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Carmi O, Gross A, Ivzan N, Franca LL, Farah N, Zalevsky Z, Mandel Y. Evaluation and Optimization of Methods for Generating High-Resolution Retinotopic Maps Using Visual Cortex Voltage-Sensitive Dye Imaging. Front Cell Neurosci 2021; 15:713538. [PMID: 34621157 PMCID: PMC8490879 DOI: 10.3389/fncel.2021.713538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/05/2021] [Indexed: 11/24/2022] Open
Abstract
The localization and measurement of neuronal activity magnitude at high spatial and temporal resolution are essential for mapping and better understanding neuronal systems and mechanisms. One such example is the generation of retinotopic maps, which correlates localized retinal stimulation with the corresponding specific visual cortex responses. Here we evaluated and compared seven different methods for extracting and localizing cortical responses from voltage-sensitive dye imaging recordings, elicited by visual stimuli projected directly on the rat retina by a customized projection system. The performance of these methods was evaluated both qualitatively and quantitatively by means of two cluster separation metrics, namely, the (adjusted) Silhouette Index (SI) and the (adjusted) Davies-Bouldin Index (DBI). These metrics were validated using simulated data, which showed that Temporally Structured Component Analysis (TSCA) outperformed all other analysis methods for localizing cortical responses and generating high-resolution retinotopic maps. The analysis methods, as well as the use of cluster separation metrics proposed here, can facilitate future research aiming to localize specific activity at high resolution in the visual cortex or other brain areas.
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Affiliation(s)
- Ori Carmi
- Faculty of Life Sciences, School of Optometry and Vision Science, Bar-Ilan University, Ramat Gan, Israel.,Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Adi Gross
- Faculty of Life Sciences, School of Optometry and Vision Science, Bar-Ilan University, Ramat Gan, Israel
| | - Nadav Ivzan
- Faculty of Life Sciences, School of Optometry and Vision Science, Bar-Ilan University, Ramat Gan, Israel
| | - Lamberto La Franca
- Faculty of Life Sciences, School of Optometry and Vision Science, Bar-Ilan University, Ramat Gan, Israel.,Department of Ophthalmology Vita-Salute San Raffaele University, Milan, Italy
| | - Nairouz Farah
- Faculty of Life Sciences, School of Optometry and Vision Science, Bar-Ilan University, Ramat Gan, Israel
| | - Zeev Zalevsky
- Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Yossi Mandel
- Faculty of Life Sciences, School of Optometry and Vision Science, Bar-Ilan University, Ramat Gan, Israel.,Bar Ilan's Institute for Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan, Israel
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2
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Omer DB, Fekete T, Ulchin Y, Hildesheim R, Grinvald A. Dynamic Patterns of Spontaneous Ongoing Activity in the Visual Cortex of Anesthetized and Awake Monkeys are Different. Cereb Cortex 2020; 29:1291-1304. [PMID: 29718200 DOI: 10.1093/cercor/bhy099] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/12/2018] [Indexed: 11/14/2022] Open
Abstract
Ongoing internal cortical activity plays a major role in perception and behavior both in animals and humans. Previously we have shown that spontaneous patterns resembling orientation-maps appear over large cortical areas in the primary visual-cortex of anesthetized cats. However, it remains unknown 1) whether spontaneous-activity in the primate also displays similar patterns and 2) whether a significant difference exists between cortical ongoing-activity in the anesthetized and awake primate. We explored these questions by combining voltage-sensitive-dye imaging with multiunit and local-field-potential recordings. Spontaneously emerging orientation and ocular-dominance maps, spanning up to 6 × 6 mm2, were readily observed in anesthetized but not in awake monkeys. Nevertheless, spontaneous correlated-activity involving orientation-domains was observed in awake monkeys. Under both anesthetized and awake conditions, spontaneous correlated-activity coincided with traveling waves. We found that spontaneous activity resembling orientation-maps in awake animals spans smaller cortical areas in each instance, but over time it appears across all of V1. Furthermore, in the awake monkey, our results suggest that the synaptic strength had been completely reorganized including connections between dissimilar elements of the functional architecture. These findings lend support to the notion that ongoing-activity has many more fast switching representations playing an important role in cortical function and behavior.
