The Experts below are selected from a list of 38376 Experts worldwide ranked by ideXlab platform
Jose M Carmena - One of the best experts on this subject based on the ideXlab platform.
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head mounted microendoscopic Calcium Imaging in dorsal premotor cortex of behaving rhesus macaque
Cell Reports, 2021Co-Authors: Anil Bollimunta, Samantha R Santacruz, Ryan W Eaton, John H Morrison, Karen A Moxon, Jose M CarmenaAbstract:Microendoscopic Calcium Imaging with one-photon miniature microscopes enables unprecedented readout of neural circuit dynamics during active behavior in rodents. In this study, we describe successful application of this technology in the rhesus macaque, demonstrating plug-and-play, head-mounted recordings of cellular-resolution Calcium dynamics from large populations of neurons simultaneously in bilateral dorsal premotor cortices during performance of a naturalistic motor reach task. Imaging is stable over several months, allowing us to longitudinally track individual neurons and monitor their relationship to motor behavior over time. We observe neuronal Calcium dynamics selective for reach direction, which we could use to decode the animal's trial-by-trial motor behavior. This work establishes head-mounted microendoscopic Calcium Imaging in macaques as a powerful approach for studying the neural circuit mechanisms underlying complex and clinically relevant behaviors, and it promises to greatly advance our understanding of human brain function, as well as its dysfunction in neurological disease.
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head mounted microendoscopic Calcium Imaging in dorsal premotor cortex of behaving rhesus macaque
bioRxiv, 2020Co-Authors: Anil Bollimunta, Samantha R Santacruz, Ryan W Eaton, John H Morrison, Karen A Moxon, Jose M Carmena, Jonathan J NassiAbstract:Summary A major effort is now underway across the brain sciences to identify, characterize and manipulate mesoscale neural circuits in order to elucidate the mechanisms underlying sensory perception, cognition and behavior. Optical Imaging technologies, in conjunction with genetically encoded sensors and actuators, serve as important tools toward these goals, allowing access to large-scale genetically defined neuronal populations. In particular, one-photon miniature microscopes, coupled with genetically encoded Calcium indicators and microendoscopic gradient-refractive index (GRIN) lenses, enable unprecedented readout of neural circuit dynamics in cortical and deep subcortical brain regions during active behavior in rodents. This has already led to breakthrough discoveries across a wide array of rodent brain regions and behaviors. However, in order to study the neural circuit mechanisms underlying more complex and clinically relevant human behaviors and cognitive functions, it is crucial to translate this technology to non-human primates. Here, we describe the first successful application of this technology in the rhesus macaque. We identified a viral strategy for robust expression of GCaMP, optimized a surgical protocol for microendoscope GRIN lens insertion, and created a chronic cranial chamber and lens mounting system for Imaging in gyral cortex. Using these methods, we demonstrate the ability to perform plug-and-play, head-mounted recordings of cellular-resolution Calcium dynamics from over 100 genetically-targeted neurons simultaneously in dorsal premotor cortex while the macaque performs a naturalistic motor reach task with the head unrestrained and freely moving. The recorded population of neurons exhibited Calcium dynamics selective to the direction of reach, which we show can be used to decode the animal’s trial-by-trial motor behavior. Recordings were stable over several months, allowing us to longitudinally track large populations of individual neurons and monitor their relationship to motor behavior over time. Finally, we demonstrate the ability to conduct simultaneous, multi-site Imaging in bilateral dorsal premotor cortices, offering an opportunity to study distributed networks underlying complex behavior and cognition. Together, this work establishes head-mounted microendoscopic Calcium Imaging in macaque as a powerful new approach for studying the neural circuit mechanisms underlying complex and clinically relevant behaviors, and promises to greatly advance our understanding of human brain function, as well as its dysfunction in neurological disease. Highlights First demonstration of head-mounted microendoscopic Calcium Imaging in behaving macaque. Surgical protocols developed for preparing the animal for Calcium Imaging, including virus injections to express GCaMP and chronic implantation of a GRIN lens to enable optical access to gyral cortex. Proof of concept plug-and-play Calcium Imaging in behaving macaques with months long stable recording capability allowing populations of individual neurons to be tracked longitudinally. Bilateral Calcium Imaging from dorsal premotor cortex exhibited dynamics selective to the animal’s direction of reach and allowed decoding of the animal’s motor behavior
Pier Luigi Dragotti - One of the best experts on this subject based on the ideXlab platform.
