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Hira R. Closed-loop experiments and brain machine interfaces with multiphoton microscopy. NEUROPHOTONICS 2024; 11:033405. [PMID: 38375331 PMCID: PMC10876015 DOI: 10.1117/1.nph.11.3.033405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
In the field of neuroscience, the importance of constructing closed-loop experimental systems has increased in conjunction with technological advances in measuring and controlling neural activity in live animals. We provide an overview of recent technological advances in the field, focusing on closed-loop experimental systems where multiphoton microscopy-the only method capable of recording and controlling targeted population activity of neurons at a single-cell resolution in vivo-works through real-time feedback. Specifically, we present some examples of brain machine interfaces (BMIs) using in vivo two-photon calcium imaging and discuss applications of two-photon optogenetic stimulation and adaptive optics to real-time BMIs. We also consider conditions for realizing future optical BMIs at the synaptic level, and their possible roles in understanding the computational principles of the brain.
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Affiliation(s)
- Riichiro Hira
- Tokyo Medical and Dental University, Graduate School of Medical and Dental Sciences, Department of Physiology and Cell Biology, Tokyo, Japan
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2
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Alegria AD, Joshi AS, Mendana JB, Khosla K, Smith KT, Auch B, Donovan M, Bischof J, Gohl DM, Kodandaramaiah SB. High-throughput genetic manipulation of multicellular organisms using a machine-vision guided embryonic microinjection robot. Genetics 2024; 226:iyae025. [PMID: 38373262 PMCID: PMC10990426 DOI: 10.1093/genetics/iyae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/02/2024] [Accepted: 01/08/2024] [Indexed: 02/21/2024] Open
Abstract
Microinjection is a technique used for transgenesis, mutagenesis, cell labeling, cryopreservation, and in vitro fertilization in multiple single and multicellular organisms. Microinjection requires specialized skills and involves rate-limiting and labor-intensive preparatory steps. Here, we constructed a machine-vision guided generalized robot that fully automates the process of microinjection in fruit fly (Drosophila melanogaster) and zebrafish (Danio rerio) embryos. The robot uses machine learning models trained to detect embryos in images of agar plates and identify specific anatomical locations within each embryo in 3D space using dual view microscopes. The robot then serially performs a microinjection in each detected embryo. We constructed and used three such robots to automatically microinject tens of thousands of Drosophila and zebrafish embryos. We systematically optimized robotic microinjection for each species and performed routine transgenesis with proficiency comparable to highly skilled human practitioners while achieving up to 4× increases in microinjection throughput in Drosophila. The robot was utilized to microinject pools of over 20,000 uniquely barcoded plasmids into 1,713 embryos in 2 days to rapidly generate more than 400 unique transgenic Drosophila lines. This experiment enabled a novel measurement of the number of independent germline integration events per successfully injected embryo. Finally, we showed that robotic microinjection of cryoprotective agents in zebrafish embryos significantly improves vitrification rates and survival of cryopreserved embryos post-thaw as compared to manual microinjection. We anticipate that the robot can be used to carry out microinjection for genome-wide manipulation and cryopreservation at scale in a wide range of organisms.
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Affiliation(s)
- Andrew D Alegria
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amey S Joshi
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jorge Blanco Mendana
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kanav Khosla
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kieran T Smith
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Benjamin Auch
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Margaret Donovan
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - John Bischof
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daryl M Gohl
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Suhasa B Kodandaramaiah
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
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3
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Li K, Gong H, Qiu J, Li R, Zhao Q, Zhao X, Sun M. Neuron Contact Detection Based on Pipette Precise Positioning for Robotic Brain-Slice Patch Clamps. SENSORS (BASEL, SWITZERLAND) 2023; 23:8144. [PMID: 37836974 PMCID: PMC10575430 DOI: 10.3390/s23198144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/09/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
A patch clamp is the "gold standard" method for studying ion-channel biophysics and pharmacology. Due to the complexity of the operation and the heavy reliance on experimenter experience, more and more researchers are focusing on patch-clamp automation. The existing automated patch-clamp system focuses on the process of completing the experiment; the detection method in each step is relatively simple, and the robustness of the complex brain film environment is lacking, which will increase the detection error in the microscopic environment, affecting the success rate of the automated patch clamp. To address these problems, we propose a method that is suitable for the contact between pipette tips and neuronal cells in automated patch-clamp systems. It mainly includes two key steps: precise positioning of pipettes and contact judgment. First, to obtain the precise coordinates of the tip of the pipette, we use the Mixture of Gaussian (MOG) algorithm for motion detection to focus on the tip area under the microscope. We use the object detection model to eliminate the encirclement frame of the pipette tip to reduce the influence of different shaped tips, and then use the sweeping line algorithm to accurately locate the pipette tip. We also use the object detection model to obtain a three-dimensional bounding frame of neuronal cells. When the microscope focuses on the maximum plane of the cell, which is the height in the middle of the enclosing frame, we detect the focus of the tip of the pipette to determine whether the contact between the tip and the cell is successful, because the cell and the pipette will be at the same height at this time. We propose a multitasking network CU-net that can judge the focus of pipette tips in complex contexts. Finally, we design an automated contact sensing process in combination with resistance constraints and apply it to our automated patch-clamp system. The experimental results show that our method can increase the success rate of pipette contact with cells in patch-clamp experiments.
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Affiliation(s)
- Ke Li
- Institute of Robotics and Automatic Information System, Tianjin Key Laboratory of Intelligent Robotics, Nankai University, Tianjin 300350, China; (K.L.); (H.G.); (J.Q.); (R.L.); (Q.Z.); (X.Z.)
- Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, Shenzhen 518083, China
| | - Huiying Gong
- Institute of Robotics and Automatic Information System, Tianjin Key Laboratory of Intelligent Robotics, Nankai University, Tianjin 300350, China; (K.L.); (H.G.); (J.Q.); (R.L.); (Q.Z.); (X.Z.)
- Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, Shenzhen 518083, China
| | - Jinyu Qiu
- Institute of Robotics and Automatic Information System, Tianjin Key Laboratory of Intelligent Robotics, Nankai University, Tianjin 300350, China; (K.L.); (H.G.); (J.Q.); (R.L.); (Q.Z.); (X.Z.)
- Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, Shenzhen 518083, China
| | - Ruimin Li
- Institute of Robotics and Automatic Information System, Tianjin Key Laboratory of Intelligent Robotics, Nankai University, Tianjin 300350, China; (K.L.); (H.G.); (J.Q.); (R.L.); (Q.Z.); (X.Z.)
- Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, Shenzhen 518083, China
| | - Qili Zhao
- Institute of Robotics and Automatic Information System, Tianjin Key Laboratory of Intelligent Robotics, Nankai University, Tianjin 300350, China; (K.L.); (H.G.); (J.Q.); (R.L.); (Q.Z.); (X.Z.)
- Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, Shenzhen 518083, China
| | - Xin Zhao
- Institute of Robotics and Automatic Information System, Tianjin Key Laboratory of Intelligent Robotics, Nankai University, Tianjin 300350, China; (K.L.); (H.G.); (J.Q.); (R.L.); (Q.Z.); (X.Z.)
- Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, Shenzhen 518083, China
| | - Mingzhu Sun
- Institute of Robotics and Automatic Information System, Tianjin Key Laboratory of Intelligent Robotics, Nankai University, Tianjin 300350, China; (K.L.); (H.G.); (J.Q.); (R.L.); (Q.Z.); (X.Z.)
- Institute of Intelligence Technology and Robotic Systems, Shenzhen Research Institute of Nankai University, Shenzhen 518083, China
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Dacre J, Sánchez Rivera M, Schiemann J, Currie S, Ammer JJ, Duguid I. A cranial implant for stabilizing whole-cell patch-clamp recordings in behaving rodents. J Neurosci Methods 2023; 390:109827. [PMID: 36871604 PMCID: PMC10375832 DOI: 10.1016/j.jneumeth.2023.109827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 02/14/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND In vivo patch-clamp recording techniques provide access to the sub- and suprathreshold membrane potential dynamics of individual neurons during behavior. However, maintaining recording stability throughout behavior is a significant challenge, and while methods for head restraint are commonly used to enhance stability, behaviorally related brain movement relative to the skull can severely impact the success rate and duration of whole-cell patch-clamp recordings. NEW METHOD We developed a low-cost, biocompatible, and 3D-printable cranial implant capable of locally stabilizing brain movement, while permitting equivalent access to the brain when compared to a conventional craniotomy. RESULTS Experiments in head-restrained behaving mice demonstrate that the cranial implant can reliably reduce the amplitude and speed of brain displacements, significantly improving the success rate of recordings across repeated bouts of motor behavior. COMPARISON WITH EXISTING METHOD(S) Our solution offers an improvement on currently available strategies for brain stabilization. Due to its small size, the implant can be retrofitted to most in vivo electrophysiology recording setups, providing a low cost, easily implementable solution for increasing intracellular recording stability in vivo. CONCLUSIONS By facilitating stable whole-cell patch-clamp recordings in vivo, biocompatible 3D printed implants should accelerate the investigation of single neuron computations underlying behavior.
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Affiliation(s)
- Joshua Dacre
- Centre for Discovery Brain Sciences and Patrick Wild Centre, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Michelle Sánchez Rivera
- Centre for Discovery Brain Sciences and Patrick Wild Centre, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Julia Schiemann
- Centre for Discovery Brain Sciences and Patrick Wild Centre, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Stephen Currie
- Centre for Discovery Brain Sciences and Patrick Wild Centre, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Julian J Ammer
- Centre for Discovery Brain Sciences and Patrick Wild Centre, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Ian Duguid
- Centre for Discovery Brain Sciences and Patrick Wild Centre, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, UK.
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Huang J, Liang S, Li L, Li X, Liao X, Hu Q, Zhang C, Jia H, Chen X, Wang M, Li R. Daily two-photon neuronal population imaging with targeted single-cell electrophysiology and subcellular imaging in auditory cortex of behaving mice. Front Cell Neurosci 2023; 17:1142267. [PMID: 36937184 PMCID: PMC10020347 DOI: 10.3389/fncel.2023.1142267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Quantitative and mechanistic understanding of learning and long-term memory at the level of single neurons in living brains require highly demanding techniques. A specific need is to precisely label one cell whose firing output property is pinpointed amidst a functionally characterized large population of neurons through the learning process and then investigate the distribution and properties of dendritic inputs. Here, we disseminate an integrated method of daily two-photon neuronal population Ca2+ imaging through an auditory associative learning course, followed by targeted single-cell loose-patch recording and electroporation of plasmid for enhanced chronic Ca2+ imaging of dendritic spines in the targeted cell. Our method provides a unique solution to the demand, opening a solid path toward the hard-cores of how learning and long-term memory are physiologically carried out at the level of single neurons and synapses.