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Affiliation(s)
- David B Omer
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Fekete
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Yigal Ulchin
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Rina Hildesheim
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Amiram Grinvald
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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3
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Macknik SL, Alexander RG, Caballero O, Chanovas J, Nielsen KJ, Nishimura N, Schaffer CB, Slovin H, Babayoff A, Barak R, Tang S, Ju N, Yazdan-Shahmorad A, Alonso JM, Malinskiy E, Martinez-Conde S. Advanced Circuit and Cellular Imaging Methods in Nonhuman Primates. J Neurosci 2019; 39:8267-8274. [PMID: 31619496 PMCID: PMC6794937 DOI: 10.1523/jneurosci.1168-19.2019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 12/15/2022] Open
Abstract
Novel genetically encoded tools and advanced microscopy methods have revolutionized neural circuit analyses in insects and rodents over the last two decades. Whereas numerous technical hurdles originally barred these methodologies from success in nonhuman primates (NHPs), current research has started to overcome those barriers. In some cases, methodological advances developed with NHPs have even surpassed their precursors. One such advance includes new ultra-large imaging windows on NHP cortex, which are larger than the entire rodent brain and allow analysis unprecedented ultra-large-scale circuits. NHP imaging chambers now remain patent for periods longer than a mouse's lifespan, allowing for long-term all-optical interrogation of identified circuits and neurons over timeframes that are relevant to human cognitive development. Here we present some recent imaging advances brought forth by research teams using macaques and marmosets. These include technical developments in optogenetics; voltage-, calcium- and glutamate-sensitive dye imaging; two-photon and wide-field optical imaging; viral delivery; and genetic expression of indicators and light-activated proteins that result in the visualization of tens of thousands of identified cortical neurons in NHPs. We describe a subset of the many recent advances in circuit and cellular imaging tools in NHPs focusing here primarily on the research presented during the corresponding mini-symposium at the 2019 Society for Neuroscience annual meeting.
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Affiliation(s)
- Stephen L Macknik
- State University of New York Downstate Medical Center, Health Science Center at Brooklyn, New York 11203,
| | - Robert G Alexander
- State University of New York Downstate Medical Center, Health Science Center at Brooklyn, New York 11203
| | - Olivya Caballero
- State University of New York Downstate Medical Center, Health Science Center at Brooklyn, New York 11203
| | - Jordi Chanovas
- State University of New York Downstate Medical Center, Health Science Center at Brooklyn, New York 11203
| | - Kristina J Nielsen
- Zanvyl Krieger Mind/Brain Institute, Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland 21218
| | - Nozomi Nishimura
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853
| | - Chris B Schaffer
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853
| | - Hamutal Slovin
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Amit Babayoff
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Ravid Barak
- The Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Shiming Tang
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, and Peking University-International Data Group-McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Niansheng Ju
- Peking-Tsinghua Center for Life Sciences, School of Life Sciences, and Peking University-International Data Group-McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Azadeh Yazdan-Shahmorad
- Department of Bioengineering, University of Washington, Seattle, Washington 98195
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98195
| | - Jose-Manuel Alonso
- State University of New York, College of Optometry, New York, New York 10036, and
| | | | - Susana Martinez-Conde
- State University of New York Downstate Medical Center, Health Science Center at Brooklyn, New York 11203
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Gross A, Ivzan NH, Farah N, Mandel Y. High-resolution VSDI retinotopic mapping via a DLP-based projection system. BIOMEDICAL OPTICS EXPRESS 2019; 10:5117-5129. [PMID: 31646034 PMCID: PMC6788600 DOI: 10.1364/boe.10.005117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/14/2019] [Accepted: 08/17/2019] [Indexed: 06/10/2023]
Abstract
High-resolution recording of visual cortex activity is an important tool for vision research. Using a customized digital mirror device (DMD) - based system equipped with retinal imaging, we projected visual stimuli directly on the rat retina and recorded cortical responses by voltage-sensitive dye imaging. We obtained robust cortical responses and generated high-resolution retinotopic maps at an unprecedented retinal resolution of 4.6 degrees in the field of view, while further distinguishing between normal and pathological retinal areas. This system is a useful tool for studying the cortical response to localized retinal stimulation and may shed light on various cortical plasticity processes.
