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Yuan A, Colonell J, Lebedeva A, Okun M, Charles AS, Harris TD. Multi-day Neuron Tracking in High Density Electrophysiology Recordings using EMD. bioRxiv 2024:2023.08.03.551724. [PMID: 38260339 PMCID: PMC10802241 DOI: 10.1101/2023.08.03.551724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Accurate tracking of the same neurons across multiple days is crucial for studying changes in neuronal activity during learning and adaptation. Advances in high density extracellular electrophysiology recording probes, such as Neuropixels, provide a promising avenue to accomplish this goal. Identifying the same neurons in multiple recordings is, however, complicated by non-rigid movement of the tissue relative to the recording sites (drift) and loss of signal from some neurons. Here we propose a neuron tracking method that can identify the same cells independent of firing statistics, that are used by most existing methods. Our method is based on between-day non-rigid alignment of spike sorted clusters. We verified the same cell identity in mice using measured visual receptive fields. This method succeeds on datasets separated from one to 47 days, with an 84% average recovery rate.
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Affiliation(s)
- Augustine(Xiaoran) Yuan
- Janelia Research Campus, Howard Hughes Medical Institute, USA
- Department of Biomedical Engineering, Center for Imaging Science Institute, Kavli Neuroscience Discovery Institute, Johns Hopkins University, USA
| | | | - Anna Lebedeva
- Sainsbury Wellcome Centre, University College London, UK
| | - Michael Okun
- Department of Psychology and Neuroscience Institute, University of Sheffield, UK
| | - Adam S. Charles
- Department of Biomedical Engineering, Center for Imaging Science Institute, Kavli Neuroscience Discovery Institute, Johns Hopkins University, USA
| | - Timothy D. Harris
- Janelia Research Campus, Howard Hughes Medical Institute, USA
- Department of Biomedical Engineering, Center for Imaging Science Institute, Kavli Neuroscience Discovery Institute, Johns Hopkins University, USA
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2
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Ye Z, Shelton AM, Shaker JR, Boussard J, Colonell J, Birman D, Manavi S, Chen S, Windolf C, Hurwitz C, Namima T, Pedraja F, Weiss S, Raducanu B, Ness TV, Jia X, Mastroberardino G, Rossi LF, Carandini M, Häusser M, Einevoll GT, Laurent G, Sawtell NB, Bair W, Pasupathy A, Lopez CM, Dutta B, Paninski L, Siegle JH, Koch C, Olsen SR, Harris TD, Steinmetz NA. Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings. bioRxiv 2024:2023.08.23.554527. [PMID: 37662298 PMCID: PMC10473688 DOI: 10.1101/2023.08.23.554527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
To understand the neural basis of behavior, it is essential to sensitively and accurately measure neural activity at single neuron and single spike resolution. Extracellular electrophysiology delivers this, but it has biases in the neurons it detects and it imperfectly resolves their action potentials. To minimize these limitations, we developed a silicon probe with much smaller and denser recording sites than previous designs, called Neuropixels Ultra (NP Ultra). This device samples neuronal activity at ultra-high spatial density (~10 times higher than previous probes) with low noise levels, while trading off recording span. NP Ultra is effectively an implantable voltage-sensing camera that captures a planar image of a neuron's electrical field. We use a spike sorting algorithm optimized for these probes to demonstrate that the yield of visually-responsive neurons in recordings from mouse visual cortex improves up to ~3-fold. We show that NP Ultra can record from small neuronal structures including axons and dendrites. Recordings across multiple brain regions and four species revealed a subset of extracellular action potentials with unexpectedly small spatial spread and axon-like features. We share a large-scale dataset of these brain-wide recordings in mice as a resource for studies of neuronal biophysics. Finally, using ground-truth identification of three major inhibitory cortical cell types, we found that these cell types were discriminable with approximately 75% success, a significant improvement over lower-resolution recordings. NP Ultra improves spike sorting performance, detection of subcellular compartments, and cell type classification to enable more powerful dissection of neural circuit activity during behavior.