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Affiliation(s)
- Junjie Huang
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
| | - Susu Liang
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
| | - Longhui Li
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
| | - Xingyi Li
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
| | - Xiang Liao
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
| | - Qianshuo Hu
- School of Artificial Intelligence, Chongqing University of Technology, Chongqing, China
| | - Chunqing Zhang
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Hongbo Jia
- School of Physical Science and Technology, Advanced Institute for Brain and Intelligence, Guangxi University, Nanning, China
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Leibniz Institute for Neurobiology, Magdeburg, Germany
- Institute of Neuroscience and the SyNergy Cluster, Technical University Munich, Munich, Germany
| | - Xiaowei Chen
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
- Guangyang Bay Laboratory, Chongqing Institute for Brain and Intelligence, Chongqing, China
- Xiaowei Chen,
| | - Meng Wang
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
- Meng Wang,
| | - Ruijie Li
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
- School of Physical Science and Technology, Advanced Institute for Brain and Intelligence, Guangxi University, Nanning, China
- *Correspondence: Ruijie Li,
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6
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Discovering sparse control strategies in neural activity. PLoS Comput Biol 2022; 18:e1010072. [PMID: 35622828 PMCID: PMC9140285 DOI: 10.1371/journal.pcbi.1010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 04/01/2022] [Indexed: 11/19/2022] Open
Abstract
Biological circuits such as neural or gene regulation networks use internal states to map sensory input to an adaptive repertoire of behavior. Characterizing this mapping is a major challenge for systems biology. Though experiments that probe internal states are developing rapidly, organismal complexity presents a fundamental obstacle given the many possible ways internal states could map to behavior. Using C. elegans as an example, we propose a protocol for systematic perturbation of neural states that limits experimental complexity and could eventually help characterize collective aspects of the neural-behavioral map. We consider experimentally motivated small perturbations—ones that are most likely to preserve natural dynamics and are closer to internal control mechanisms—to neural states and their impact on collective neural activity. Then, we connect such perturbations to the local information geometry of collective statistics, which can be fully characterized using pairwise perturbations. Applying the protocol to a minimal model of C. elegans neural activity, we find that collective neural statistics are most sensitive to a few principal perturbative modes. Dominant eigenvalues decay initially as a power law, unveiling a hierarchy that arises from variation in individual neural activity and pairwise interactions. Highest-ranking modes tend to be dominated by a few, “pivotal” neurons that account for most of the system’s sensitivity, suggesting a sparse mechanism of collective control.
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7
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Joshi AS, Alegria AD, Auch B, Khosla K, Mendana JB, Liu K, Bischof J, Gohl DM, Kodandaramaiah SB. Multiscale, multi-perspective imaging assisted robotic microinjection of 3D biological structures. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2021; 2021:4844-4850. [PMID: 34892294 PMCID: PMC8966898 DOI: 10.1109/embc46164.2021.9630858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Microinjection is a widely used technique employed by biologists with applications in transgenesis, cryopreservation, mutagenesis, labeling/dye injection and in-vitro fertilization. However, microinjection is an extremely laborious manual procedure, which makes it a critical bottleneck in the field and thus ripe for automation. Here, we present a computer-guided robot that automates the targeted microinjection of Drosophila melanogaster and zebrafish (Danio rerio) embryos, two important model organisms in biological research. The robot uses a series of cameras to image an agar plate containing embryos at multiple magnifications and perspectives. This imaging is combined with machine learning and computer vision algorithms to pinpoint a location on the embryo for targeted microinjection with microscale precision. We demonstrate the utility of this microinjection robot to successfully microinject Drosophila melanogaster and zebrafish embryos. Results obtained indicate that the robotic microinjection approach can significantly increase the throughput of microinjection as compared to manual microinjection while maintaining survival rates comparable to human operators. In the future, this robotic platform can be used to perform high throughput microinjection experiments and can be extended to automatically microinject a host of organisms such as roundworms (Caenorhabditis elegans), mosquito (Culicidae) embryos, sea urchins (Echinoidea) and frog (Xenopus) oocytes.
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Affiliation(s)
- Amey S. Joshi
- Department of Mechanical Engineering, University of Minnesota Twin Cities, Minneapolis, USA
| | - Andrew D. Alegria
- Department of Mechanical Engineering, University of Minnesota Twin Cities, Minneapolis, USA
| | - Benjamin Auch
- University of Minnesota Genomic Center, University of Minnesota Twin Cities, Minneapolis, USA
| | - Kanav Khosla
- Department of Mechanical Engineering, University of Minnesota Twin Cities, Minneapolis, USA
| | - Jorge Blanco Mendana
- University of Minnesota Genomic Center, University of Minnesota Twin Cities, Minneapolis, USA
| | - Kunpeng Liu
- Department of Mechanical Engineering, University of Minnesota Twin Cities, Minneapolis, USA
| | - John Bischof
- Department of Mechanical Engineering, University of Minnesota Twin Cities, Minneapolis, USA
- Department of Biomedical Engineering, University of Minnesota Twin Cities, Minneapolis, USA
| | - Daryl M. Gohl
- University of Minnesota Genomic Center, University of Minnesota Twin Cities, Minneapolis, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota Twin Cities, Minneapolis, USA
| | - Suhasa B. Kodandaramaiah
- Department of Mechanical Engineering, University of Minnesota Twin Cities, Minneapolis, USA
- Department of Biomedical Engineering, University of Minnesota Twin Cities, Minneapolis, USA
- Department of Neuroscience, University of Minnesota Twin Cities, Minneapolis, USA
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8
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Sjöström PJ. Grand Challenge at the Frontiers of Synaptic Neuroscience. Front Synaptic Neurosci 2021; 13:748937. [PMID: 34759809 PMCID: PMC8575031 DOI: 10.3389/fnsyn.2021.748937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/22/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- P. Jesper Sjöström
- Department of Medicine, Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, The Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, QC, Canada
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Miranda C, Howell MR, Lusk JF, Marschall E, Eshima J, Anderson T, Smith BS. Automated microscope-independent fluorescence-guided micropipette. BIOMEDICAL OPTICS EXPRESS 2021; 12:4689-4699. [PMID: 34513218 PMCID: PMC8407805 DOI: 10.1364/boe.431372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Glass micropipette electrodes are commonly used to provide high resolution recordings of neurons. Although it is the gold standard for single cell recordings, it is highly dependent on the skill of the electrophysiologist. Here, we demonstrate a method of guiding micropipette electrodes to neurons by collecting fluorescence at the aperture, using an intra-electrode tapered optical fiber. The use of a tapered fiber for excitation and collection of fluorescence at the micropipette tip couples the feedback mechanism directly to the distance between the target and electrode. In this study, intra-electrode tapered optical fibers provide a targeted robotic approach to labeled neurons that is independent of microscopy.