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Affiliation(s)
- Adi Gross
- Faculty of Life Sciences, School of Optometry and Vision Science, Bar-Ilan University, Ramat Gan, 5290002, Israel
- These authors equally contributed to this research
| | - Nadav H. Ivzan
- Faculty of Life Sciences, School of Optometry and Vision Science, Bar-Ilan University, Ramat Gan, 5290002, Israel
- These authors equally contributed to this research
| | - Nairouz Farah
- Faculty of Life Sciences, School of Optometry and Vision Science, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Yossi Mandel
- Faculty of Life Sciences, School of Optometry and Vision Science, Bar-Ilan University, Ramat Gan, 5290002, Israel
- Bar Ilan’s Institute for Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan, 5290002, Israel
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Fekete T, Van de Cruys S, Ekroll V, van Leeuwen C. In the interest of saving time: a critique of discrete perception. Neurosci Conscious 2018; 2018:niy003. [PMID: 30042856 PMCID: PMC6007149 DOI: 10.1093/nc/niy003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 01/31/2018] [Accepted: 02/05/2018] [Indexed: 11/13/2022] Open
Abstract
A recently proposed model of sensory processing suggests that perceptual experience is updated in discrete steps. We show that the data advanced to support discrete perception are in fact compatible with a continuous account of perception. Physiological and psychophysical constraints, moreover, as well as our awake-primate imaging data, imply that human neuronal networks cannot support discrete updates of perceptual content at the maximal update rates consistent with phenomenology. A more comprehensive approach to understanding the physiology of perception (and experience at large) is therefore called for, and we briefly outline our take on the problem.
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Affiliation(s)
- Tomer Fekete
- Brain and Cognition Unit, KU Leuven, Tiensestraat 102, Leuven, 3000, Belgium
| | - Sander Van de Cruys
- Brain and Cognition Unit, KU Leuven, Tiensestraat 102, Leuven, 3000, Belgium
| | - Vebjørn Ekroll
- Brain and Cognition Unit, KU Leuven, Tiensestraat 102, Leuven, 3000, Belgium
| | - Cees van Leeuwen
- Brain and Cognition Unit, KU Leuven, Tiensestraat 102, Leuven, 3000, Belgium
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6
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Chemla S, Muller L, Reynaud A, Takerkart S, Destexhe A, Chavane F. Improving voltage-sensitive dye imaging: with a little help from computational approaches. NEUROPHOTONICS 2017; 4:031215. [PMID: 28573154 PMCID: PMC5438098 DOI: 10.1117/1.nph.4.3.031215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/24/2017] [Indexed: 05/29/2023]
Abstract
Voltage-sensitive dye imaging (VSDI) is a key neurophysiological recording tool because it reaches brain scales that remain inaccessible to other techniques. The development of this technique from in vitro to the behaving nonhuman primate has only been made possible thanks to the long-lasting, visionary work of Amiram Grinvald. This work has opened new scientific perspectives to the great benefit to the neuroscience community. However, this unprecedented technique remains largely under-utilized, and many future possibilities await for VSDI to reveal new functional operations. One reason why this tool has not been used extensively is the inherent complexity of the signal. For instance, the signal reflects mainly the subthreshold neuronal population response and is not linked to spiking activity in a straightforward manner. Second, VSDI gives access to intracortical recurrent dynamics that are intrinsically complex and therefore nontrivial to process. Computational approaches are thus necessary to promote our understanding and optimal use of this powerful technique. Here, we review such approaches, from computational models to dissect the mechanisms and origin of the recorded signal, to advanced signal processing methods to unravel new neuronal interactions at mesoscopic scale. Only a stronger development of interdisciplinary approaches can bridge micro- to macroscales.