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Affiliation(s)
- Zhiwen Ye
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Andrew M. Shelton
- MindScope Program, Allen Institute, Seattle, WA, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Jordan R. Shaker
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Julien Boussard
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Daniel Birman
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Sahar Manavi
- MindScope Program, Allen Institute, Seattle, WA, USA
| | - Susu Chen
- Janelia Research Campus, Ashburn, VA, USA
| | - Charlie Windolf
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Cole Hurwitz
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Tomoyuki Namima
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, Seattle, WA, USA
| | - Federico Pedraja
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Shahaf Weiss
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | | | | | - Xiaoxuan Jia
- Center for Life Sciences & IDG/McGovern Institute for Brain Research, Tsinghua University, China
| | - Giulia Mastroberardino
- UCL Institute of Ophthalmology, University College London, London, UK
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - L. Federico Rossi
- Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - Matteo Carandini
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Michael Häusser
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Gaute T. Einevoll
- Norwegian University of Life Sciences, Ås, Norway
- University of Oslo, Oslo, Norway
| | - Gilles Laurent
- Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Nathaniel B. Sawtell
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Wyeth Bair
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, Seattle, WA, USA
| | - Anitha Pasupathy
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, Seattle, WA, USA
| | | | | | - Liam Paninski
- Department of Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Christof Koch
- MindScope Program, Allen Institute, Seattle, WA, USA
| | - Shawn R. Olsen
- MindScope Program, Allen Institute, Seattle, WA, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Timothy D. Harris
- Janelia Research Campus, Ashburn, VA, USA
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD, USA
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3
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Chen S, Liu Y, Wang ZA, Colonell J, Liu LD, Hou H, Tien NW, Wang T, Harris T, Druckmann S, Li N, Svoboda K. Brain-wide neural activity underlying memory-guided movement. Cell 2024; 187:676-691.e16. [PMID: 38306983 DOI: 10.1016/j.cell.2023.12.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 09/19/2023] [Accepted: 12/27/2023] [Indexed: 02/04/2024]
Abstract
Behavior relies on activity in structured neural circuits that are distributed across the brain, but most experiments probe neurons in a single area at a time. Using multiple Neuropixels probes, we recorded from multi-regional loops connected to the anterior lateral motor cortex (ALM), a circuit node mediating memory-guided directional licking. Neurons encoding sensory stimuli, choices, and actions were distributed across the brain. However, choice coding was concentrated in the ALM and subcortical areas receiving input from the ALM in an ALM-dependent manner. Diverse orofacial movements were encoded in the hindbrain; midbrain; and, to a lesser extent, forebrain. Choice signals were first detected in the ALM and the midbrain, followed by the thalamus and other brain areas. At movement initiation, choice-selective activity collapsed across the brain, followed by new activity patterns driving specific actions. Our experiments provide the foundation for neural circuit models of decision-making and movement initiation.
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Affiliation(s)
- Susu Chen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Yi Liu
- Stanford University, Palo Alto, CA, USA
| | | | - Jennifer Colonell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Liu D Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Baylor College of Medicine, Houston, TX, USA
| | - Han Hou
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Nai-Wen Tien
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Tim Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Timothy Harris
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Johns Hopkins University, Baltimore, MD, USA
| | - Shaul Druckmann
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Stanford University, Palo Alto, CA, USA.
| | - Nuo Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Baylor College of Medicine, Houston, TX, USA.
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA; Allen Institute for Neural Dynamics, Seattle, WA, USA.
