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Szarka G, Ganczer A, Balogh M, Tengölics ÁJ, Futácsi A, Kenyon G, Pan F, Kovács-Öller T, Völgyi B. Gap junctions fine-tune ganglion cell signals to equalize response kinetics within a given electrically coupled array. iScience 2024; 27:110099. [PMID: 38947503 PMCID: PMC11214328 DOI: 10.1016/j.isci.2024.110099] [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: 01/04/2024] [Revised: 03/06/2024] [Accepted: 05/22/2024] [Indexed: 07/02/2024] Open
Abstract
Retinal ganglion cells (RGCs) summate inputs and forward a spike train code to the brain in the form of either maintained spiking (sustained) or a quickly decaying brief spike burst (transient). We report diverse response transience values across the RGC population and, contrary to the conventional transient/sustained scheme, responses with intermediary characteristics are the most abundant. Pharmacological tests showed that besides GABAergic inhibition, gap junction (GJ)-mediated excitation also plays a pivotal role in shaping response transience and thus visual coding. More precisely GJs connecting RGCs to nearby amacrine and RGCs play a defining role in the process. These GJs equalize kinetic features, including the response transience of transient OFF alpha (tOFFα) RGCs across a coupled array. We propose that GJs in other coupled neuron ensembles in the brain are also critical in the harmonization of response kinetics to enhance the population code and suit a corresponding task.
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Affiliation(s)
- Gergely Szarka
- University of Pécs, Szentágothai Research Centre, Pécs, Hungary
- University of Pécs, Department of Neurobiology, Pécs, Hungary
- MTA-PTE NAP 2 Retinal Electrical Synapses Research Group, Pécs, Hungary
- Center for Neuroscience, University of Pécs, Pécs, Hungary
- SzKK Imaging Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Alma Ganczer
- University of Pécs, Szentágothai Research Centre, Pécs, Hungary
- University of Pécs, Department of Neurobiology, Pécs, Hungary
- MTA-PTE NAP 2 Retinal Electrical Synapses Research Group, Pécs, Hungary
- Center for Neuroscience, University of Pécs, Pécs, Hungary
| | - Márton Balogh
- University of Pécs, Szentágothai Research Centre, Pécs, Hungary
- University of Pécs, Department of Neurobiology, Pécs, Hungary
- MTA-PTE NAP 2 Retinal Electrical Synapses Research Group, Pécs, Hungary
- Center for Neuroscience, University of Pécs, Pécs, Hungary
| | - Ádám Jonatán Tengölics
- University of Pécs, Szentágothai Research Centre, Pécs, Hungary
- University of Pécs, Department of Neurobiology, Pécs, Hungary
- MTA-PTE NAP 2 Retinal Electrical Synapses Research Group, Pécs, Hungary
- Center for Neuroscience, University of Pécs, Pécs, Hungary
| | - Anett Futácsi
- University of Pécs, Szentágothai Research Centre, Pécs, Hungary
- MTA-PTE NAP 2 Retinal Electrical Synapses Research Group, Pécs, Hungary
- Center for Neuroscience, University of Pécs, Pécs, Hungary
- SzKK Imaging Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | | | - Feng Pan
- The Hong Kong Polytechnic University, Hong Kong, China
| | - Tamás Kovács-Öller
- University of Pécs, Szentágothai Research Centre, Pécs, Hungary
- University of Pécs, Department of Neurobiology, Pécs, Hungary
- MTA-PTE NAP 2 Retinal Electrical Synapses Research Group, Pécs, Hungary
- Center for Neuroscience, University of Pécs, Pécs, Hungary
- SzKK Imaging Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Béla Völgyi
- University of Pécs, Szentágothai Research Centre, Pécs, Hungary
- University of Pécs, Department of Neurobiology, Pécs, Hungary
- MTA-PTE NAP 2 Retinal Electrical Synapses Research Group, Pécs, Hungary
- Center for Neuroscience, University of Pécs, Pécs, Hungary
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2
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Pachitariu M, Sridhar S, Pennington J, Stringer C. Spike sorting with Kilosort4. Nat Methods 2024; 21:914-921. [PMID: 38589517 PMCID: PMC11093732 DOI: 10.1038/s41592-024-02232-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/01/2024] [Indexed: 04/10/2024]
Abstract
Spike sorting is the computational process of extracting the firing times of single neurons from recordings of local electrical fields. This is an important but hard problem in neuroscience, made complicated by the nonstationarity of the recordings and the dense overlap in electrical fields between nearby neurons. To address the spike-sorting problem, we have been openly developing the Kilosort framework. Here we describe the various algorithmic steps introduced in different versions of Kilosort. We also report the development of Kilosort4, a version with substantially improved performance due to clustering algorithms inspired by graph-based approaches. To test the performance of Kilosort, we developed a realistic simulation framework that uses densely sampled electrical fields from real experiments to generate nonstationary spike waveforms and realistic noise. We found that nearly all versions of Kilosort outperformed other algorithms on a variety of simulated conditions and that Kilosort4 performed best in all cases, correctly identifying even neurons with low amplitudes and small spatial extents in high drift conditions.
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Affiliation(s)
| | - Shashwat Sridhar
- HHMI, Ashburn, VA, USA
- Department of Ophthalmology, University Medical Center Göttingen, Göttingen, Germany
| | - Jacob Pennington
- HHMI, Ashburn, VA, USA
- Department of Mathematics, Washington State University, Vancouver, WA, USA
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3
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Zhang X, Dou Z, Kim SH, Upadhyay G, Havert D, Kang S, Kazemi K, Huang K, Aydin O, Huang R, Rahman S, Ellis‐Mohr A, Noblet HA, Lim KH, Chung HJ, Gritton HJ, Saif MTA, Kong HJ, Beggs JM, Gazzola M. Mind In Vitro Platforms: Versatile, Scalable, Robust, and Open Solutions to Interfacing with Living Neurons. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306826. [PMID: 38161217 PMCID: PMC10953569 DOI: 10.1002/advs.202306826] [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: 09/18/2023] [Revised: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Motivated by the unexplored potential of in vitro neural systems for computing and by the corresponding need of versatile, scalable interfaces for multimodal interaction, an accurate, modular, fully customizable, and portable recording/stimulation solution that can be easily fabricated, robustly operated, and broadly disseminated is presented. This approach entails a reconfigurable platform that works across multiple industry standards and that enables a complete signal chain, from neural substrates sampled through micro-electrode arrays (MEAs) to data acquisition, downstream analysis, and cloud storage. Built-in modularity supports the seamless integration of electrical/optical stimulation and fluidic interfaces. Custom MEA fabrication leverages maskless photolithography, favoring the rapid prototyping of a variety of configurations, spatial topologies, and constitutive materials. Through a dedicated analysis and management software suite, the utility and robustness of this system are demonstrated across neural cultures and applications, including embryonic stem cell-derived and primary neurons, organotypic brain slices, 3D engineered tissue mimics, concurrent calcium imaging, and long-term recording. Overall, this technology, termed "mind in vitro" to underscore the computing inspiration, provides an end-to-end solution that can be widely deployed due to its affordable (>10× cost reduction) and open-source nature, catering to the expanding needs of both conventional and unconventional electrophysiology.