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Affiliation(s)
- Sandrine Chemla
- Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), UMR-7289 Institut de Neurosciences de la Timone, Marseille, France
| | - Lyle Muller
- Salk Institute for Biological Studies, Computational Neurobiology Laboratory, La Jolla, California, United States
| | - Alexandre Reynaud
- McGill University, McGill Vision Research, Department of Ophthalmology, Montreal, Quebec, Canada
| | - Sylvain Takerkart
- Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), UMR-7289 Institut de Neurosciences de la Timone, Marseille, France
| | - Alain Destexhe
- Unit for Neurosciences, Information and Complexity (UNIC), Centre National de la Recherche Scientifique (CNRS), UPR-3293, Gif-sur-Yvette, France
- The European Institute for Theoretical Neuroscience (EITN), Paris, France
| | - Frédéric Chavane
- Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), UMR-7289 Institut de Neurosciences de la Timone, Marseille, France
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Zhao C, Hata R, Okamura JY, Wang G. Differences in spatial and temporal frequency interactions between central and peripheral parts of the feline area 18. Eur J Neurosci 2016; 44:2635-2645. [PMID: 27529598 DOI: 10.1111/ejn.13372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/14/2016] [Accepted: 08/05/2016] [Indexed: 12/01/2022]
Abstract
The visual system demonstrates significant differences in information processing abilities between the central and peripheral parts of the visual field. Optical imaging based on intrinsic signals was used to investigate the difference in stimulus spatial and temporal frequency interactions related to receptive field eccentricity in the cat area 18. Changing either the spatial or the temporal frequency of grating stimuli had a significant impact on responses in the cortical areas corresponding to the centre of the visual field and more peripheral parts at 10 degrees eccentricity. The cortical region corresponding to the centre of the gaze was tuned to 0.4 cycles per degree (c/deg) for spatial frequency and 2 Hz for temporal frequency. In contrast, the cortical region corresponding to the periphery of the visual field was tuned to a lower spatial frequency of 0.15 c/deg and a higher temporal frequency of 4 Hz. Interestingly, when we simultaneously changed both the spatial frequency and the temporal frequency of the grating stimuli, the responses were significantly different from those estimated with an assumption of independence between the spatial and temporal frequency in the cortical region corresponding to the periphery of the visual field. However, in the cortical area corresponding to the centre of the gaze, spatial frequency showed significant independence from temporal frequency. These properties support the notion of relative specialization of visual information processing for peripheral representations in cortical areas.
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Affiliation(s)
- Chunzhen Zhao
- Department of Information Science and Biomedical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima, 890-0065, Japan.,Laboratory for Cognitive Neuroscience, Weifang Medical University, Weifang, China
| | - Ryosuke Hata
- Department of Information Science and Biomedical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima, 890-0065, Japan
| | - Jun-Ya Okamura
- Department of Information Science and Biomedical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima, 890-0065, Japan
| | - Gang Wang
- Department of Information Science and Biomedical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima, 890-0065, Japan. .,Laboratory for Cognitive Neuroscience, Weifang Medical University, Weifang, China.
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8
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Raguet H, Monier C, Foubert L, Ferezou I, Fregnac Y, Peyré G. Spatially Structured Sparse Morphological Component Separation for voltage-sensitive dye optical imaging. J Neurosci Methods 2015; 257:76-96. [PMID: 26434707 DOI: 10.1016/j.jneumeth.2015.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/23/2015] [Accepted: 09/23/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Voltage-sensitive dye optical imaging is a promising technique for studying in vivo neural assemblies dynamics where functional clustering can be visualized in the imaging plane. Its practical potential is however limited by many artifacts. NEW METHOD We present a novel method, that we call "SMCS" (Spatially Structured Sparse Morphological Component Separation), to separate the relevant biological signal from noise and artifacts. It extends Generalized Linear Models (GLM) by using a set of convex non-smooth regularization priors adapted to the morphology of the sources and artifacts to capture. RESULTS We make use of first order proximal splitting algorithms to solve the corresponding large scale optimization problem. We also propose an automatic parameters selection procedure based on statistical risk estimation methods. COMPARISON WITH EXISTING METHODS We compare this method with blank subtraction and GLM methods on both synthetic and real data. It shows encouraging perspectives for the observation of complex cortical dynamics. CONCLUSIONS This work shows how recent advances in source separation can be integrated into a biophysical model of VSDOI. Going beyond GLM methods is important to capture transient cortical events such as propagating waves.
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Affiliation(s)
- Hugo Raguet
- CNRS and Ceremade, Université Paris-Dauphine, Place du Maréchal De Lattre De Tassigny, 75775 Paris Cedex 16, France.
| | - Cyril Monier
- Unit of Neuroscience, Information and Complexity, CNRS UPR-3293, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
| | - Luc Foubert
- Unit of Neuroscience, Information and Complexity, CNRS UPR-3293, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
| | - Isabelle Ferezou
- Unit of Neuroscience, Information and Complexity, CNRS UPR-3293, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
| | - Yves Fregnac
- Unit of Neuroscience, Information and Complexity, CNRS UPR-3293, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
| | - Gabriel Peyré
- CNRS and Ceremade, Université Paris-Dauphine, Place du Maréchal De Lattre De Tassigny, 75775 Paris Cedex 16, France.