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Affiliation(s)
- Christopher Miranda
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Madeleine R. Howell
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Joel F. Lusk
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Ethan Marschall
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Jarrett Eshima
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
| | - Trent Anderson
- University of Arizona, College of Medicine – Phoenix, Phoenix, AZ 85004, USA
| | - Barbara S. Smith
- Arizona State University, School of Biological and Health Systems Engineering, Tempe, AZ 85210, USA
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10
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Machine Learning-Based Pipette Positional Correction for Automatic Patch Clamp In Vitro. eNeuro 2021; 8:8/4/ENEURO.0051-21.2021. [PMID: 34312222 PMCID: PMC8318343 DOI: 10.1523/eneuro.0051-21.2021] [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: 02/02/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 11/21/2022] Open
Abstract
Patch clamp electrophysiology is a common technique used in neuroscience to understand individual neuron behavior, allowing one to record current and voltage changes with superior spatiotemporal resolution compared with most electrophysiology methods. While patch clamp experiments produce high fidelity electrophysiology data, the technique is onerous and labor intensive. Despite the emergence of patch clamp systems that automate key stages in the typical patch clamp procedure, full automation remains elusive. Patch clamp pipettes can miss the target cell during automated experiments because of positioning errors in the robotic manipulators, which can easily exceed the diameter of a neuron. Further, when patching in acute brain slices, the inherent light scattering from non-uniform brain tissue can complicate pipette tip identification. We present a convolutional neural network (CNN), based on ResNet101, to identify and correct pipette positioning errors before each patch clamp attempt, thereby preventing the deleterious effects of and accumulation of positioning errors. This deep-learning-based pipette detection method enabled superior localization of the pipette within 0.62 ± 0.58 μm, resulting in improved cell detection success rate and whole-cell patch clamp success rates by 71% and 59%, respectively, compared with the state-of-the-art cross-correlation method. Furthermore, this technique reduced the average time for pipette correction by 81%. This technique enables real-time correction of pipette position during patch clamp experiments with similar accuracy and quality of recording to manual patch clamp, making notable progress toward full human-out-of-the-loop automation for patch clamp electrophysiology.
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11
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Landry CR, Yip MC, Kolb I, Stoy WA, Gonzalez MM, Forest CR. Method for Rapid Enzymatic Cleaning for Reuse of Patch Clamp Pipettes: Increasing Throughput by Eliminating Manual Pipette Replacement between Patch Clamp Attempts. Bio Protoc 2021; 11:e4085. [PMID: 34395724 PMCID: PMC8329470 DOI: 10.21769/bioprotoc.4085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 11/02/2022] Open
Abstract
The whole-cell patch-clamp method is a gold standard for single-cell analysis of electrical activity, cellular morphology, and gene expression. Prior to our discovery that patch-clamp pipettes could be cleaned and reused, experimental throughput and automation were limited by the need to replace pipettes manually after each experiment. This article presents an optimized protocol for pipette cleaning, which enables it to be performed quickly (< 30 s), resulting in a high yield of whole-cell recording success rate (> 90%) for over 100 reuses of a single pipette. For most patch-clamp experiments (< 30 whole-cell recordings per day), this method enables a single pipette to be used for an entire day of experiments. In addition, we describe easily implementable hardware and software as well as troubleshooting tips to help other labs implement this method in their own experiments. Pipette cleaning enables patch-clamp experiments to be performed with higher throughput, whether manually or in an automated fashion, by eliminating the tedious and skillful task of replacing pipettes. From our experience with numerous electrophysiology laboratories, pipette cleaning can be integrated into existing patch-clamp setups in approximately one day using the hardware and software described in this article. Graphic abstract: Rapid enzymatic cleaning for reuse of patch-clamp pipettes.
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Affiliation(s)
- Corey R. Landry
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, USA
| | - Mighten C. Yip
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, USA
| | - Ilya Kolb
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, USA
| | | | - Mercedes M. Gonzalez
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, USA
| | - Craig R. Forest
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, USA
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12
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Abstract
Membrane potential (Vmem) is a fundamental biophysical signal present in all cells. Vmem signals range in time from milliseconds to days, and they span lengths from microns to centimeters. Vmem affects many cellular processes, ranging from neurotransmitter release to cell cycle control to tissue patterning. However, existing tools are not suitable for Vmem quantification in many of these areas. In this review, we outline the diverse biology of Vmem, drafting a wish list of features for a Vmem sensing platform. We then use these guidelines to discuss electrode-based and optical platforms for interrogating Vmem. On the one hand, electrode-based strategies exhibit excellent quantification but are most effective in short-term, cellular recordings. On the other hand, optical strategies provide easier access to diverse samples but generally only detect relative changes in Vmem. By combining the respective strengths of these technologies, recent advances in optical quantification of absolute Vmem enable new inquiries into Vmem biology.