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Affiliation(s)
- Xiaotian Zhang
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Zhi Dou
- Department of Mechanical Science and EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Seung Hyun Kim
- Department of Mechanical Science and EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Gaurav Upadhyay
- Department of Mechanical Science and EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Daniel Havert
- Department of PhysicsIndiana University BloomingtonBloomingtonIN47405USA
| | - Sehong Kang
- Department of Mechanical Science and EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Kimia Kazemi
- Department of Mechanical Science and EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Kai‐Yu Huang
- Department of Chemical and Biomolecular EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Onur Aydin
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Raymond Huang
- Department of Mechanical Science and EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Saeedur Rahman
- Department of Mechanical Science and EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Austin Ellis‐Mohr
- Department of Electrical and Computer EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Hayden A. Noblet
- Molecular and Integrative PhysiologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
- Neuroscience ProgramUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Ki H. Lim
- Molecular and Integrative PhysiologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Hee Jung Chung
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
- Molecular and Integrative PhysiologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
- Neuroscience ProgramUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Howard J. Gritton
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
- Department of Comparative BiosciencesUniversity of Illinois at Urbana–ChampaignUrbanaIL61802USA
| | - M. Taher A. Saif
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
- Department of Mechanical Science and EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - Hyun Joon Kong
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
- Department of Chemical and Biomolecular EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
| | - John M. Beggs
- Department of PhysicsIndiana University BloomingtonBloomingtonIN47405USA
| | - Mattia Gazzola
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
- Department of Mechanical Science and EngineeringUniversity of Illinois at Urbana–ChampaignUrbanaIL61801USA
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4
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Shokri M, Gogliettino AR, Hottowy P, Sher A, Litke AM, Chichilnisky EJ, Pequito S, Muratore D. Spike sorting in the presence of stimulation artifacts: a dynamical control systems approach. J Neural Eng 2024; 21:016022. [PMID: 38271715 PMCID: PMC10853761 DOI: 10.1088/1741-2552/ad228f] [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: 07/05/2023] [Revised: 11/08/2023] [Accepted: 01/25/2024] [Indexed: 01/27/2024]
Abstract
Objective. Bi-directional electronic neural interfaces, capable of both electrical recording and stimulation, communicate with the nervous system to permit precise calibration of electrical inputs by capturing the evoked neural responses. However, one significant challenge is that stimulation artifacts often mask the actual neural signals. To address this issue, we introduce a novel approach that employs dynamical control systems to detect and decipher electrically evoked neural activity despite the presence of electrical artifacts.Approach. Our proposed method leverages the unique spatiotemporal patterns of neural activity and electrical artifacts to distinguish and identify individual neural spikes. We designed distinctive dynamical models for both the stimulation artifact and each neuron observed during spontaneous neural activity. We can estimate which neurons were active by analyzing the recorded voltage responses across multiple electrodes post-stimulation. This technique also allows us to exclude signals from electrodes heavily affected by stimulation artifacts, such as the stimulating electrode itself, yet still accurately differentiate between evoked spikes and electrical artifacts.Main results. We applied our method to high-density multi-electrode recordings from the primate retina in anex vivosetup, using a grid of 512 electrodes. Through repeated electrical stimulations at varying amplitudes, we were able to construct activation curves for each neuron. The curves obtained with our method closely resembled those derived from manual spike sorting. Additionally, the stimulation thresholds we estimated strongly agreed with those determined through manual analysis, demonstrating high reliability (R2=0.951for human 1 andR2=0.944for human 2).Significance. Our method can effectively separate evoked neural spikes from stimulation artifacts by exploiting the distinct spatiotemporal propagation patterns captured by a dense, large-scale multi-electrode array. This technique holds promise for future applications in real-time closed-loop stimulation systems and for managing multi-channel stimulation strategies.
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Affiliation(s)
- Mohammad Shokri
- Delft Center for Systems and Control, Delft University of Technology, Delft 2628 CN, The Netherlands
| | - Alex R Gogliettino
- Neurosciences PhD Program, Stanford University, Stanford, CA 94305, United States of America
- Hansen Experimental Physics Laboratory, Stanford University, Stanford, CA 94305, United States of America
| | - Paweł Hottowy
- Faculty of Physics and Applied Computer Science, AGH University of Krakow, Krakow, Poland
| | - Alexander Sher
- Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, CA, United States of America
| | - Alan M Litke
- Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, CA, United States of America
| | - E J Chichilnisky
- Departments of Neurosurgery and Ophthalmology, Stanford University, Stanford, CA 94305, United States of America
| | - Sérgio Pequito
- Division of Systems and Control, Department of Information Technology, Uppsala University, 751 05 Uppsala, Sweden
| | - Dante Muratore
- Microelectronics Department, Delft University of Technology, Delft 2628 CN, The Netherlands
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5
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Chong HR, Ranjbar-Slamloo Y, Ho MZH, Ouyang X, Kamigaki T. Functional alterations of the prefrontal circuit underlying cognitive aging in mice. Nat Commun 2023; 14:7254. [PMID: 37945561 PMCID: PMC10636129 DOI: 10.1038/s41467-023-43142-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Executive function is susceptible to aging. How aging impacts the circuit-level computations underlying executive function remains unclear. Using calcium imaging and optogenetic manipulation during memory-guided behavior, we show that working-memory coding and the relevant recurrent connectivity in the mouse medial prefrontal cortex (mPFC) are altered as early as middle age. Population activity in the young adult mPFC exhibits dissociable yet overlapping patterns between tactile and auditory modalities, enabling crossmodal memory coding concurrent with modality-dependent coding. In middle age, however, crossmodal coding remarkably diminishes while modality-dependent coding persists, and both types of coding decay in advanced age. Resting-state functional connectivity, especially among memory-coding neurons, decreases already in middle age, suggesting deteriorated recurrent circuits for memory maintenance. Optogenetic inactivation reveals that the middle-aged mPFC exhibits heightened vulnerability to perturbations. These findings elucidate functional alterations of the prefrontal circuit that unfold in middle age and deteriorate further as a hallmark of cognitive aging.
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Affiliation(s)
- Huee Ru Chong
- Neuroscience & Mental Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Yadollah Ranjbar-Slamloo
- Neuroscience & Mental Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Malcolm Zheng Hao Ho
- Neuroscience & Mental Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
- IGP-Neuroscience, Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, 308232, Singapore
| | - Xuan Ouyang
- Neuroscience & Mental Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Tsukasa Kamigaki
- Neuroscience & Mental Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
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6
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Kim S, Jeon J, Ganbat D, Kim T, Shin K, Hong S, Hong J. Alteration of Neural Network and Hippocampal Slice Activation through Exosomes Derived from 5XFAD Nasal Lavage Fluid. Int J Mol Sci 2023; 24:14064. [PMID: 37762366 PMCID: PMC10531257 DOI: 10.3390/ijms241814064] [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: 08/09/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Exosomes, key mediators of intercellular transmission of pathogenic proteins, such as amyloid-beta and tau, significantly influence the progression and exacerbation of Alzheimer's disease (AD) pathology. Present in a variety of biological fluids, including cerebrospinal fluid, blood, saliva, and nasal lavage fluid (NLF), exosomes underscore their potential as integral mediators of AD pathology. By serving as vehicles for disease-specific molecules, exosomes could unveil valuable insights into disease identification and progression. This study emphasizes the imperative to investigate the impacts of exosomes on neural networks to enhance our comprehension of intracerebral neuronal communication and its implications for neurological disorders like AD. After harvesting exosomes derived from NLF of 5XFAD mice, we utilized a high-density multielectrode array (HD-MEA) system, the novel technology enabling concurrent recordings from thousands of neurons in primary cortical neuron cultures and organotypic hippocampal slices. The ensuing results revealed a surge in neuronal firing rates and disoriented neural connectivity, reflecting the effects provoked by pathological amyloid-beta oligomer treatment. The local field potentials in the exosome-treated hippocampal brain slices also exhibited aberrant rhythmicity, along with an elevated level of current source density. While this research is an initial exploration, it highlights the potential of exosomes in modulating neural networks under AD conditions and endorses the HD-MEA as an efficacious tool for exosome studies.
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Affiliation(s)
- Sangseong Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jaekyong Jeon
- Department of Pharmacy, Hanyang University, Ansan 15588, Republic of Korea; (J.J.); (D.G.)
| | - Dulguun Ganbat
- Department of Pharmacy, Hanyang University, Ansan 15588, Republic of Korea; (J.J.); (D.G.)
| | - Taewoon Kim
- Department of Bionanotechnology, Graduate School, Hanyang University, Seoul 04763, Republic of Korea; (T.K.); (K.S.)
| | - Kyusoon Shin
- Department of Bionanotechnology, Graduate School, Hanyang University, Seoul 04763, Republic of Korea; (T.K.); (K.S.)
| | - Sungho Hong
- Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Okinawa 904-0495, Japan;
| | - Jongwook Hong
- Department of Bionanotechnology, Graduate School, Hanyang University, Seoul 04763, Republic of Korea; (T.K.); (K.S.)