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able an activity based level set segmentation algorithm for two photon Calcium Imaging data
bioRxiv, 2017Co-Authors: Stephanie Reynolds, Therese Abrahamsson, Renaud Schuck, Jesper P Sjostrom, Simon R Schultz, Pier Luigi DragottiAbstract:We present an algorithm for detecting the location of cells from two-photon Calcium Imaging data. In our framework, multiple coupled active contours evolve, guided by a model-based cost function, to identify cell boundaries. An active contour seeks to partition a local region into two subregions, a cell interior and exterior, in which all pixels have maximally ‘similar’ time courses. This simple, local model allows contours to be evolved predominantly independently. When contours are sufficiently close, their evolution is coupled, in a manner that permits overlap. We illustrate the ability of the proposed method to demix overlapping cells on real data. The proposed framework is flexible, incorporating no prior information regarding a cell9s morphology or stereotypical temporal activity, which enables the detection of cells with diverse properties. We demonstrate algorithm performance on a challenging mouse in vitro dataset, containing synchronously spiking cells, and a manually labelled mouse in vivo dataset, on which ABLE achieves a 67.5% success rate.
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able an activity based level set segmentation algorithm for two photon Calcium Imaging data
eNeuro, 2017Co-Authors: Stephanie Reynolds, Therese Abrahamsson, Renaud Schuck, Jesper P Sjostrom, Simon R Schultz, Pier Luigi DragottiAbstract:Abstract We present an algorithm for detecting the location of cells from two-photon Calcium Imaging data. In our framework, multiple coupled active contours evolve, guided by a model-based cost function, to identify cell boundaries. An active contour seeks to partition a local region into two subregions, a cell interior and exterior, in which all pixels have maximally “similar” time courses. This simple, local model allows contours to be evolved predominantly independently. When contours are sufficiently close, their evolution is coupled, in a manner that permits overlap. We illustrate the ability of the proposed method to demix overlapping cells on real data. The proposed framework is flexible, incorporating no prior information regarding a cell’s morphology or stereotypical temporal activity, which enables the detection of cells with diverse properties. We demonstrate algorithm performance on a challenging mouse in vitro dataset, containing synchronously spiking cells, and a manually labelled mouse in vivo dataset, on which ABLE (the proposed method) achieves a 67.5% success rate.
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a finite rate of innovation algorithm for fast and accurate spike detection from two photon Calcium Imaging
Journal of Neural Engineering, 2013Co-Authors: Jon Onativia, Simon R Schultz, Pier Luigi DragottiAbstract:Objective. Inferring the times of sequences of action potentials (APs) (spike trains) from neurophysiological data is a key problem in computational neuroscience. The detection of APs from two-photon Imaging of Calcium signals offers certain advantages over traditional electrophysiological approaches, as up to thousands of spatially and immunohistochemically defined neurons can be recorded simultaneously. However, due to noise, dye buffering and the limited sampling rates in common microscopy configurations, accurate detection of APs from Calcium time series has proved to be a difficult problem. Approach. Here we introduce a novel approach to the problem making use of finite rate of innovation (FRI) theory (Vetterli et al 2002 IEEE Trans. Signal Process. 50 1417‐28). For Calcium transients well fit by a single exponential, the problem is reduced to reconstructing a stream of decaying exponentials. Signals made of a combination of exponentially decaying functions with different onset times are a subclass of FRI signals, for which much theory has recently been developed by the signal processing community. Main results. We demonstrate for the first time the use of FRI theory to retrieve the timing of APs from Calcium transient time series. The final algorithm is fast, non-iterative and parallelizable. Spike inference can be performed in real-time for a population of neurons and does not require any training phase or learning to initialize parameters. Significance. The algorithm has been tested with both real data (obtained by simultaneous electrophysiology and multiphoton Imaging of Calcium signals in cerebellar Purkinje cell dendrites), and surrogate data, and outperforms several recently proposed methods for spike train inference from Calcium Imaging data. (Some figures may appear in colour only in the online journal)
John H Morrison - One of the best experts on this subject based on the ideXlab platform.