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4
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Trautmann EM, Hesse JK, Stine GM, Xia R, Zhu S, O'Shea DJ, Karsh B, Colonell J, Lanfranchi FF, Vyas S, Zimnik A, Steinmann NA, Wagenaar DA, Andrei A, Lopez CM, O'Callaghan J, Putzeys J, Raducanu BC, Welkenhuysen M, Churchland M, Moore T, Shadlen M, Shenoy K, Tsao D, Dutta B, Harris T. Large-scale high-density brain-wide neural recording in nonhuman primates. bioRxiv 2023:2023.02.01.526664. [PMID: 37205406 PMCID: PMC10187172 DOI: 10.1101/2023.02.01.526664] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
High-density, integrated silicon electrodes have begun to transform systems neuroscience, by enabling large-scale neural population recordings with single cell resolution. Existing technologies, however, have provided limited functionality in nonhuman primate species such as macaques, which offer close models of human cognition and behavior. Here, we report the design, fabrication, and performance of Neuropixels 1.0-NHP, a high channel count linear electrode array designed to enable large-scale simultaneous recording in superficial and deep structures within the macaque or other large animal brain. These devices were fabricated in two versions: 4416 electrodes along a 45 mm shank, and 2496 along a 25 mm shank. For both versions, users can programmatically select 384 channels, enabling simultaneous multi-area recording with a single probe. We demonstrate recording from over 3000 single neurons within a session, and simultaneous recordings from over 1000 neurons using multiple probes. This technology represents a significant increase in recording access and scalability relative to existing technologies, and enables new classes of experiments involving fine-grained electrophysiological characterization of brain areas, functional connectivity between cells, and simultaneous brain-wide recording at scale.
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5
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Lillvis JL, Otsuna H, Ding X, Pisarev I, Kawase T, Colonell J, Rokicki K, Goina C, Gao R, Hu A, Wang K, Bogovic J, Milkie DE, Meienberg L, Mensh BD, Boyden ES, Saalfeld S, Tillberg PW, Dickson BJ. Rapid reconstruction of neural circuits using tissue expansion and light sheet microscopy. eLife 2022; 11:81248. [DOI: 10.7554/elife.81248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Brain function is mediated by the physiological coordination of a vast, intricately connected network of molecular and cellular components. The physiological properties of neural network components can be quantified with high throughput. The ability to assess many animals per study has been critical in relating physiological properties to behavior. By contrast, the synaptic structure of neural circuits is presently quantifiable only with low throughput. This low throughput hampers efforts to understand how variations in network structure relate to variations in behavior. For neuroanatomical reconstruction there is a methodological gulf between electron-microscopic (EM) methods, which yield dense connectomes at considerable expense and low throughput, and light-microscopic (LM) methods, which provide molecular and cell-type specificity at high throughput but without synaptic resolution. To bridge this gulf, we developed a high-throughput analysis pipeline and imaging protocol using tissue expansion and light sheet microscopy (ExLLSM) to rapidly reconstruct selected circuits across many animals with single-synapse resolution and molecular contrast. Using Drosophila to validate this approach, we demonstrate that it yields synaptic counts similar to those obtained by EM, enables synaptic connectivity to be compared across sex and experience, and can be used to correlate structural connectivity, functional connectivity, and behavior. This approach fills a critical methodological gap in studying variability in the structure and function of neural circuits across individuals within and between species.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Edward S Boyden
- MIT McGovern Institute for Brain Research, Massachusetts Institute of Technology
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6
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Lee KH, Ni YL, Colonell J, Karsh B, Putzeys J, Pachitariu M, Harris TD, Meister M. Electrode pooling can boost the yield of extracellular recordings with switchable silicon probes. Nat Commun 2021; 12:5245. [PMID: 34475396 PMCID: PMC8413349 DOI: 10.1038/s41467-021-25443-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/28/2021] [Indexed: 11/09/2022] Open
Abstract
State-of-the-art silicon probes for electrical recording from neurons have thousands of recording sites. However, due to volume limitations there are typically many fewer wires carrying signals off the probe, which restricts the number of channels that can be recorded simultaneously. To overcome this fundamental constraint, we propose a method called electrode pooling that uses a single wire to serve many recording sites through a set of controllable switches. Here we present the framework behind this method and an experimental strategy to support it. We then demonstrate its feasibility by implementing electrode pooling on the Neuropixels 1.0 electrode array and characterizing its effect on signal and noise. Finally we use simulations to explore the conditions under which electrode pooling saves wires without compromising the content of the recordings. We make recommendations on the design of future devices to take advantage of this strategy.