- Department of Medical and Digital Engineering, Graduate School, Hanyang University, Seoul 04763, Republic of Korea
- Department of Bionanoengineering, Hanyang University, Ansan 15588, Republic of Korea
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7
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Yu H, Qi Y, Pan G. NeuSort: an automatic adaptive spike sorting approach with neuromorphic models. J Neural Eng 2023; 20:056006. [PMID: 37659393 DOI: 10.1088/1741-2552/acf61d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 09/01/2023] [Indexed: 09/04/2023]
Abstract
Objective.Spike sorting, a critical step in neural data processing, aims to classify spiking events from single electrode recordings based on different waveforms. This study aims to develop a novel online spike sorter, NeuSort, using neuromorphic models, with the ability to adaptively adjust to changes in neural signals, including waveform deformations and the appearance of new neurons.Approach.NeuSort leverages a neuromorphic model to emulate template-matching processes. This model incorporates plasticity learning mechanisms inspired by biological neural systems, facilitating real-time adjustments to online parameters.Results.Experimental findings demonstrate NeuSort's ability to track neuron activities amidst waveform deformations and identify new neurons in real-time. NeuSort excels in handling non-stationary neural signals, significantly enhancing its applicability for long-term spike sorting tasks. Moreover, its implementation on neuromorphic chips guarantees ultra-low energy consumption during computation.Significance.NeuSort caters to the demand for real-time spike sorting in brain-machine interfaces through a neuromorphic approach. Its unsupervised, automated spike sorting process makes it a plug-and-play solution for online spike sorting.
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Affiliation(s)
- Hang Yu
- State Key Lab of Brain-Machine Intelligence, Hangzhou, People's Republic of China
- College of Computer Science and Technology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yu Qi
- State Key Lab of Brain-Machine Intelligence, Hangzhou, People's Republic of China
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital, Hangzhou, People's Republic of China
- MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Gang Pan
- State Key Lab of Brain-Machine Intelligence, Hangzhou, People's Republic of China
- College of Computer Science and Technology, Zhejiang University, Hangzhou, People's Republic of China
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8
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Seifert M, Roberts PA, Kafetzis G, Osorio D, Baden T. Birds multiplex spectral and temporal visual information via retinal On- and Off-channels. Nat Commun 2023; 14:5308. [PMID: 37652912 PMCID: PMC10471707 DOI: 10.1038/s41467-023-41032-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 08/18/2023] [Indexed: 09/02/2023] Open
Abstract
In vertebrate vision, early retinal circuits divide incoming visual information into functionally opposite elementary signals: On and Off, transient and sustained, chromatic and achromatic. Together these signals can yield an efficient representation of the scene for transmission to the brain via the optic nerve. However, this long-standing interpretation of retinal function is based on mammals, and it is unclear whether this functional arrangement is common to all vertebrates. Here we show that male poultry chicks use a fundamentally different strategy to communicate information from the eye to the brain. Rather than using functionally opposite pairs of retinal output channels, chicks encode the polarity, timing, and spectral composition of visual stimuli in a highly correlated manner: fast achromatic information is encoded by Off-circuits, and slow chromatic information overwhelmingly by On-circuits. Moreover, most retinal output channels combine On- and Off-circuits to simultaneously encode, or multiplex, both achromatic and chromatic information. Our results from birds conform to evidence from fish, amphibians, and reptiles which retain the full ancestral complement of four spectral types of cone photoreceptors.
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Affiliation(s)
- Marvin Seifert
- School of Life Sciences, University of Sussex, Brighton, UK.
| | - Paul A Roberts
- School of Life Sciences, University of Sussex, Brighton, UK
| | | | - Daniel Osorio
- School of Life Sciences, University of Sussex, Brighton, UK.
| | - Tom Baden
- School of Life Sciences, University of Sussex, Brighton, UK.
- Institute of Ophthalmic Research, University of Tübingen, Tübingen, Germany.
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9
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Celiker C, Weissova K, Cerna KA, Oppelt J, Dorgau B, Gambin FM, Sebestikova J, Lako M, Sernagor E, Liskova P, Barta T. Light-responsive microRNA molecules in human retinal organoids are differentially regulated by distinct wavelengths of light. iScience 2023; 26:107237. [PMID: 37485345 PMCID: PMC10362355 DOI: 10.1016/j.isci.2023.107237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/30/2023] [Accepted: 06/25/2023] [Indexed: 07/25/2023] Open
Abstract
Cells in the human retina must rapidly adapt to constantly changing visual stimuli. This fast adaptation to varying levels and wavelengths of light helps to regulate circadian rhythms and allows for adaptation to high levels of illumination, thereby enabling the rest of the visual system to remain responsive. It has been shown that retinal microRNA (miRNA) molecules play a key role in regulating these processes. However, despite extensive research using various model organisms, light-regulated miRNAs in human retinal cells remain unknown. Here, we aim to characterize these miRNAs. We generated light-responsive human retinal organoids that express miRNA families and clusters typically found in the retina. Using an in-house developed photostimulation device, we identified a subset of light-regulated miRNAs. Importantly, we found that these miRNAs are differentially regulated by distinct wavelengths of light and have a rapid turnover, highlighting the dynamic and adaptive nature of the human retina.
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Affiliation(s)
- Canan Celiker
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Kamila Weissova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Brno, Czech Republic
| | - Katerina Amruz Cerna
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jan Oppelt
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Philadelphia, PA, USA
| | - Birthe Dorgau
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Francisco Molina Gambin
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jana Sebestikova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Majlinda Lako
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Evelyne Sernagor
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Tomas Barta
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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10
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Donoghue K, Toreyin H. A Proof-of-Concept Numerical Ising Machine for Neural Spike Localization. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-5. [PMID: 38083117 DOI: 10.1109/embc40787.2023.10340471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Identifying the physical locations of neurons based on the spike waveforms captured by multiple recording channels, namely spike localization, can potentially enhance spike sorting accuracy. This study proposes a new method for spike localization, where the problem is first described as a nonconvex optimization problem and then the optimization is attempted heuristically via a numerical Ising solver. The paper first presents a quadratic unconstrained binary optimization (QUBO) formulation of spike localization. Then, a MATLAB solver simulating an Ising machine is written to solve the QUBO. The proposed method is evaluated on a 2D toy problem consisting of two electrodes and a single spike event, where the neuron location search is conducted in three different regions placed at increasing distances from the electrodes. The results indicate that the neuron can be accurately identified when in one of the nearest nodes to the electrodes, whereas the accuracy decreases to 87.5% and 75% as the search region distance increases. The study for the first time formulates the spike localization problem as a QUBO and demonstrates the feasibility of solving the resultant non-convex optimization problem heuristically using an Ising machine.Clinical Relevance- High channel-count implantable neural monitoring systems allow tracking large brain regions at the cost of increased data volumes to transmit and power dissipation. The new spike localization approach presented can potentially decrease the data volume and power consumption by enabling high accuracy spike localization at the implantable system.
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11
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Ghazal M, Scholaert C, Dumortier C, Lefebvre C, Barois N, Janel S, Tarhan MC, Colin M, Buée L, Halliez S, Pecqueur S, Coffinier Y, Alibart F, Yger P. Precision of neuronal localization in 2D cell cultures by using high-performance electropolymerized microelectrode arrays correlated with optical imaging. Biomed Phys Eng Express 2023; 9. [PMID: 36745905 DOI: 10.1088/2057-1976/acb93e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/06/2023] [Indexed: 02/08/2023]
Abstract
Recently, the development of electronic devices to extracellularly record the simultaneous electrical activities of numerous neurons has been blooming, opening new possibilities to interface and decode neuronal activity. In this work, we tested how the use of EDOT electropolymerization to tune post-fabrication materials could optimize the cell/electrode interface of such devices. Our results showed an improved signal-to-noise ratio, better biocompatibility, and a higher number of neurons detected in comparison with gold electrodes. Then, using such enhanced recordings with 2D neuronal cultures combined with fluorescent optical imaging, we checked the extent to which the positions of the recorded neurons could be estimated solely via their extracellular signatures. Our results showed that assuming neurons behave as monopoles, positions could be estimated with a precision of approximately tens of micrometers.