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head mounted microendoscopic Calcium Imaging in dorsal premotor cortex of behaving rhesus macaque
Cell Reports, 2021Co-Authors: Anil Bollimunta, Samantha R Santacruz, Ryan W Eaton, John H Morrison, Karen A Moxon, Jose M CarmenaAbstract:Microendoscopic Calcium Imaging with one-photon miniature microscopes enables unprecedented readout of neural circuit dynamics during active behavior in rodents. In this study, we describe successful application of this technology in the rhesus macaque, demonstrating plug-and-play, head-mounted recordings of cellular-resolution Calcium dynamics from large populations of neurons simultaneously in bilateral dorsal premotor cortices during performance of a naturalistic motor reach task. Imaging is stable over several months, allowing us to longitudinally track individual neurons and monitor their relationship to motor behavior over time. We observe neuronal Calcium dynamics selective for reach direction, which we could use to decode the animal's trial-by-trial motor behavior. This work establishes head-mounted microendoscopic Calcium Imaging in macaques as a powerful approach for studying the neural circuit mechanisms underlying complex and clinically relevant behaviors, and it promises to greatly advance our understanding of human brain function, as well as its dysfunction in neurological disease.
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head mounted microendoscopic Calcium Imaging in dorsal premotor cortex of behaving rhesus macaque
bioRxiv, 2020Co-Authors: Anil Bollimunta, Samantha R Santacruz, Ryan W Eaton, John H Morrison, Karen A Moxon, Jose M Carmena, Jonathan J NassiAbstract:Summary A major effort is now underway across the brain sciences to identify, characterize and manipulate mesoscale neural circuits in order to elucidate the mechanisms underlying sensory perception, cognition and behavior. Optical Imaging technologies, in conjunction with genetically encoded sensors and actuators, serve as important tools toward these goals, allowing access to large-scale genetically defined neuronal populations. In particular, one-photon miniature microscopes, coupled with genetically encoded Calcium indicators and microendoscopic gradient-refractive index (GRIN) lenses, enable unprecedented readout of neural circuit dynamics in cortical and deep subcortical brain regions during active behavior in rodents. This has already led to breakthrough discoveries across a wide array of rodent brain regions and behaviors. However, in order to study the neural circuit mechanisms underlying more complex and clinically relevant human behaviors and cognitive functions, it is crucial to translate this technology to non-human primates. Here, we describe the first successful application of this technology in the rhesus macaque. We identified a viral strategy for robust expression of GCaMP, optimized a surgical protocol for microendoscope GRIN lens insertion, and created a chronic cranial chamber and lens mounting system for Imaging in gyral cortex. Using these methods, we demonstrate the ability to perform plug-and-play, head-mounted recordings of cellular-resolution Calcium dynamics from over 100 genetically-targeted neurons simultaneously in dorsal premotor cortex while the macaque performs a naturalistic motor reach task with the head unrestrained and freely moving. The recorded population of neurons exhibited Calcium dynamics selective to the direction of reach, which we show can be used to decode the animal’s trial-by-trial motor behavior. Recordings were stable over several months, allowing us to longitudinally track large populations of individual neurons and monitor their relationship to motor behavior over time. Finally, we demonstrate the ability to conduct simultaneous, multi-site Imaging in bilateral dorsal premotor cortices, offering an opportunity to study distributed networks underlying complex behavior and cognition. Together, this work establishes head-mounted microendoscopic Calcium Imaging in macaque as a powerful new approach for studying the neural circuit mechanisms underlying complex and clinically relevant behaviors, and promises to greatly advance our understanding of human brain function, as well as its dysfunction in neurological disease. Highlights First demonstration of head-mounted microendoscopic Calcium Imaging in behaving macaque. Surgical protocols developed for preparing the animal for Calcium Imaging, including virus injections to express GCaMP and chronic implantation of a GRIN lens to enable optical access to gyral cortex. Proof of concept plug-and-play Calcium Imaging in behaving macaques with months long stable recording capability allowing populations of individual neurons to be tracked longitudinally. Bilateral Calcium Imaging from dorsal premotor cortex exhibited dynamics selective to the animal’s direction of reach and allowed decoding of the animal’s motor behavior
Ryan W Eaton - One of the best experts on this subject based on the ideXlab platform.