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Affiliation(s)
- Julia R Lazzari-Dean
- Department of Chemistry, University of California, Berkeley, California 94720, USA; ,
| | - Anneliese M M Gest
- Department of Chemistry, University of California, Berkeley, California 94720, USA; ,
| | - Evan W Miller
- Department of Chemistry, University of California, Berkeley, California 94720, USA; ,
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA
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13
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Liu JTC, Glaser AK, Bera K, True LD, Reder NP, Eliceiri KW, Madabhushi A. Harnessing non-destructive 3D pathology. Nat Biomed Eng 2021; 5:203-218. [PMID: 33589781 PMCID: PMC8118147 DOI: 10.1038/s41551-020-00681-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/17/2020] [Indexed: 02/08/2023]
Abstract
High-throughput methods for slide-free three-dimensional (3D) pathological analyses of whole biopsies and surgical specimens offer the promise of modernizing traditional histology workflows and delivering improvements in diagnostic performance. Advanced optical methods now enable the interrogation of orders of magnitude more tissue than previously possible, where volumetric imaging allows for enhanced quantitative analyses of cell distributions and tissue structures that are prognostic and predictive. Non-destructive imaging processes can simplify laboratory workflows, potentially reducing costs, and can ensure that samples are available for subsequent molecular assays. However, the large size of the feature-rich datasets that they generate poses challenges for data management and computer-aided analysis. In this Perspective, we provide an overview of the imaging technologies that enable 3D pathology, and the computational tools-machine learning, in particular-for image processing and interpretation. We also discuss the integration of various other diagnostic modalities with 3D pathology, along with the challenges and opportunities for clinical adoption and regulatory approval.
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Affiliation(s)
- Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Kaustav Bera
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nicholas P Reder
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Kevin W Eliceiri
- Department of Medical Physics, University of Wisconsin, Madison, WI, USA.
- Department of Biomedical Engineering, University of Wisconsin, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
| | - Anant Madabhushi
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA.
- Louis Stokes Cleveland Veterans Administration Medical Center, Cleveland, OH, USA.
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14
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Noguchi A, Ikegaya Y, Matsumoto N. In Vivo Whole-Cell Patch-Clamp Methods: Recent Technical Progress and Future Perspectives. SENSORS (BASEL, SWITZERLAND) 2021; 21:1448. [PMID: 33669656 PMCID: PMC7922023 DOI: 10.3390/s21041448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 02/01/2023]
Abstract
Brain functions are fundamental for the survival of organisms, and they are supported by neural circuits consisting of a variety of neurons. To investigate the function of neurons at the single-cell level, researchers often use whole-cell patch-clamp recording techniques. These techniques enable us to record membrane potentials (including action potentials) of individual neurons of not only anesthetized but also actively behaving animals. This whole-cell recording method enables us to reveal how neuronal activities support brain function at the single-cell level. In this review, we introduce previous studies using in vivo patch-clamp recording techniques and recent findings primarily regarding neuronal activities in the hippocampus for behavioral function. We further discuss how we can bridge the gap between electrophysiology and biochemistry.
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Affiliation(s)
- Asako Noguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; (A.N.); (Y.I.)
| | - Yuji Ikegaya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; (A.N.); (Y.I.)
- Institute for AI and Beyond, The University of Tokyo, Tokyo 113-0033, Japan
- Center for Information and Neural Networks, National Institute of Information and Communications Technology, Suita City, Osaka 565-0871, Japan
| | - Nobuyoshi Matsumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; (A.N.); (Y.I.)
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15
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Abstract
Intact and functioning brain enables quantification of neural activities directly associated with real world such as visual and auditory information. In vivo patch clamp can record different types of neuronal activity, such as spiking responses, membrane potential dynamics, and synaptic currents (e.g., EPSC, IPSC) in either anesthetized or awake or even free moving animals. Researchers can not only directly measure these neuronal activities but also quantify and unravel synaptic contribution from excitatory and inhibitory circuits. Here, we describe the requirements and standard protocols to perform in vivo patch clamp recording. The key factors of successful recording based on references and our experiences are also provided.
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Affiliation(s)
- Yi Zhou
- Department of Neurobiology, School of Basic Medical Sciences, Army Medical University, Chongqing, China.