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Affiliation(s)
- Mahdi Ghazal
- Institut d'Électronique, Microélectronique et Nanotechnologie (IEMN), CNRS, UMR 8520, F-59652 Villeneuve d'Ascq, France
| | - Corentin Scholaert
- Institut d'Électronique, Microélectronique et Nanotechnologie (IEMN), CNRS, UMR 8520, F-59652 Villeneuve d'Ascq, France
| | - Corentin Dumortier
- Lille Neurosciences & Cognition (lilNCog)-U1172 (INSERM, Lille), Univ Lille, CHU Lille 59045 Lille, France
| | - Camille Lefebvre
- Lille Neurosciences & Cognition (lilNCog)-U1172 (INSERM, Lille), Univ Lille, CHU Lille 59045 Lille, France
| | - Nicolas Barois
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Sebastien Janel
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Mehmet Cagatay Tarhan
- Institut d'Électronique, Microélectronique et Nanotechnologie (IEMN), CNRS, UMR 8520, F-59652 Villeneuve d'Ascq, France
| | - Morvane Colin
- Lille Neurosciences & Cognition (lilNCog)-U1172 (INSERM, Lille), Univ Lille, CHU Lille 59045 Lille, France
| | - Luc Buée
- Lille Neurosciences & Cognition (lilNCog)-U1172 (INSERM, Lille), Univ Lille, CHU Lille 59045 Lille, France
| | - Sophie Halliez
- Lille Neurosciences & Cognition (lilNCog)-U1172 (INSERM, Lille), Univ Lille, CHU Lille 59045 Lille, France
| | - Sebastien Pecqueur
- Institut d'Électronique, Microélectronique et Nanotechnologie (IEMN), CNRS, UMR 8520, F-59652 Villeneuve d'Ascq, France
| | - Yannick Coffinier
- Institut d'Électronique, Microélectronique et Nanotechnologie (IEMN), CNRS, UMR 8520, F-59652 Villeneuve d'Ascq, France
| | - Fabien Alibart
- Institut d'Électronique, Microélectronique et Nanotechnologie (IEMN), CNRS, UMR 8520, F-59652 Villeneuve d'Ascq, France
- Laboratoire Nanotechnologies & Nanosystèmes (LN2), CNRS, Université de Sherbrooke, J1X0A5, Sherbrooke, Canada
| | - Pierre Yger
- Lille Neurosciences & Cognition (lilNCog)-U1172 (INSERM, Lille), Univ Lille, CHU Lille 59045 Lille, France
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
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12
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Edge computing on TPU for brain implant signal analysis. Neural Netw 2023; 162:212-224. [PMID: 36921432 DOI: 10.1016/j.neunet.2023.02.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/18/2023] [Accepted: 02/23/2023] [Indexed: 03/04/2023]
Abstract
The ever-increasing number of recording sites of silicon-based probes imposes a great challenge for detecting and evaluating single-unit activities in an accurate and efficient manner. Currently separate solutions are available for high precision offline evaluation and separate solutions for embedded systems where computational resources are more limited. We propose a deep learning-based spike sorting system, that utilizes both unsupervised and supervised paradigms to learn a general feature embedding space and detect neural activity in raw data as well as predict the feature vectors for sorting. The unsupervised component uses contrastive learning to extract features from individual waveforms, while the supervised component is based on the MobileNetV2 architecture. One of the key advantages of our system is that it can be trained on multiple, diverse datasets simultaneously, resulting in greater generalizability than previous deep learning-based models. We demonstrate that the proposed model does not only reaches the accuracy of current state-of-art offline spike sorting methods but has the unique potential to run on edge Tensor Processing Units (TPUs), specialized chips designed for artificial intelligence and edge computing. We compare our model performance with state of art solutions on paired datasets as well as on hybrid recordings as well. The herein demonstrated system paves the way to the integration of deep learning-based spike sorting algorithms into wearable electronic devices, which will be a crucial element of high-end brain-computer interfaces.
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13
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Abstract
Visual information processing in the retina requires the rhythmic expression of clock genes. The intrinsic retinal circadian clock is independent of the master clock located in the hypothalamic suprachiasmatic nucleus and emerges from retinal cells, including glia. Less clear is how glial oscillators influence the daily regulation of visual information processing in the mouse retina. Here, we demonstrate that the adult conditional deletion of the gene Bmal1 in GLAST-positive glial cells alters retinal physiology. Specifically, such deletion was sufficient to lower the amplitude of the electroretinogram b-wave recorded under light-adapted conditions. Furthermore, recordings from > 20,000 retinal ganglion cells (RGCs), the retina output, showed a non-uniform effect on RGCs activity in response to light across different cell types and over a 24-h period. Overall, our results suggest a new role of a glial circadian gene in adjusting mammalian retinal output throughout the night-day cycle.
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14
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Gill BJA, Khan FA, Goldberg AR, Merricks EM, Wu X, Sosunov AA, Sudhakar TD, Dovas A, Lado W, Michalak AJ, Teoh JJ, Liou JY, Frankel WN, McKhann GM, Canoll P, Schevon CA. Single unit analysis and wide-field imaging reveal alterations in excitatory and inhibitory neurons in glioma. Brain 2022; 145:3666-3680. [PMID: 35552612 PMCID: PMC10202150 DOI: 10.1093/brain/awac168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 02/05/2022] [Accepted: 04/27/2022] [Indexed: 11/14/2022] Open
Abstract
While several studies have attributed the development of tumour-associated seizures to an excitatory-inhibitory imbalance, we have yet to resolve the spatiotemporal interplay between different types of neuron in glioma-infiltrated cortex. Herein, we combined methods for single unit analysis of microelectrode array recordings with wide-field optical mapping of Thy1-GCaMP pyramidal cells in an ex vivo acute slice model of diffusely infiltrating glioma. This enabled simultaneous tracking of individual neurons from both excitatory and inhibitory populations throughout seizure-like events. Moreover, our approach allowed for observation of how the crosstalk between these neurons varied spatially, as we recorded across an extended region of glioma-infiltrated cortex. In tumour-bearing slices, we observed marked alterations in single units classified as putative fast-spiking interneurons, including reduced firing, activity concentrated within excitatory bursts and deficits in local inhibition. These results were correlated with increases in overall excitability. Mechanistic perturbation of this system with the mTOR inhibitor AZD8055 revealed increased firing of putative fast-spiking interneurons and restoration of local inhibition, with concomitant decreases in overall excitability. Altogether, our findings suggest that diffusely infiltrating glioma affect the interplay between excitatory and inhibitory neuronal populations in a reversible manner, highlighting a prominent role for functional mechanisms linked to mTOR activation.
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Affiliation(s)
- Brian J A Gill
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Farhan A Khan
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexander R Goldberg
- Department of Pathology and Cell Biology, Irving Cancer Research Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Edward M Merricks
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xiaoping Wu
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Alexander A Sosunov
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tejaswi D Sudhakar
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Athanassios Dovas
- Department of Pathology and Cell Biology, Irving Cancer Research Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wudu Lado
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrew J Michalak
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jia Jie Teoh
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jyun-you Liou
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Wayne N Frankel
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Guy M McKhann
- Department of Neurological Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Irving Cancer Research Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Catherine A Schevon
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
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15
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Naughton JR, Varela JA, Connolly TJ, Shepard S, Dodge TE, Kempa K, Burns MJ, Christianson JP, Naughton MJ. Suppression of crosstalk in multielectrode arrays with local shielding. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.948337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Electrical crosstalk can constrain the performance of multielectrode arrays in electro- and neurophysiology, in terms of both stimulation and recording. This is especially so at high electrode density, desirable for spatiotemporal mapping of bioelectrical signals from multiple cells. Channel interference due to crosstalk is currently only partially addressed, via continuous interleaved sampling or post-data acquisition spike sorting. Here, we show that a locally-shielded electrode architecture significantly suppresses crosstalk, and enables multi-site recording at high electrode density without the need for spike sorting. Arrays of shielded electrodes, prepared by micro- and nanofabrication techniques in a vertically-oriented coaxial geometry, demonstrate at least a 400 times improvement in spatial density over the unshielded case.