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head mounted microendoscopic Calcium Imaging in dorsal premotor cortex of behaving rhesus macaque
Cell Reports, 2021Co-Authors: Anil Bollimunta, Samantha R Santacruz, Ryan W Eaton, John H Morrison, Karen A Moxon, Jose M CarmenaAbstract:Microendoscopic Calcium Imaging with one-photon miniature microscopes enables unprecedented readout of neural circuit dynamics during active behavior in rodents. In this study, we describe successful application of this technology in the rhesus macaque, demonstrating plug-and-play, head-mounted recordings of cellular-resolution Calcium dynamics from large populations of neurons simultaneously in bilateral dorsal premotor cortices during performance of a naturalistic motor reach task. Imaging is stable over several months, allowing us to longitudinally track individual neurons and monitor their relationship to motor behavior over time. We observe neuronal Calcium dynamics selective for reach direction, which we could use to decode the animal's trial-by-trial motor behavior. This work establishes head-mounted microendoscopic Calcium Imaging in macaques as a powerful approach for studying the neural circuit mechanisms underlying complex and clinically relevant behaviors, and it promises to greatly advance our understanding of human brain function, as well as its dysfunction in neurological disease.
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head mounted microendoscopic Calcium Imaging in dorsal premotor cortex of behaving rhesus macaque
bioRxiv, 2020Co-Authors: Anil Bollimunta, Samantha R Santacruz, Ryan W Eaton, John H Morrison, Karen A Moxon, Jose M Carmena, Jonathan J NassiAbstract:Summary A major effort is now underway across the brain sciences to identify, characterize and manipulate mesoscale neural circuits in order to elucidate the mechanisms underlying sensory perception, cognition and behavior. Optical Imaging technologies, in conjunction with genetically encoded sensors and actuators, serve as important tools toward these goals, allowing access to large-scale genetically defined neuronal populations. In particular, one-photon miniature microscopes, coupled with genetically encoded Calcium indicators and microendoscopic gradient-refractive index (GRIN) lenses, enable unprecedented readout of neural circuit dynamics in cortical and deep subcortical brain regions during active behavior in rodents. This has already led to breakthrough discoveries across a wide array of rodent brain regions and behaviors. However, in order to study the neural circuit mechanisms underlying more complex and clinically relevant human behaviors and cognitive functions, it is crucial to translate this technology to non-human primates. Here, we describe the first successful application of this technology in the rhesus macaque. We identified a viral strategy for robust expression of GCaMP, optimized a surgical protocol for microendoscope GRIN lens insertion, and created a chronic cranial chamber and lens mounting system for Imaging in gyral cortex. Using these methods, we demonstrate the ability to perform plug-and-play, head-mounted recordings of cellular-resolution Calcium dynamics from over 100 genetically-targeted neurons simultaneously in dorsal premotor cortex while the macaque performs a naturalistic motor reach task with the head unrestrained and freely moving. The recorded population of neurons exhibited Calcium dynamics selective to the direction of reach, which we show can be used to decode the animal’s trial-by-trial motor behavior. Recordings were stable over several months, allowing us to longitudinally track large populations of individual neurons and monitor their relationship to motor behavior over time. Finally, we demonstrate the ability to conduct simultaneous, multi-site Imaging in bilateral dorsal premotor cortices, offering an opportunity to study distributed networks underlying complex behavior and cognition. Together, this work establishes head-mounted microendoscopic Calcium Imaging in macaque as a powerful new approach for studying the neural circuit mechanisms underlying complex and clinically relevant behaviors, and promises to greatly advance our understanding of human brain function, as well as its dysfunction in neurological disease. Highlights First demonstration of head-mounted microendoscopic Calcium Imaging in behaving macaque. Surgical protocols developed for preparing the animal for Calcium Imaging, including virus injections to express GCaMP and chronic implantation of a GRIN lens to enable optical access to gyral cortex. Proof of concept plug-and-play Calcium Imaging in behaving macaques with months long stable recording capability allowing populations of individual neurons to be tracked longitudinally. Bilateral Calcium Imaging from dorsal premotor cortex exhibited dynamics selective to the animal’s direction of reach and allowed decoding of the animal’s motor behavior
Karen A Moxon - One of the best experts on this subject based on the ideXlab platform.