| | - He Li
- Department of Physiology, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhongju Xiao
- Department of Physiology, Southern Medical University, Guangzhou, Guangdong, China
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16
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Alegria A, Joshi A, O'Brien J, Kodandaramaiah SB. Single neuron recording: progress towards high-throughput analysis. BIOELECTRONICS IN MEDICINE 2020; 3:33-36. [PMID: 33169092 PMCID: PMC7604670 DOI: 10.2217/bem-2020-0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/10/2020] [Indexed: 11/21/2022]
Affiliation(s)
- Andrew Alegria
- Department of Mechanical Engineering, University of Minnesota, Twin Cities, MN 55455, USA
| | - Amey Joshi
- Department of Mechanical Engineering, University of Minnesota, Twin Cities, MN 55455, USA
| | - Jacob O'Brien
- Department of Mechanical Engineering, University of Minnesota, Twin Cities, MN 55455, USA
| | - Suhasa B Kodandaramaiah
- Department of Mechanical Engineering, University of Minnesota, Twin Cities, MN 55455, USA
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, MN 55455, USA
- Department of Neuroscience, University of Minnesota, Twin Cities, MN 55455, USA
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17
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Peng Y, Mittermaier FX, Planert H, Schneider UC, Alle H, Geiger JRP. High-throughput microcircuit analysis of individual human brains through next-generation multineuron patch-clamp. eLife 2019; 8:48178. [PMID: 31742558 PMCID: PMC6894931 DOI: 10.7554/elife.48178] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022] Open
Abstract
Comparing neuronal microcircuits across different brain regions, species and individuals can reveal common and divergent principles of network computation. Simultaneous patch-clamp recordings from multiple neurons offer the highest temporal and subthreshold resolution to analyse local synaptic connectivity. However, its establishment is technically complex and the experimental performance is limited by high failure rates, long experimental times and small sample sizes. We introduce an in vitro multipatch setup with an automated pipette pressure and cleaning system facilitating recordings of up to 10 neurons simultaneously and sequential patching of additional neurons. We present hardware and software solutions that increase the usability, speed and data throughput of multipatch experiments which allowed probing of 150 synaptic connections between 17 neurons in one human cortical slice and screening of over 600 connections in tissue from a single patient. This method will facilitate the systematic analysis of microcircuits and allow unprecedented assessment of inter-individual variability.
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Affiliation(s)
- Yangfan Peng
- Institute of Neurophysiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Henrike Planert
- Institute of Neurophysiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Henrik Alle
- Institute of Neurophysiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
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18
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Shull G, Haffner C, Huttner WB, Kodandaramaiah SB, Taverna E. Robotic platform for microinjection into single cells in brain tissue. EMBO Rep 2019; 20:e47880. [PMID: 31469223 PMCID: PMC6776899 DOI: 10.15252/embr.201947880] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/23/2019] [Accepted: 08/07/2019] [Indexed: 01/02/2023] Open
Abstract
Microinjection into single cells in brain tissue is a powerful technique to study and manipulate neural stem cells. However, such microinjection requires expertise and is a low-throughput process. We developed the "Autoinjector", a robot that utilizes images from a microscope to guide a microinjection needle into tissue to deliver femtoliter volumes of liquids into single cells. The Autoinjector enables microinjection of hundreds of cells within a single organotypic slice, resulting in an overall yield that is an order of magnitude greater than manual microinjection. The Autoinjector successfully targets both apical progenitors (APs) and newborn neurons in the embryonic mouse and human fetal telencephalon. We used the Autoinjector to systematically study gap-junctional communication between neural progenitors in the embryonic mouse telencephalon and found that apical contact is a characteristic feature of the cells that are part of a gap junction-coupled cluster. The throughput and versatility of the Autoinjector will render microinjection an accessible high-performance single-cell manipulation technique and will provide a powerful new platform for performing single-cell analyses in tissue for bioengineering and biophysics applications.
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Affiliation(s)
- Gabriella Shull
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, MN, USA.,Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Christiane Haffner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Suhasa B Kodandaramaiah
- Department of Biomedical Engineering, University of Minnesota, Twin Cities, MN, USA.,Department of Mechanical Engineering, University of Minnesota, Twin Cities, MN, USA
| | - Elena Taverna
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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19
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Obien MEJ, Frey U. Large-Scale, High-Resolution Microelectrode Arrays for Interrogation of Neurons and Networks. ADVANCES IN NEUROBIOLOGY 2019; 22:83-123. [PMID: 31073933 DOI: 10.1007/978-3-030-11135-9_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
High-density microelectrode arrays (HD-MEAs) are increasingly being used for the observation and manipulation of neurons and networks in vitro. Large-scale electrode arrays allow for long-term extracellular recording of the electrical activity from thousands of neurons simultaneously. Beyond population activity, it has also become possible to extract information of single neurons at subcellular level (e.g., the propagation of action potentials along axons). In effect, HD-MEAs have become an electrical imaging platform for label-free extraction of the structure and activation of cells in cultures and tissues. The quality of HD-MEA data depends on the resolution of the electrode array and the signal-to-noise ratio. In this chapter, we begin with an introduction to HD-MEA signals. We provide an overview of the developments on complementary metal-oxide-semiconductor or CMOS-based HD-MEA technology. We also discuss the factors affecting the performance of HD-MEAs and the trending application requirements that drive the efforts for future devices. We conclude with an outlook on the potential of HD-MEAs for advancing basic neuroscience and drug discovery.
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Affiliation(s)
- Marie Engelene J Obien
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
- MaxWell Biosystems, Basel, Switzerland.
| | - Urs Frey
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- MaxWell Biosystems, Basel, Switzerland
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20
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Suk HJ, Boyden ES, van Welie I. Advances in the automation of whole-cell patch clamp technology. J Neurosci Methods 2019; 326:108357. [PMID: 31336060 DOI: 10.1016/j.jneumeth.2019.108357] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/05/2019] [Accepted: 07/10/2019] [Indexed: 12/22/2022]
Abstract
Electrophysiology is the study of neural activity in the form of local field potentials, current flow through ion channels, calcium spikes, back propagating action potentials and somatic action potentials, all measurable on a millisecond timescale. Despite great progress in imaging technologies and sensor proteins, none of the currently available tools allow imaging of neural activity on a millisecond timescale and beyond the first few hundreds of microns inside the brain. The patch clamp technique has been an invaluable tool since its inception several decades ago and has generated a wealth of knowledge about the nature of voltage- and ligand-gated ion channels, sub-threshold and supra-threshold activity, and characteristics of action potentials related to higher order functions. Many techniques that evolve to be standardized tools in the biological sciences go through a period of transformation in which they become, at least to some degree, automated, in order to improve reproducibility, throughput and standardization. The patch clamp technique is currently undergoing this transition, and in this review, we will discuss various aspects of this transition, covering advances in automated patch clamp technology both in vitro and in vivo.