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16
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Radmanesh M, Rezaei AA, Jalili M, Hashemi A, Goudarzi MM. Online spike sorting via deep contractive autoencoder. Neural Netw 2022; 155:39-49. [DOI: 10.1016/j.neunet.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 07/03/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022]
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17
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Bod RB, Rokai J, Meszéna D, Fiáth R, Ulbert I, Márton G. From End to End: Gaining, Sorting, and Employing High-Density Neural Single Unit Recordings. Front Neuroinform 2022; 16:851024. [PMID: 35769832 PMCID: PMC9236662 DOI: 10.3389/fninf.2022.851024] [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: 01/08/2022] [Accepted: 05/06/2022] [Indexed: 11/15/2022] Open
Abstract
The meaning behind neural single unit activity has constantly been a challenge, so it will persist in the foreseeable future. As one of the most sourced strategies, detecting neural activity in high-resolution neural sensor recordings and then attributing them to their corresponding source neurons correctly, namely the process of spike sorting, has been prevailing so far. Support from ever-improving recording techniques and sophisticated algorithms for extracting worthwhile information and abundance in clustering procedures turned spike sorting into an indispensable tool in electrophysiological analysis. This review attempts to illustrate that in all stages of spike sorting algorithms, the past 5 years innovations' brought about concepts, results, and questions worth sharing with even the non-expert user community. By thoroughly inspecting latest innovations in the field of neural sensors, recording procedures, and various spike sorting strategies, a skeletonization of relevant knowledge lays here, with an initiative to get one step closer to the original objective: deciphering and building in the sense of neural transcript.
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Affiliation(s)
- Réka Barbara Bod
- Laboratory of Experimental Neurophysiology, Department of Physiology, Faculty of Medicine, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureş, Târgu Mureş, Romania
| | - János Rokai
- Integrative Neuroscience Group, Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Budapest, Hungary
- School of PhD Studies, Semmelweis University, Budapest, Hungary
| | - Domokos Meszéna
- Integrative Neuroscience Group, Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Richárd Fiáth
- Integrative Neuroscience Group, Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - István Ulbert
- Integrative Neuroscience Group, Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Gergely Márton
- Integrative Neuroscience Group, Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
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18
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Dorgau B, Georgiou M, Chaudhary A, Moya-Molina M, Collin J, Queen R, Hilgen G, Davey T, Hewitt P, Schmitt M, Kustermann S, Pognan F, Steel DH, Sernagor E, Armstrong L, Lako M. Human Retinal Organoids Provide a Suitable Tool for Toxicological Investigations: A Comprehensive Validation Using Drugs and Compounds Affecting the Retina. Stem Cells Transl Med 2022; 11:159-177. [PMID: 35298655 PMCID: PMC8929478 DOI: 10.1093/stcltm/szab010] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/13/2021] [Indexed: 12/04/2022] Open
Abstract
Retinal drug toxicity screening is essential for the development of safe treatment strategies for a large number of diseases. To this end, retinal organoids derived from human pluripotent stem cells (hPSCs) provide a suitable screening platform due to their similarity to the human retina and the ease of generation in large-scale formats. In this study, two hPSC cell lines were differentiated to retinal organoids, which comprised all key retinal cell types in multiple nuclear and synaptic layers. Single-cell RNA-Seq of retinal organoids indicated the maintenance of retinal ganglion cells and development of bipolar cells: both cell types segregated into several subtypes. Ketorolac, digoxin, thioridazine, sildenafil, ethanol, and methanol were selected as key compounds to screen on retinal organoids because of their well-known retinal toxicity profile described in the literature. Exposure of the hPSC-derived retinal organoids to digoxin, thioridazine, and sildenafil resulted in photoreceptor cell death, while digoxin and thioridazine additionally affected all other cell types, including Müller glia cells. All drug treatments caused activation of astrocytes, indicated by dendrites sprouting into neuroepithelium. The ability to respond to light was preserved in organoids although the number of responsive retinal ganglion cells decreased after drug exposure. These data indicate similar drug effects in organoids to those reported in in vivo models and/or in humans, thus providing the first robust experimental evidence of their suitability for toxicological studies.
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Affiliation(s)
- Birthe Dorgau
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
- Newcells Biotech, Biosphere, Newcastle Helix, Newcastle upon Tyne, UK
| | - Maria Georgiou
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Alexander Chaudhary
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Marina Moya-Molina
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
- Newcells Biotech, Biosphere, Newcastle Helix, Newcastle upon Tyne, UK
| | - Joseph Collin
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Rachel Queen
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Gerrit Hilgen
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
- Northumbria University, Applied Sciences, Faculty of Health and Life Science, Newcastle upon Tyne, UK
| | - Tracey Davey
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
- Electron Microscopy Research Services, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Stefan Kustermann
- Pharmaceutical Sciences, F. Hoffmann-La Roche, Pharma Research and Early Development, Roche Innovation Center Basel, Switzerland
| | | | - David H Steel
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Evelyne Sernagor
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Lyle Armstrong
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
- Newcells Biotech, Biosphere, Newcastle Helix, Newcastle upon Tyne, UK
| | - Majlinda Lako
- Newcastle University, Biosciences Institute, Faculty of Medical Sciences, Newcastle upon Tyne, UK
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19
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Hilgen G, Kartsaki E, Kartysh V, Cessac B, Sernagor E. A novel approach to the functional classification of retinal ganglion cells. Open Biol 2022; 12:210367. [PMID: 35259949 PMCID: PMC8905177 DOI: 10.1098/rsob.210367] [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] [Indexed: 01/09/2023] Open
Abstract
Retinal neurons are remarkedly diverse based on structure, function and genetic identity. Classifying these cells is a challenging task, requiring multimodal methodology. Here, we introduce a novel approach for retinal ganglion cell (RGC) classification, based on pharmacogenetics combined with immunohistochemistry and large-scale retinal electrophysiology. Our novel strategy allows grouping of cells sharing gene expression and understanding how these cell classes respond to basic and complex visual scenes. Our approach consists of several consecutive steps. First, the spike firing frequency is increased in RGCs co-expressing a certain gene (Scnn1a or Grik4) using excitatory DREADDs (designer receptors exclusively activated by designer drugs) in order to single out activity originating specifically from these cells. Their spike location is then combined with post hoc immunostaining, to unequivocally characterize their anatomical and functional features. We grouped these isolated RGCs into multiple clusters based on spike train similarities. Using this novel approach, we were able to extend the pre-existing list of Grik4-expressing RGC types to a total of eight and, for the first time, we provide a phenotypical description of 13 Scnn1a-expressing RGCs. The insights and methods gained here can guide not only RGC classification but neuronal classification challenges in other brain regions as well.
