for Brain and Cognition, Universitat Pompeu Fabra, 08002, Barcelona, Spain.
- Department of Information and Communication Technologies, Universitat Pompeu Fabra, 08002, Barcelona, Spain.
| | - Tyler Cash-Padgett
- Department of Neuroscience, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN55455, USA
| | - Maya Zhe Wang
- Department of Neuroscience, Center for Magnetic Resonance Research, University of Minnesota, Minneapolis, MN55455, USA
| | - Benjamin Y Hayden
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rubén Moreno-Bote
- Center for Brain and Cognition, Universitat Pompeu Fabra, 08002, Barcelona, Spain
- Department of Information and Communication Technologies, Universitat Pompeu Fabra, 08002, Barcelona, Spain
- Serra Húnter Fellow Programme, Universitat Pompeu Fabra, Barcelona, Spain
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Stoll FM, Rudebeck PH. Preferences reveal dissociable encoding across prefrontal-limbic circuits. Neuron 2024; 112:2241-2256.e8. [PMID: 38640933 PMCID: PMC11223984 DOI: 10.1016/j.neuron.2024.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 12/04/2023] [Accepted: 03/19/2024] [Indexed: 04/21/2024]
Abstract
Individual preferences for the flavor of different foods and fluids exert a strong influence on behavior. Most current theories posit that preferences are integrated with other state variables in the orbitofrontal cortex (OFC), which is thought to derive the relative subjective value of available options to guide choice behavior. Here, we report that instead of a single integrated valuation system in the OFC, another complementary one is centered in the ventrolateral prefrontal cortex (vlPFC) in macaques. Specifically, we found that the OFC and vlPFC preferentially represent outcome flavor and outcome probability, respectively, and that preferences are separately integrated into value representations in these areas. In addition, the vlPFC, but not the OFC, represented the probability of receiving the available outcome flavors separately, with the difference between these representations reflecting the degree of preference for each flavor. Thus, both the vlPFC and OFC exhibit dissociable but complementary representations of subjective value, both of which are necessary for decision-making.
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Affiliation(s)
- Frederic M Stoll
- Nash Family Department of Neuroscience, Lipschultz Center for Cognitive Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Peter H Rudebeck
- Nash Family Department of Neuroscience, Lipschultz Center for Cognitive Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Sharma D, Lupkin SM, McGinty VB. Orbitofrontal high-gamma reflects spike-dissociable value and decision mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587758. [PMID: 38617349 PMCID: PMC11014579 DOI: 10.1101/2024.04.02.587758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The orbitofrontal cortex (OFC) plays a crucial role in value-based decision-making. While previous research has focused on spiking activity in OFC neurons, the role of OFC local field potentials (LFPs) in decision-making remains unclear. LFPs are important because they can reflect synaptic and subthreshold activity not directly coupled to spiking, and because they are potential targets for less invasive forms of brain-machine interface (BMI). We recorded LFPs and spiking activity using multi-channel vertical probes while monkeys performed a two-option value-based decision-making task. We compared the value- and decision-coding properties of high-gamma range LFPs (HG, 50-150 Hz) to the coding properties of spiking multi-unit activity (MUA) recorded concurrently on the same electrodes. Results show that HG and MUA both represent the values of decision targets, and that their representations have similar temporal profiles in a trial. However, we also identified value-coding properties of HG that were dissociable from the concurrently-measured MUA. On average across channels, HG amplitude increased monotonically with value, whereas the average value encoding in MUA was net neutral. HG also encoded a signal consistent with a comparison between the values of the two targets, a signal which was much weaker in MUA. In individual channels, HG was better able to predict choice outcomes than MUA; however, when simultaneously recorded channels were combined in population-based decoder, MUA provided more accurate predictions than HG. Interestingly, HG value representations were accentuated in channels in or near shallow cortical layers, suggesting a dissociation between neuronal sources of HG and MUA. In summary, we find that HG signals are dissociable from MUA with respect to cognitive variables encoded in prefrontal cortex, evident in the monotonic encoding of value, stronger encoding of value comparisons, and more accurate predictions about behavior. High-frequency LFPs may therefore be a viable - or even preferable - target for BMIs to assist cognitive function, opening the possibility for less invasive access to mental contents that would otherwise be observable only with spike-based measures.
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Affiliation(s)
- Dixit Sharma
- Center for Molecular and Behavioral Neuroscience, Rutgers University – Newark
- Graduate Program in Neuroscience, Rutgers University – Newark
| | - Shira M. Lupkin
- Center for Molecular and Behavioral Neuroscience, Rutgers University – Newark
- Graduate Program in Neuroscience, Rutgers University – Newark
| | - Vincent B. McGinty
- Center for Molecular and Behavioral Neuroscience, Rutgers University – Newark
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Fan S, Dal Monte O, Nair AR, Fagan NA, Chang SWC. Closed-loop microstimulations of the orbitofrontal cortex during real-life gaze interaction enhance dynamic social attention. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572176. [PMID: 38187638 PMCID: PMC10769221 DOI: 10.1101/2023.12.18.572176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The prefrontal cortex is extensively involved in social exchange. During dyadic gaze interaction, multiple prefrontal areas exhibit neuronal encoding of social gaze events and context-specific mutual eye contact, supported by a widespread neural mechanism of social gaze monitoring. To explore causal manipulation of real-life gaze interaction, we applied weak closed-loop microstimulations that were precisely triggered by specific social gaze events to three prefrontal areas in monkeys. Microstimulations of orbitofrontal cortex (OFC), but not dorsomedial prefrontal or anterior cingulate cortex, enhanced momentary dynamic social attention in the spatial dimension by decreasing distance of one's gaze fixations relative to partner monkey's eyes. In the temporal dimension, microstimulations of OFC reduced the inter-looking interval for attending to another agent and the latency to reciprocate other's directed gaze. These findings demonstrate that primate OFC serves as a functionally accessible node in controlling dynamic social attention and suggest its potential for a therapeutic brain interface.
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Affiliation(s)
- Siqi Fan
- Department of Psychology, Yale University, New Haven, CT 06520, USA
- The Rockefeller University, New York, NY 10065, USA
| | - Olga Dal Monte
- Department of Psychology, Yale University, New Haven, CT 06520, USA
- Department of Psychology, University of Turin, 10124 Torino, Italy
| | - Amrita R. Nair
- Department of Psychology, Yale University, New Haven, CT 06520, USA
| | | | - Steve W. C. Chang
- Department of Psychology, Yale University, New Haven, CT 06520, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
- Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
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