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Affiliation(s)
- Kyu Hyun Lee
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA
| | - Yu-Li Ni
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA
| | | | - Bill Karsh
- HHMI Janelia Research Campus, Ashburn, VA, USA
| | | | | | | | - Markus Meister
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA.
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7
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Steinmetz NA, Aydin C, Lebedeva A, Okun M, Pachitariu M, Bauza M, Beau M, Bhagat J, Böhm C, Broux M, Chen S, Colonell J, Gardner RJ, Karsh B, Kloosterman F, Kostadinov D, Mora-Lopez C, O'Callaghan J, Park J, Putzeys J, Sauerbrei B, van Daal RJJ, Vollan AZ, Wang S, Welkenhuysen M, Ye Z, Dudman JT, Dutta B, Hantman AW, Harris KD, Lee AK, Moser EI, O'Keefe J, Renart A, Svoboda K, Häusser M, Haesler S, Carandini M, Harris TD. Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings. Science 2021. [PMID: 33859006 DOI: 10.1101/2020.10.27.358291] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Measuring the dynamics of neural processing across time scales requires following the spiking of thousands of individual neurons over milliseconds and months. To address this need, we introduce the Neuropixels 2.0 probe together with newly designed analysis algorithms. The probe has more than 5000 sites and is miniaturized to facilitate chronic implants in small mammals and recording during unrestrained behavior. High-quality recordings over long time scales were reliably obtained in mice and rats in six laboratories. Improved site density and arrangement combined with newly created data processing methods enable automatic post hoc correction for brain movements, allowing recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior, even in small animals such as mice.
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Affiliation(s)
- Nicholas A Steinmetz
- UCL Institute of Ophthalmology, University College London, London, UK.
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | | | - Anna Lebedeva
- Sainsbury Wellcome Centre, University College London, London, UK
| | - Michael Okun
- Centre for Systems Neuroscience and Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Marius Pachitariu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Marius Bauza
- Sainsbury Wellcome Centre, University College London, London, UK
| | - Maxime Beau
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Jai Bhagat
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Claudia Böhm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Susu Chen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jennifer Colonell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Richard J Gardner
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bill Karsh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Fabian Kloosterman
- Neuroelectronics Research Flanders, Leuven, Belgium
- IMEC, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
- Brain and Cognition, KU Leuven, Leuven, Belgium
| | - Dimitar Kostadinov
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | | | | | - Junchol Park
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Britton Sauerbrei
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Rik J J van Daal
- ATLAS Neuroengineering, Leuven, Belgium
- Neuroelectronics Research Flanders, Leuven, Belgium
- Micro- and Nanosystems, KU Leuven, Leuven, Belgium
| | - Abraham Z Vollan
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Zhiwen Ye
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Joshua T Dudman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Adam W Hantman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Kenneth D Harris
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Albert K Lee
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Edvard I Moser
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - John O'Keefe
- Sainsbury Wellcome Centre, University College London, London, UK
| | | | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Michael Häusser
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Sebastian Haesler
- Neuroelectronics Research Flanders, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Matteo Carandini
- UCL Institute of Ophthalmology, University College London, London, UK.
| | - Timothy D Harris
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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8
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Steinmetz NA, Aydin C, Lebedeva A, Okun M, Pachitariu M, Bauza M, Beau M, Bhagat J, Böhm C, Broux M, Chen S, Colonell J, Gardner RJ, Karsh B, Kloosterman F, Kostadinov D, Mora-Lopez C, O'Callaghan J, Park J, Putzeys J, Sauerbrei B, van Daal RJJ, Vollan AZ, Wang S, Welkenhuysen M, Ye Z, Dudman JT, Dutta B, Hantman AW, Harris KD, Lee AK, Moser EI, O'Keefe J, Renart A, Svoboda K, Häusser M, Haesler S, Carandini M, Harris TD. Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings. Science 2021; 372:eabf4588. [PMID: 33859006 PMCID: PMC8244810 DOI: 10.1126/science.abf4588] [Citation(s) in RCA: 307] [Impact Index Per Article: 102.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/01/2021] [Indexed: 12/22/2022]
Abstract
Measuring the dynamics of neural processing across time scales requires following the spiking of thousands of individual neurons over milliseconds and months. To address this need, we introduce the Neuropixels 2.0 probe together with newly designed analysis algorithms. The probe has more than 5000 sites and is miniaturized to facilitate chronic implants in small mammals and recording during unrestrained behavior. High-quality recordings over long time scales were reliably obtained in mice and rats in six laboratories. Improved site density and arrangement combined with newly created data processing methods enable automatic post hoc correction for brain movements, allowing recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior, even in small animals such as mice.