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Affiliation(s)
- Gerrit Hilgen
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK,Health and Life Sciences, Applied Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Evgenia Kartsaki
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK,Université Côte d'Azur, Inria, Biovision team and Neuromod Institute, 06902 Sophia Antipolis Cedex, France
| | - Viktoriia Kartysh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), 1090 Vienna, Austria,Research Centre for Molecular Medicine (CeMM) of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Bruno Cessac
- Université Côte d'Azur, Inria, Biovision team and Neuromod Institute, 06902 Sophia Antipolis Cedex, France
| | - Evelyne Sernagor
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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20
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Shabestari PS, Buccino AP, Kumar SS, Pedrocchi A, Hierlemann A. A modulated template-matching approach to improve spike sorting of bursting neurons. IEEE BIOMEDICAL CIRCUITS AND SYSTEMS CONFERENCE : HEALTHCARE TECHNOLOGY : [PROCEEDINGS]. IEEE BIOMEDICAL CIRCUITS AND SYSTEMS CONFERENCE 2021; 2021:9644995. [PMID: 35018369 PMCID: PMC7612198 DOI: 10.1109/biocas49922.2021.9644995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In extracellular neural electrophysiology, individual spikes have to be assigned to their cell of origin in a procedure called "spike sorting". Spike sorting is an unsupervised problem, since no ground-truth information is generally available. Here, we focus on improving spike sorting performance, particularly during periods of high synchronous activity or so-called "bursting". Bursting entails systematic changes in spike shapes and amplitudes and remains a challenge for current spike sorting schemes. We use realistic simulated bursting recordings of high-density micro-electrode arrays (HD-MEAs) and we present a fully automated algorithm based on template matching with a focus on recovering missed spikes during bursts. To compare and benchmark spike-sorting performance after applying our method, we used ground-truth information of simulated recordings. We show that our approach can be effective in improving spike sorting performance during bursting. Further validation with experimental recordings is necessary.
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Affiliation(s)
- Payam S. Shabestari
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Electronics, Informatics, and Biomedical Engineering, Politecnico di Milano, Milan, Italy
| | - Alessio P. Buccino
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sreedhar S. Kumar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Alessandra Pedrocchi
- Department of Electronics, Informatics, and Biomedical Engineering, Politecnico di Milano, Milan, Italy
| | - Andreas Hierlemann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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21
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Qin Y, Zhang N, Chen Y, Tan Y, Yang Z, Shi Y, Luo C, Liu T, Yao D. Probing the Functional and Structural Connectivity Underlying EEG Traveling Waves. Brain Topogr 2021; 35:66-78. [PMID: 34291338 DOI: 10.1007/s10548-021-00862-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 06/27/2021] [Indexed: 11/29/2022]
Abstract
Neural oscillations play an important role in the maintenance of brain function by regulating multi-scale neural activity. Characterizing the traveling properties of EEG is helpful for understanding the spatiotemporal dynamics of neural oscillations. However, traveling EEG based on non-invasive approach has little been investigated, and the relationship with brain intrinsic connectivity is not well known. In this study, traveling EEG of different frequency bands on the scalp in terms of the center of mass (EEG-CM) was examined. Then, two quantitative indexes describing the spatiotemporal features of EEG-CM were proposed, i.e., the traveling lateralization and velocity of EEG-CM. Further, based on simultaneous EEG-MRI approach, the relationship between traveling EEG-CM and the resting-state functional networks, as well as the microstructural connectivity of white matter was investigated. The results showed that there was similar spatial distribution of EEG-CM under different frequency bands, while the velocity of rhythmic EEG-CM increased in higher frequency bands. The lateralization of EEG-CM in low frequency bands (< 30 Hz) demonstrated negative relationship with the basal ganglia network (BGN). In addition, the velocity of the traveling EEG-CM was associated with the fractional anisotropy (FA) in corpus callosum and corona radiate. These results provided valid quantitative EEG index for understanding the spatiotemporal characteristics of the scalp EEG, and implied that the EEG dynamics were representations of functional and structural organization of cortical and subcortical structures.
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Affiliation(s)
- Yun Qin
- MOE Key Lab for NeuroInformation, The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China.,Sichuan Institute for Brain Science and Brain-Inspired Intelligence, Chengdu, P.R. China
| | - Nan Zhang
- MOE Key Lab for NeuroInformation, The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Chen
- MOE Key Lab for NeuroInformation, The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - Yue Tan
- MOE Key Lab for NeuroInformation, The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhenglin Yang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Yi Shi
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Cheng Luo
- MOE Key Lab for NeuroInformation, The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Tiejun Liu
- MOE Key Lab for NeuroInformation, The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China.,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China.,Sichuan Institute for Brain Science and Brain-Inspired Intelligence, Chengdu, P.R. China
| | - Dezhong Yao
- MOE Key Lab for NeuroInformation, The Clinical Hospital of Chengdu Brain Science Institute, University of Electronic Science and Technology of China, Chengdu, China. .,School of Life Science and Technology, Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China. .,Sichuan Institute for Brain Science and Brain-Inspired Intelligence, Chengdu, P.R. China.
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22
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Toosi R, Akhaee MA, Dehaqani MRA. An automatic spike sorting algorithm based on adaptive spike detection and a mixture of skew-t distributions. Sci Rep 2021; 11:13925. [PMID: 34230517 PMCID: PMC8260722 DOI: 10.1038/s41598-021-93088-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/07/2021] [Indexed: 11/09/2022] Open
Abstract
Developing high-density electrodes for recording large ensembles of neurons provides a unique opportunity for understanding the mechanism of the neuronal circuits. Nevertheless, the change of brain tissue around chronically implanted neural electrodes usually causes spike wave-shape distortion and raises the crucial issue of spike sorting with an unstable structure. The automatic spike sorting algorithms have been developed to extract spikes from these big extracellular data. However, due to the spike wave-shape instability, there have been a lack of robust spike detection procedures and clustering to overcome the spike loss problem. Here, we develop an automatic spike sorting algorithm based on adaptive spike detection and a mixture of skew-t distributions to address these distortions and instabilities. The adaptive detection procedure applies to the detected spikes, consists of multi-point alignment and statistical filtering for removing mistakenly detected spikes. The detected spikes are clustered based on the mixture of skew-t distributions to deal with non-symmetrical clusters and spike loss problems. The proposed algorithm improves the performance of the spike sorting in both terms of precision and recall, over a broad range of signal-to-noise ratios. Furthermore, the proposed algorithm has been validated on different datasets and demonstrates a general solution to precise spike sorting, in vitro and in vivo.
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Affiliation(s)
- Ramin Toosi
- School of Electrical and Computer Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Mohammad Ali Akhaee
- School of Electrical and Computer Engineering, College of Engineering, University of Tehran, Tehran, Iran.
| | - Mohammad-Reza A Dehaqani
- School of Electrical and Computer Engineering, College of Engineering, University of Tehran, Tehran, Iran. .,Cognitive Systems Laboratory, Control and Intelligent Processing Center of Excellence (CIPCE), School of Electrical and Computer Engineering, College of Engineering, University of Tehran, Tehran, Iran. .,School of Cognitive Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
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23
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Chen K, Jiang Y, Wu Z, Zheng N, Wang H, Hong H. HTsort: Enabling Fast and Accurate Spike Sorting on Multi-Electrode Arrays. Front Comput Neurosci 2021; 15:657151. [PMID: 34234663 PMCID: PMC8255361 DOI: 10.3389/fncom.2021.657151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
Spike sorting is used to classify the spikes (action potentials acquired by physiological electrodes), aiming to identify their respective firing units. Now it has been developed to classify the spikes recorded by multi-electrode arrays (MEAs), with the improvement of micro-electrode technology. However, how to improve classification accuracy and maintain low time complexity simultaneously becomes a difficulty. A fast and accurate spike sorting approach named HTsort is proposed for high-density multi-electrode arrays in this paper. Several improvements have been introduced to the traditional pipeline that is composed of threshold detection and clustering method. First, the divide-and-conquer method is employed to utilize electrode spatial information to achieve pre-clustering. Second, the clustering method HDBSCAN (hierarchical density-based spatial clustering of applications with noise) is used to classify spikes and detect overlapping events (multiple spikes firing simultaneously). Third, the template merging method is used to merge redundant exported templates according to the template similarity and the spatial distribution of electrodes. Finally, the template matching method is used to resolve overlapping events. Our approach is validated on simulation data constructed by ourselves and publicly available data and compared to other state-of-the-art spike sorters. We found that the proposed HTsort has a more favorable trade-off between accuracy and time consumption. Compared with MountainSort and SpykingCircus, the time consumption is reduced by at least 40% when the number of electrodes is 64 and below. Compared with HerdingSpikes, the classification accuracy can typically improve by more than 10%. Meanwhile, HTsort exhibits stronger robustness against background noise than other sorters. Our more sophisticated spike sorter would facilitate neurophysiologists to complete spike sorting more quickly and accurately.