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9
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Nortmann N, Rekauzke S, Onat S, König P, Jancke D. Primary visual cortex represents the difference between past and present. Cereb Cortex 2015; 25:1427-40. [PMID: 24343889 PMCID: PMC4428292 DOI: 10.1093/cercor/bht318] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The visual system is confronted with rapidly changing stimuli in everyday life. It is not well understood how information in such a stream of input is updated within the brain. We performed voltage-sensitive dye imaging across the primary visual cortex (V1) to capture responses to sequences of natural scene contours. We presented vertically and horizontally filtered natural images, and their superpositions, at 10 or 33 Hz. At low frequency, the encoding was found to represent not the currently presented images, but differences in orientation between consecutive images. This was in sharp contrast to more rapid sequences for which we found an ongoing representation of current input, consistent with earlier studies. Our finding that for slower image sequences, V1 does no longer report actual features but represents their relative difference in time counteracts the view that the first cortical processing stage must always transfer complete information. Instead, we show its capacities for change detection with a new emphasis on the role of automatic computation evolving in the 100-ms range, inevitably affecting information transmission further downstream.
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Affiliation(s)
- Nora Nortmann
- Optical Imaging Group, Institut für Neuroinformatik, Ruhr-University Bochum, 44780 Bochum, Germany
- Bernstein Group for Computational Neuroscience, Ruhr-University Bochum, 44780 Bochum, Germany
- Institute of Cognitive Science, University of Osnabrück, 49069 Osnabrück, Germany
| | - Sascha Rekauzke
- Optical Imaging Group, Institut für Neuroinformatik, Ruhr-University Bochum, 44780 Bochum, Germany
- Bernstein Group for Computational Neuroscience, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Selim Onat
- Institute of Cognitive Science, University of Osnabrück, 49069 Osnabrück, Germany
| | - Peter König
- Institute of Cognitive Science, University of Osnabrück, 49069 Osnabrück, Germany
- Department of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Dirk Jancke
- Optical Imaging Group, Institut für Neuroinformatik, Ruhr-University Bochum, 44780 Bochum, Germany
- Bernstein Group for Computational Neuroscience, Ruhr-University Bochum, 44780 Bochum, Germany
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Takerkart S, Katz P, Garcia F, Roux S, Reynaud A, Chavane F. Vobi One: a data processing software package for functional optical imaging. Front Neurosci 2014; 8:2. [PMID: 24478623 PMCID: PMC3901006 DOI: 10.3389/fnins.2014.00002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/04/2014] [Indexed: 11/13/2022] Open
Abstract
Optical imaging is the only technique that allows to record the activity of a neuronal population at the mesoscopic scale. A large region of the cortex (10-20 mm diameter) is directly imaged with a CCD camera while the animal performs a behavioral task, producing spatio-temporal data with an unprecedented combination of spatial and temporal resolutions (respectively, tens of micrometers and milliseconds). However, researchers who have developed and used this technique have relied on heterogeneous software and methods to analyze their data. In this paper, we introduce Vobi One, a software package entirely dedicated to the processing of functional optical imaging data. It has been designed to facilitate the processing of data and the comparison of different analysis methods. Moreover, it should help bring good analysis practices to the community because it relies on a database and a standard format for data handling and it provides tools that allow producing reproducible research. Vobi One is an extension of the BrainVISA software platform, entirely written with the Python programming language, open source and freely available for download at https://trac.int.univ-amu.fr/vobi_one.
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Affiliation(s)
- Sylvain Takerkart
- Institut de Neurosciences de la Timone UMR 7289, CNRS - Aix Marseille Université Marseille, France
| | - Philippe Katz
- Institut de Neurosciences de la Timone UMR 7289, CNRS - Aix Marseille Université Marseille, France ; LabISEN, Vision Department, Institut Supérieur de lElectronique et du Numérique Brest, France
| | - Flavien Garcia
- Institut de Neurosciences de la Timone UMR 7289, CNRS - Aix Marseille Université Marseille, France
| | - Sébastien Roux
- Institut de Neurosciences de la Timone UMR 7289, CNRS - Aix Marseille Université Marseille, France
| | - Alexandre Reynaud
- McGill Vision Research, Department of Ophtalmology, McGill University Montréal, QC, Canada
| | - Frédéric Chavane
- Institut de Neurosciences de la Timone UMR 7289, CNRS - Aix Marseille Université Marseille, France
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