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Affiliation(s)
- Nicholas A Steinmetz
- UCL Institute of Ophthalmology, University College London, London, UK.
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | | | - Anna Lebedeva
- Sainsbury Wellcome Centre, University College London, London, UK
| | - Michael Okun
- Centre for Systems Neuroscience and Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Marius Pachitariu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Marius Bauza
- Sainsbury Wellcome Centre, University College London, London, UK
| | - Maxime Beau
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Jai Bhagat
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Claudia Böhm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Susu Chen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jennifer Colonell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Richard J Gardner
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Bill Karsh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Fabian Kloosterman
- Neuroelectronics Research Flanders, Leuven, Belgium
- IMEC, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
- Brain and Cognition, KU Leuven, Leuven, Belgium
| | - Dimitar Kostadinov
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | | | | | - Junchol Park
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Britton Sauerbrei
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Rik J J van Daal
- ATLAS Neuroengineering, Leuven, Belgium
- Neuroelectronics Research Flanders, Leuven, Belgium
- Micro- and Nanosystems, KU Leuven, Leuven, Belgium
| | - Abraham Z Vollan
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Zhiwen Ye
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Joshua T Dudman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Adam W Hantman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Kenneth D Harris
- UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Albert K Lee
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Edvard I Moser
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - John O'Keefe
- Sainsbury Wellcome Centre, University College London, London, UK
| | | | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Michael Häusser
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Sebastian Haesler
- Neuroelectronics Research Flanders, Leuven, Belgium
- Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium
| | - Matteo Carandini
- UCL Institute of Ophthalmology, University College London, London, UK.
| | - Timothy D Harris
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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9
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Bogovic JA, Otsuna H, Heinrich L, Ito M, Jeter J, Meissner G, Nern A, Colonell J, Malkesman O, Ito K, Saalfeld S. An unbiased template of the Drosophila brain and ventral nerve cord. PLoS One 2020; 15:e0236495. [PMID: 33382698 PMCID: PMC7774840 DOI: 10.1371/journal.pone.0236495] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 07/07/2020] [Indexed: 12/03/2022] Open
Abstract
The fruit fly Drosophila melanogaster is an important model organism for neuroscience with a wide array of genetic tools that enable the mapping of individual neurons and neural subtypes. Brain templates are essential for comparative biological studies because they enable analyzing many individuals in a common reference space. Several central brain templates exist for Drosophila, but every one is either biased, uses sub-optimal tissue preparation, is imaged at low resolution, or does not account for artifacts. No publicly available Drosophila ventral nerve cord template currently exists. In this work, we created high-resolution templates of the Drosophila brain and ventral nerve cord using the best-available technologies for imaging, artifact correction, stitching, and template construction using groupwise registration. We evaluated our central brain template against the four most competitive, publicly available brain templates and demonstrate that ours enables more accurate registration with fewer local deformations in shorter time.