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Affiliation(s)
- Keming Chen
- Key Laboratory of Radio Frequency Circuit and System, Hangzhou Dianzi University, Hangzhou, China
| | - Yangtao Jiang
- Key Laboratory of Radio Frequency Circuit and System, Hangzhou Dianzi University, Hangzhou, China
| | - Zhanxiong Wu
- Key Laboratory of Radio Frequency Circuit and System, Hangzhou Dianzi University, Hangzhou, China
| | - Nenggan Zheng
- Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, China
| | - Haochuan Wang
- Key Laboratory of Radio Frequency Circuit and System, Hangzhou Dianzi University, Hangzhou, China
| | - Hui Hong
- Key Laboratory of Radio Frequency Circuit and System, Hangzhou Dianzi University, Hangzhou, China
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24
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Duplicate Detection of Spike Events: A Relevant Problem in Human Single-Unit Recordings. Brain Sci 2021; 11:brainsci11060761. [PMID: 34201115 PMCID: PMC8228483 DOI: 10.3390/brainsci11060761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022] Open
Abstract
Single-unit recordings in the brain of behaving human subjects provide a unique opportunity to advance our understanding of neural mechanisms of cognition. These recordings are exclusively performed in medical centers during diagnostic or therapeutic procedures. The presence of medical instruments along with other aspects of the hospital environment limit the control of electrical noise compared to animal laboratory environments. Here, we highlight the problem of an increased occurrence of simultaneous spike events on different recording channels in human single-unit recordings. Most of these simultaneous events were detected in clusters previously labeled as artifacts and showed similar waveforms. These events may result from common external noise sources or from different micro-electrodes recording activity from the same neuron. To address the problem of duplicate recorded events, we introduce an open-source algorithm to identify these artificial spike events based on their synchronicity and waveform similarity. Applying our method to a comprehensive dataset of human single-unit recordings, we demonstrate that our algorithm can substantially increase the data quality of these recordings. Given our findings, we argue that future studies of single-unit activity recorded under noisy conditions should employ algorithms of this kind to improve data quality.
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25
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Buccino AP, Einevoll GT. MEArec: A Fast and Customizable Testbench Simulator for Ground-truth Extracellular Spiking Activity. Neuroinformatics 2021; 19:185-204. [PMID: 32648042 PMCID: PMC7782412 DOI: 10.1007/s12021-020-09467-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
When recording neural activity from extracellular electrodes, both in vivo and in vitro, spike sorting is a required and very important processing step that allows for identification of single neurons’ activity. Spike sorting is a complex algorithmic procedure, and in recent years many groups have attempted to tackle this problem, resulting in numerous methods and software packages. However, validation of spike sorting techniques is complicated. It is an inherently unsupervised problem and it is hard to find universal metrics to evaluate performance. Simultaneous recordings that combine extracellular and patch-clamp or juxtacellular techniques can provide ground-truth data to evaluate spike sorting methods. However, their utility is limited by the fact that only a few cells can be measured at the same time. Simulated ground-truth recordings can provide a powerful alternative mean to rank the performance of spike sorters. We present here MEArec, a Python-based software which permits flexible and fast simulation of extracellular recordings. MEArec allows users to generate extracellular signals on various customizable electrode designs and can replicate various problematic aspects for spike sorting, such as bursting, spatio-temporal overlapping events, and drifts. We expect MEArec will provide a common testbench for spike sorting development and evaluation, in which spike sorting developers can rapidly generate and evaluate the performance of their algorithms.
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Affiliation(s)
- Alessio Paolo Buccino
- Centre for Integrative Neuroplasticity (CINPLA), University of Oslo, Oslo, Norway. .,Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland.
| | - Gaute Tomas Einevoll
- Centre for Integrative Neuroplasticity (CINPLA), University of Oslo, Oslo, Norway.,Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
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26
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Li W, Qin S, Lu Y, Wang H, Xu Z, Wu T. A facile and comprehensive algorithm for electrical response identification in mouse retinal ganglion cells. PLoS One 2021; 16:e0246547. [PMID: 33705406 PMCID: PMC7951861 DOI: 10.1371/journal.pone.0246547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 01/20/2021] [Indexed: 12/01/2022] Open
Abstract
Retinal prostheses can restore the basic visual function of patients with retinal degeneration, which relies on effective electrical stimulation to evoke the physiological activities of retinal ganglion cells (RGCs). Current electrical stimulation strategies have defects such as unstable effects and insufficient stimulation positions, therefore, it is crucial to determine the optimal pulse parameters for precise and safe electrical stimulation. Biphasic voltages (cathode-first) with a pulse width of 25 ms and different amplitudes were used to ex vivo stimulate RGCs of three wild-type (WT) mice using a commercial microelectrode array (MEA) recording system. An algorithm is developed to automatically realize both spike-sorting and electrical response identification for the spike signals recorded. Measured from three WT mouse retinas, the total numbers of RGC units and responsive RGC units were 1193 and 151, respectively. In addition, the optimal pulse amplitude range for electrical stimulation was determined to be 0.43 V-1.3 V. The processing results of the automatic algorithm we proposed shows high consistency with those using traditional manual processing. We anticipate the new algorithm can not only speed up the elaborate electrophysiological data processing, but also optimize pulse parameters for the electrical stimulation strategy of neural prostheses.
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Affiliation(s)
- Wanying Li
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shan Qin
- Shenzhen Shekou People’s Hospital, Shenzhen, China
| | - Yijie Lu
- Shenzhen Aier Eye Hospital, Shenzhen, China
| | - Hao Wang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhen Xu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- * E-mail: (TZW); (ZX)
| | - Tianzhun Wu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- * E-mail: (TZW); (ZX)
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27
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Zerti D, Hilgen G, Dorgau B, Collin J, Ader M, Armstrong L, Sernagor E, Lako M. Transplanted pluripotent stem cell-derived photoreceptor precursors elicit conventional and unusual light responses in mice with advanced retinal degeneration. STEM CELLS (DAYTON, OHIO) 2021; 39:882-896. [PMID: 33657251 DOI: 10.1002/stem.3365] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 02/19/2021] [Indexed: 11/09/2022]
Abstract
Retinal dystrophies often lead to blindness. Developing therapeutic interventions to restore vision is therefore of paramount importance. Here we demonstrate the ability of pluripotent stem cell-derived cone precursors to engraft and restore light responses in the Pde6brd1 mouse, an end-stage photoreceptor degeneration model. Our data show that up to 1.5% of precursors integrate into the host retina, differentiate into cones, and engraft in close apposition to the host bipolar cells. Half of the transplanted mice exhibited visual behavior and of these 33% showed binocular light sensitivity. The majority of retinal ganglion cells exhibited contrast-sensitive ON, OFF or ON-OFF light responses and even motion sensitivity; however, quite a few exhibited unusual responses (eg, light-induced suppression), presumably reflecting remodeling of the neural retina. Our data indicate that despite relatively low engraftment yield, pluripotent stem cell-derived cone precursors can elicit light responsiveness even at advanced degeneration stages. Further work is needed to improve engraftment yield and counteract retinal remodeling to achieve useful clinical applications.