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Affiliation(s)
- Ho-Jun Suk
- Health Sciences and Technology, MIT, Cambridge, MA 02139, USA; Media Lab, MIT, Cambridge, MA 02139, USA; McGovern Institute, MIT, Cambridge, MA 02139, USA
| | - Edward S Boyden
- Media Lab, MIT, Cambridge, MA 02139, USA; McGovern Institute, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
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21
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Kolb I, Landry CR, Yip MC, Lewallen CF, Stoy WA, Lee J, Felouzis A, Yang B, Boyden ES, Rozell CJ, Forest CR. PatcherBot: a single-cell electrophysiology robot for adherent cells and brain slices. J Neural Eng 2019; 16:046003. [PMID: 30970335 DOI: 10.1088/1741-2552/ab1834] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVE Intracellular patch-clamp electrophysiology, one of the most ubiquitous, high-fidelity techniques in biophysics, remains laborious and low-throughput. While previous efforts have succeeded at automating some steps of the technique, here we demonstrate a robotic 'PatcherBot' system that can perform many patch-clamp recordings sequentially, fully unattended. APPROACH Comprehensive automation is accomplished by outfitting the robot with machine vision, and cleaning pipettes instead of manually exchanging them. MAIN RESULTS the PatcherBot can obtain data at a rate of 16 cells per hour and work with no human intervention for up to 3 h. We demonstrate the broad applicability and scalability of this system by performing hundreds of recordings in tissue culture cells and mouse brain slices with no human supervision. Using the PatcherBot, we also discovered that pipette cleaning can be improved by a factor of three. SIGNIFICANCE The system is potentially transformative for applications that depend on many high-quality measurements of single cells, such as drug screening, protein functional characterization, and multimodal cell type investigations.
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Affiliation(s)
- Ilya Kolb
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, United States of America
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22
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Holst GL, Stoy W, Yang B, Kolb I, Kodandaramaiah SB, Li L, Knoblich U, Zeng H, Haider B, Boyden ES, Forest CR. Autonomous patch-clamp robot for functional characterization of neurons in vivo: development and application to mouse visual cortex. J Neurophysiol 2019; 121:2341-2357. [PMID: 30969898 DOI: 10.1152/jn.00738.2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Patch clamping is the gold standard measurement technique for cell-type characterization in vivo, but it has low throughput, is difficult to scale, and requires highly skilled operation. We developed an autonomous robot that can acquire multiple consecutive patch-clamp recordings in vivo. In practice, 40 pipettes loaded into a carousel are sequentially filled and inserted into the brain, localized to a cell, used for patch clamping, and disposed. Automated visual stimulation and electrophysiology software enables functional cell-type classification of whole cell-patched cells, as we show for 37 cells in the anesthetized mouse in visual cortex (V1) layer 5. We achieved 9% yield, with 5.3 min per attempt over hundreds of trials. The highly variable and low-yield nature of in vivo patch-clamp recordings will benefit from such a standardized, automated, quantitative approach, allowing development of optimal algorithms and enabling scaling required for large-scale studies and integration with complementary techniques. NEW & NOTEWORTHY In vivo patch-clamp is the gold standard for intracellular recordings, but it is a very manual and highly skilled technique. The robot in this work demonstrates the most automated in vivo patch-clamp experiment to date, by enabling production of multiple, serial intracellular recordings without human intervention. The robot automates pipette filling, wire threading, pipette positioning, neuron hunting, break-in, delivering sensory stimulus, and recording quality control, enabling in vivo cell-type characterization.
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Affiliation(s)
- Gregory L Holst
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology , Atlanta, Georgia
| | - William Stoy
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology , Atlanta, Georgia
| | - Bo Yang
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology , Atlanta, Georgia
| | - Ilya Kolb
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology , Atlanta, Georgia
| | | | - Lu Li
- Allen Institute for Brain Science , Seattle, Washington
| | - Ulf Knoblich
- Allen Institute for Brain Science , Seattle, Washington
| | - Hongkui Zeng
- Allen Institute for Brain Science , Seattle, Washington
| | - Bilal Haider
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology , Atlanta, Georgia
| | - Edward S Boyden
- Media Arts and Sciences, Massachusetts Institute of Technology , Cambridge, Massachusetts.,McGovern Institute, Massachusetts Institute of Technology , Cambridge, Massachusetts.,Koch Institute, Massachusetts Institute of Technology , Cambridge, Massachusetts
| | - Craig R Forest
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology , Atlanta, Georgia
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23
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Obien MEJ, Hierlemann A, Frey U. Accurate signal-source localization in brain slices by means of high-density microelectrode arrays. Sci Rep 2019; 9:788. [PMID: 30692552 PMCID: PMC6349853 DOI: 10.1038/s41598-018-36895-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022] Open
Abstract
Extracellular recordings by means of high-density microelectrode arrays (HD-MEAs) have become a powerful tool to resolve subcellular details of single neurons in active networks grown from dissociated cells. To extend the application of this technology to slice preparations, we developed models describing how extracellular signals, produced by neuronal cells in slices, are detected by microelectrode arrays. The models help to analyze and understand the electrical-potential landscape in an in vitro HD-MEA-recording scenario based on point-current sources. We employed two modeling schemes, (i) a simple analytical approach, based on the method of images (MoI), and (ii) an approach, based on finite-element methods (FEM). We compared and validated the models with large-scale, high-spatiotemporal-resolution recordings of slice preparations by means of HD-MEAs. We then developed a model-based localization algorithm and compared the performance of MoI and FEM models. Both models provided accurate localization results and a comparable and negligible systematic error, when the point source was in saline, a condition similar to cell-culture experiments. Moreover, the relative random error in the x-y-z-localization amounted only up to 4.3% for z-distances up to 200 μm from the HD-MEA surface. In tissue, the systematic errors of both, MoI and FEM models were significantly higher, and a pre-calibration was required. Nevertheless, the FEM values proved to be closer to the tissue experimental results, yielding 5.2 μm systematic mean error, compared to 22.0 μm obtained with MoI. These results suggest that the medium volume or "saline height", the brain slice thickness and anisotropy, and the location of the reference electrode, which were included in the FEM model, considerably affect the extracellular signal and localization performance, when the signal source is at larger distance to the array. After pre-calibration, the relative random error of the z-localization in tissue was only 3% for z-distances up to 200 μm. We then applied the model and related detailed understanding of extracellular recordings to achieve an electrically-guided navigation of a stimulating micropipette, solely based on the measured HD-MEA signals, and managed to target spontaneously active neurons in an acute brain slice for electroporation.