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head mounted microendoscopic Calcium Imaging in dorsal premotor cortex of behaving rhesus macaque
Cell Reports, 2021Co-Authors: Anil Bollimunta, Samantha R Santacruz, Ryan W Eaton, John H Morrison, Karen A Moxon, Jose M CarmenaAbstract:Microendoscopic Calcium Imaging with one-photon miniature microscopes enables unprecedented readout of neural circuit dynamics during active behavior in rodents. In this study, we describe successful application of this technology in the rhesus macaque, demonstrating plug-and-play, head-mounted recordings of cellular-resolution Calcium dynamics from large populations of neurons simultaneously in bilateral dorsal premotor cortices during performance of a naturalistic motor reach task. Imaging is stable over several months, allowing us to longitudinally track individual neurons and monitor their relationship to motor behavior over time. We observe neuronal Calcium dynamics selective for reach direction, which we could use to decode the animal's trial-by-trial motor behavior. This work establishes head-mounted microendoscopic Calcium Imaging in macaques as a powerful approach for studying the neural circuit mechanisms underlying complex and clinically relevant behaviors, and it promises to greatly advance our understanding of human brain function, as well as its dysfunction in neurological disease.
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head mounted microendoscopic Calcium Imaging in dorsal premotor cortex of behaving rhesus macaque
bioRxiv, 2020Co-Authors: Anil Bollimunta, Samantha R Santacruz, Ryan W Eaton, John H Morrison, Karen A Moxon, Jose M Carmena, Jonathan J NassiAbstract:Summary A major effort is now underway across the brain sciences to identify, characterize and manipulate mesoscale neural circuits in order to elucidate the mechanisms underlying sensory perception, cognition and behavior. Optical Imaging technologies, in conjunction with genetically encoded sensors and actuators, serve as important tools toward these goals, allowing access to large-scale genetically defined neuronal populations. In particular, one-photon miniature microscopes, coupled with genetically encoded Calcium indicators and microendoscopic gradient-refractive index (GRIN) lenses, enable unprecedented readout of neural circuit dynamics in cortical and deep subcortical brain regions during active behavior in rodents. This has already led to breakthrough discoveries across a wide array of rodent brain regions and behaviors. However, in order to study the neural circuit mechanisms underlying more complex and clinically relevant human behaviors and cognitive functions, it is crucial to translate this technology to non-human primates. Here, we describe the first successful application of this technology in the rhesus macaque. We identified a viral strategy for robust expression of GCaMP, optimized a surgical protocol for microendoscope GRIN lens insertion, and created a chronic cranial chamber and lens mounting system for Imaging in gyral cortex. Using these methods, we demonstrate the ability to perform plug-and-play, head-mounted recordings of cellular-resolution Calcium dynamics from over 100 genetically-targeted neurons simultaneously in dorsal premotor cortex while the macaque performs a naturalistic motor reach task with the head unrestrained and freely moving. The recorded population of neurons exhibited Calcium dynamics selective to the direction of reach, which we show can be used to decode the animal’s trial-by-trial motor behavior. Recordings were stable over several months, allowing us to longitudinally track large populations of individual neurons and monitor their relationship to motor behavior over time. Finally, we demonstrate the ability to conduct simultaneous, multi-site Imaging in bilateral dorsal premotor cortices, offering an opportunity to study distributed networks underlying complex behavior and cognition. Together, this work establishes head-mounted microendoscopic Calcium Imaging in macaque as a powerful new approach for studying the neural circuit mechanisms underlying complex and clinically relevant behaviors, and promises to greatly advance our understanding of human brain function, as well as its dysfunction in neurological disease. Highlights First demonstration of head-mounted microendoscopic Calcium Imaging in behaving macaque. Surgical protocols developed for preparing the animal for Calcium Imaging, including virus injections to express GCaMP and chronic implantation of a GRIN lens to enable optical access to gyral cortex. Proof of concept plug-and-play Calcium Imaging in behaving macaques with months long stable recording capability allowing populations of individual neurons to be tracked longitudinally. Bilateral Calcium Imaging from dorsal premotor cortex exhibited dynamics selective to the animal’s direction of reach and allowed decoding of the animal’s motor behavior