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Affiliation(s)
- John A. Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Hideo Otsuna
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Larissa Heinrich
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Masayoshi Ito
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Jennifer Jeter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Geoffrey Meissner
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Aljoscha Nern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Jennifer Colonell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Oz Malkesman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Kei Ito
- Institute of Zoology, University of Cologne, Germany
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
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10
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Gao R, Asano SM, Upadhyayula S, Pisarev I, Milkie DE, Liu TL, Singh V, Graves A, Huynh GH, Zhao Y, Bogovic J, Colonell J, Ott CM, Zugates C, Tappan S, Rodriguez A, Mosaliganti KR, Sheu SH, Pasolli HA, Pang S, Xu CS, Megason SG, Hess H, Lippincott-Schwartz J, Hantman A, Rubin GM, Kirchhausen T, Saalfeld S, Aso Y, Boyden ES, Betzig E. Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution. Science 2019; 363:eaau8302. [PMID: 30655415 PMCID: PMC6481610 DOI: 10.1126/science.aau8302] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022]
Abstract
Optical and electron microscopy have made tremendous inroads toward understanding the complexity of the brain. However, optical microscopy offers insufficient resolution to reveal subcellular details, and electron microscopy lacks the throughput and molecular contrast to visualize specific molecular constituents over millimeter-scale or larger dimensions. We combined expansion microscopy and lattice light-sheet microscopy to image the nanoscale spatial relationships between proteins across the thickness of the mouse cortex or the entire Drosophila brain. These included synaptic proteins at dendritic spines, myelination along axons, and presynaptic densities at dopaminergic neurons in every fly brain region. The technology should enable statistically rich, large-scale studies of neural development, sexual dimorphism, degree of stereotypy, and structural correlations to behavior or neural activity, all with molecular contrast.
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Affiliation(s)
- Ruixuan Gao
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Shoh M Asano
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
| | - Srigokul Upadhyayula
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Igor Pisarev
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Tsung-Li Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ved Singh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Austin Graves
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Grace H Huynh
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Yongxin Zhao
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - John Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jennifer Colonell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Carolyn M Ott
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Christopher Zugates
- arivis AG, 1875 Connecticut Avenue NW, 10th floor, Washington, DC 20009, USA
| | - Susan Tappan
- MBF Bioscience, 185 Allen Brook Lane, Suite 101, Williston, VT 05495, USA
| | - Alfredo Rodriguez
- MBF Bioscience, 185 Allen Brook Lane, Suite 101, Williston, VT 05495, USA
| | - Kishore R Mosaliganti
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Shu-Hsien Sheu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - H Amalia Pasolli
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Song Pang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Harald Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | | | - Adam Hantman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Gerald M Rubin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Tom Kirchhausen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Yoshinori Aso
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Edward S Boyden
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
- MIT Center for Neurobiological Engineering, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- Koch Institute, MIT, Cambridge, MA 02139, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Physics, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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11
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Bloss EB, Cembrowski MS, Karsh B, Colonell J, Fetter RD, Spruston N. Structured Dendritic Inhibition Supports Branch-Selective Integration in CA1 Pyramidal Cells. Neuron 2016. [PMID: 26898780 DOI: 10.1016/j.neuron.2016.01.029.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Neuronal circuit function is governed by precise patterns of connectivity between specialized groups of neurons. The diversity of GABAergic interneurons is a hallmark of cortical circuits, yet little is known about their targeting to individual postsynaptic dendrites. We examined synaptic connectivity between molecularly defined inhibitory interneurons and CA1 pyramidal cell dendrites using correlative light-electron microscopy and large-volume array tomography. We show that interneurons can be highly selective in their connectivity to specific dendritic branch types and, furthermore, exhibit precisely targeted connectivity to the origin or end of individual branches. Computational simulations indicate that the observed subcellular targeting enables control over the nonlinear integration of synaptic input or the initiation and backpropagation of action potentials in a branch-selective manner. Our results demonstrate that connectivity between interneurons and pyramidal cell dendrites is more precise and spatially segregated than previously appreciated, which may be a critical determinant of how inhibition shapes dendritic computation.