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Affiliation(s)
- Marie Engelene J Obien
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- RIKEN Quantitative Biology Center, Kobe, Japan.
- MaxWell Biosystems AG, Basel, Switzerland.
| | - Andreas Hierlemann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Urs Frey
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- RIKEN Quantitative Biology Center, Kobe, Japan
- MaxWell Biosystems AG, Basel, Switzerland
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24
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25
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Kodandaramaiah SB, Flores FJ, Holst GL, Singer AC, Han X, Brown EN, Boyden ES, Forest CR. Multi-neuron intracellular recording in vivo via interacting autopatching robots. eLife 2018; 7:24656. [PMID: 29297466 PMCID: PMC5812718 DOI: 10.7554/elife.24656] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 12/19/2017] [Indexed: 11/16/2022] Open
Abstract
The activities of groups of neurons in a circuit or brain region are important for neuronal computations that contribute to behaviors and disease states. Traditional extracellular recordings have been powerful and scalable, but much less is known about the intracellular processes that lead to spiking activity. We present a robotic system, the multipatcher, capable of automatically obtaining blind whole-cell patch clamp recordings from multiple neurons simultaneously. The multipatcher significantly extends automated patch clamping, or 'autopatching’, to guide four interacting electrodes in a coordinated fashion, avoiding mechanical coupling in the brain. We demonstrate its performance in the cortex of anesthetized and awake mice. A multipatcher with four electrodes took an average of 10 min to obtain dual or triple recordings in 29% of trials in anesthetized mice, and in 18% of the trials in awake mice, thus illustrating practical yield and throughput to obtain multiple, simultaneous whole-cell recordings in vivo.
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Affiliation(s)
- Suhasa B Kodandaramaiah
- Media Lab, Massachusetts Institute of Technology, Cambridge, United States.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,G.W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, United States
| | - Francisco J Flores
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, United States.,Picower Institute for Memory and Learning, Massachusetts Institute of Technology, Cambridge, United States
| | - Gregory L Holst
- G.W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, United States
| | - Annabelle C Singer
- Media Lab, Massachusetts Institute of Technology, Cambridge, United States.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Xue Han
- Department of Biomedical Engineering, Boston University, Boston, United States
| | - Emery N Brown
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, United States.,Picower Institute for Memory and Learning, Massachusetts Institute of Technology, Cambridge, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology, Cambridge, United States.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Craig R Forest
- G.W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, United States
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26
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Annecchino LA, Schultz SR. Progress in automating patch clamp cellular physiology. Brain Neurosci Adv 2018; 2:2398212818776561. [PMID: 32166142 PMCID: PMC7058203 DOI: 10.1177/2398212818776561] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/19/2018] [Indexed: 12/30/2022] Open
Abstract
Patch clamp electrophysiology has transformed research in the life sciences over the last few decades. Since their inception, automatic patch clamp platforms have evolved considerably, demonstrating the capability to address both voltage- and ligand-gated channels, and showing the potential to play a pivotal role in drug discovery and biomedical research. Unfortunately, the cell suspension assays to which early systems were limited cannot recreate biologically relevant cellular environments, or capture higher order aspects of synaptic physiology and network dynamics. In vivo patch clamp electrophysiology has the potential to yield more biologically complex information and be especially useful in reverse engineering the molecular and cellular mechanisms of single-cell and network neuronal computation, while capturing important aspects of human disease mechanisms and possible therapeutic strategies. Unfortunately, it is a difficult procedure with a steep learning curve, which has restricted dissemination of the technique. Luckily, in vivo patch clamp electrophysiology seems particularly amenable to robotic automation. In this review, we document the development of automated patch clamp technology, from early systems based on multi-well plates through to automated planar-array platforms, and modern robotic platforms capable of performing two-photon targeted whole-cell electrophysiological recordings in vivo.
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Affiliation(s)
- Luca A. Annecchino
- Centre for Neurotechnology and Department of Bioengineering, Imperial College London, London, UK
| | - Simon R. Schultz
- Centre for Neurotechnology and Department of Bioengineering, Imperial College London, London, UK
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27
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Vogt N. Robots take over electrophysiology. Nat Methods 2017. [DOI: 10.1038/nmeth.4492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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