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Affiliation(s)
- Erik B Bloss
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Mark S Cembrowski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Bill Karsh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jennifer Colonell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Richard D Fetter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Nelson Spruston
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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12
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Bloss EB, Cembrowski MS, Karsh B, Colonell J, Fetter RD, Spruston N. Structured Dendritic Inhibition Supports Branch-Selective Integration in CA1 Pyramidal Cells. Neuron 2016; 89:1016-30. [PMID: 26898780 DOI: 10.1016/j.neuron.2016.01.029] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/14/2015] [Accepted: 01/13/2016] [Indexed: 10/22/2022]
Abstract
Neuronal circuit function is governed by precise patterns of connectivity between specialized groups of neurons. The diversity of GABAergic interneurons is a hallmark of cortical circuits, yet little is known about their targeting to individual postsynaptic dendrites. We examined synaptic connectivity between molecularly defined inhibitory interneurons and CA1 pyramidal cell dendrites using correlative light-electron microscopy and large-volume array tomography. We show that interneurons can be highly selective in their connectivity to specific dendritic branch types and, furthermore, exhibit precisely targeted connectivity to the origin or end of individual branches. Computational simulations indicate that the observed subcellular targeting enables control over the nonlinear integration of synaptic input or the initiation and backpropagation of action potentials in a branch-selective manner. Our results demonstrate that connectivity between interneurons and pyramidal cell dendrites is more precise and spatially segregated than previously appreciated, which may be a critical determinant of how inhibition shapes dendritic computation.
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Affiliation(s)
- Erik B Bloss
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Mark S Cembrowski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Bill Karsh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jennifer Colonell
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Richard D Fetter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Nelson Spruston
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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13
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Rah JC, Bas E, Colonell J, Mishchenko Y, Karsh B, Fetter RD, Myers EW, Chklovskii DB, Svoboda K, Harris TD, Isaac JTR. Thalamocortical input onto layer 5 pyramidal neurons measured using quantitative large-scale array tomography. Front Neural Circuits 2013; 7:177. [PMID: 24273494 PMCID: PMC3824245 DOI: 10.3389/fncir.2013.00177] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 10/16/2013] [Indexed: 11/13/2022] Open
Abstract
The subcellular locations of synapses on pyramidal neurons strongly influences dendritic integration and synaptic plasticity. Despite this, there is little quantitative data on spatial distributions of specific types of synaptic input. Here we use array tomography (AT), a high-resolution optical microscopy method, to examine thalamocortical (TC) input onto layer 5 pyramidal neurons. We first verified the ability of AT to identify synapses using parallel electron microscopic analysis of TC synapses in layer 4. We then use large-scale array tomography (LSAT) to measure TC synapse distribution on L5 pyramidal neurons in a 1.00 × 0.83 × 0.21 mm3 volume of mouse somatosensory cortex. We found that TC synapses primarily target basal dendrites in layer 5, but also make a considerable input to proximal apical dendrites in L4, consistent with previous work. Our analysis further suggests that TC inputs are biased toward certain branches and, within branches, synapses show significant clustering with an excess of TC synapse nearest neighbors within 5–15 μm compared to a random distribution. Thus, we show that AT is a sensitive and quantitative method to map specific types of synaptic input on the dendrites of entire neurons. We anticipate that this technique will be of wide utility for mapping functionally-relevant anatomical connectivity in neural circuits.
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Affiliation(s)
- Jong-Cheol Rah
- Howard Hughes Medical Institute, Janelia Farm Research Campus Ashburn, VA, USA ; Developmental Synaptic Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health Bethesda, MD, USA
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14
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Macklin JJ, Akerboom J, Schreiter ER, Tian L, Patel R, Mütze J, Iyer V, Karsh B, Colonell J, Harris TD, Looger LL. Two Photon Photophysics of Fluorescent Protein Calcium Indicators. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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15
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Reifenberger JG, Lipson D, Colonell J, Raz T, Pierceall B, Thompson J, Milos P. Sequencing Paired Reads using True Single Molecule Sequencing (tSMS)™ Technology. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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16
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Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Single-molecule DNA sequencing of a viral genome. Science 2008; 320:106-9. [PMID: 18388294 DOI: 10.1126/science.1150427] [Citation(s) in RCA: 519] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of >25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of >150x and with 100% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.
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Affiliation(s)
- Timothy D Harris
- Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, USA.
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17
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Natrajan A, Ferrara JD, Hays JD, Khot M, Colonell J, Youngs WJ, Sukenik CN. Conformations of [m.3.3]propellane ketones and alcohols. J Org Chem 2002. [DOI: 10.1021/jo00294a034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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