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Affiliation(s)
- Darin Zerti
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Microscopy Centre and Department of Applied Clinical Sciences and Biotechnology, University of L'Aquila, L'Aquila, Italy
| | - Gerrit Hilgen
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Birthe Dorgau
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Joseph Collin
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Marius Ader
- CRTD/Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Lyle Armstrong
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Evelyne Sernagor
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Majlinda Lako
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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28
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Passaro AP, Stice SL. Electrophysiological Analysis of Brain Organoids: Current Approaches and Advancements. Front Neurosci 2021; 14:622137. [PMID: 33510616 PMCID: PMC7835643 DOI: 10.3389/fnins.2020.622137] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/11/2020] [Indexed: 12/23/2022] Open
Abstract
Brain organoids, or cerebral organoids, have become widely used to study the human brain in vitro. As pluripotent stem cell-derived structures capable of self-organization and recapitulation of physiological cell types and architecture, brain organoids bridge the gap between relatively simple two-dimensional human cell cultures and non-human animal models. This allows for high complexity and physiological relevance in a controlled in vitro setting, opening the door for a variety of applications including development and disease modeling and high-throughput screening. While technologies such as single cell sequencing have led to significant advances in brain organoid characterization and understanding, improved functional analysis (especially electrophysiology) is needed to realize the full potential of brain organoids. In this review, we highlight key technologies for brain organoid development and characterization, then discuss current electrophysiological methods for brain organoid analysis. While electrophysiological approaches have improved rapidly for two-dimensional cultures, only in the past several years have advances been made to overcome limitations posed by the three-dimensionality of brain organoids. Here, we review major advances in electrophysiological technologies and analytical methods with a focus on advances with applicability for brain organoid analysis.
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Affiliation(s)
- Austin P. Passaro
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Division of Neuroscience, Biomedical & Health Sciences Institute, University of Georgia, Athens, GA, United States
| | - Steven L. Stice
- Regenerative Bioscience Center, University of Georgia, Athens, GA, United States
- Division of Neuroscience, Biomedical & Health Sciences Institute, University of Georgia, Athens, GA, United States
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
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29
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Buccino AP, Hurwitz CL, Garcia S, Magland J, Siegle JH, Hurwitz R, Hennig MH. SpikeInterface, a unified framework for spike sorting. eLife 2020; 9:e61834. [PMID: 33170122 PMCID: PMC7704107 DOI: 10.7554/elife.61834] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022] Open
Abstract
Much development has been directed toward improving the performance and automation of spike sorting. This continuous development, while essential, has contributed to an over-saturation of new, incompatible tools that hinders rigorous benchmarking and complicates reproducible analysis. To address these limitations, we developed SpikeInterface, a Python framework designed to unify preexisting spike sorting technologies into a single codebase and to facilitate straightforward comparison and adoption of different approaches. With a few lines of code, researchers can reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs; and more. In this paper, we provide an overview of SpikeInterface and, with applications to real and simulated datasets, demonstrate how it can be utilized to reduce the burden of manual curation and to more comprehensively benchmark automated spike sorters.
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Affiliation(s)
- Alessio P Buccino
- Department of Biosystems Science and Engineering, ETH ZurichZürichSwitzerland
- Centre for Integrative Neuroplasticity (CINPLA), University of OsloOsloNorway
| | - Cole L Hurwitz
- School of Informatics, University of EdinburghEdinburghUnited Kingdom
| | - Samuel Garcia
- Centre de Recherche en Neuroscience de Lyon, CNRSLyonFrance
| | | | | | | | - Matthias H Hennig
- School of Informatics, University of EdinburghEdinburghUnited Kingdom
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30
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Magland J, Jun JJ, Lovero E, Morley AJ, Hurwitz CL, Buccino AP, Garcia S, Barnett AH. SpikeForest, reproducible web-facing ground-truth validation of automated neural spike sorters. eLife 2020; 9:e55167. [PMID: 32427564 PMCID: PMC7237210 DOI: 10.7554/elife.55167] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/05/2020] [Indexed: 01/03/2023] Open
Abstract
Spike sorting is a crucial step in electrophysiological studies of neuronal activity. While many spike sorting packages are available, there is little consensus about which are most accurate under different experimental conditions. SpikeForest is an open-source and reproducible software suite that benchmarks the performance of automated spike sorting algorithms across an extensive, curated database of ground-truth electrophysiological recordings, displaying results interactively on a continuously-updating website. With contributions from eleven laboratories, our database currently comprises 650 recordings (1.3 TB total size) with around 35,000 ground-truth units. These data include paired intracellular/extracellular recordings and state-of-the-art simulated recordings. Ten of the most popular spike sorting codes are wrapped in a Python package and evaluated on a compute cluster using an automated pipeline. SpikeForest documents community progress in automated spike sorting, and guides neuroscientists to an optimal choice of sorter and parameters for a wide range of probes and brain regions.
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Affiliation(s)
- Jeremy Magland
- Center for Computational Mathematics, Flatiron InstituteNew YorkUnited States
| | - James J Jun
- Center for Computational Mathematics, Flatiron InstituteNew YorkUnited States
| | - Elizabeth Lovero
- Scientific Computing Core, Flatiron InstituteNew YorkUnited States
| | - Alexander J Morley
- Medical Research Council Brain Network Dynamics Unit, University of OxfordOxfordUnited Kingdom
| | - Cole Lincoln Hurwitz
- Institute for Adaptive and Neural Computation Informatics, University of EdinburghEdinburghUnited Kingdom
| | | | - Samuel Garcia
- Centre de Recherche en Neuroscience de Lyon, Université de LyonLyonFrance
| | - Alex H Barnett
- Center for Computational Mathematics, Flatiron InstituteNew YorkUnited States
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31
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Wu T, Ratkai A, Schlett K, Grand L, Yang Z. Learning to Sort: Few-shot Spike Sorting with Adversarial Representation Learning. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2019:713-716. [PMID: 31945996 DOI: 10.1109/embc.2019.8856938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Spike sorting has long been used to obtain activities of single neurons from multi-unit recordings by extracting spikes from continuous data and assigning them to putative neurons. A large body of spike sorting algorithms have been developed that typically project spikes into a low-dimensional feature space and cluster them through iterative computations. However, there is no reached consensus on the optimal feature space or the best way of segmenting spikes into clusters, which often leads to the requirement of human intervention. It is hence desirable to effectively and efficiently utilize human knowledge in spike sorting while keeping a minimum level of manual intervention. Furthermore, the iterative computations that are commonly involved during clustering are inherently slow and hinder real-time processing of large-scale recordings. In this paper, we propose a novel few-shot spike sorting paradigm that employs a deep adversarial representation neural network to learn from a handful of annotated spikes and robustly classify unseen spikes sharing similar properties to the labeled ones. Once trained, the deep neural network can implement a parametric function that encodes analytically the categorical distribution of spike clusters, which can be significantly accelerated by GPUs and support processing hundreds of thousands of recording channels in real time. The paradigm also includes a clustering routine termed DidacticSortto aid users for labeling spikes that will be used to train the deep neural network. We have validated the performance of the proposed paradigm with both synthetic and in vitro datasets.
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32
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Gill BJA, Wu X, Khan FA, Sosunov AA, Liou JY, Dovas A, Eissa TL, Banu MA, Bateman LM, McKhann GM, Canoll P, Schevon C. Ex vivo multi-electrode analysis reveals spatiotemporal dynamics of ictal behavior at the infiltrated margin of glioma. Neurobiol Dis 2019; 134:104676. [PMID: 31731042 PMCID: PMC8147009 DOI: 10.1016/j.nbd.2019.104676] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/22/2019] [Accepted: 11/11/2019] [Indexed: 01/02/2023] Open
Abstract
The purpose of this study is to develop a platform in which the cellular and molecular underpinnings of chronic focal neocortical lesional epilepsy can be explored and use it to characterize seizure-like events (SLEs) in an ex vivo model of infiltrating high-grade glioma. Microelectrode arrays were used to study electrophysiologic changes in ex vivo acute brain slices from a PTEN/p53 deleted, PDGF-B driven mouse model of high-grade glioma. Electrode locations were co-registered to the underlying histology to ascertain the influence of the varying histologic landscape on the observed electrophysiologic changes. Peritumoral, infiltrated, and tumor sites were sampled in tumor-bearing slices. Following the addition of zero Mg2+ solution, all three histologic regions in tumor-bearing slices showed significantly greater increases in firing rates when compared to the control sites. Tumor-bearing slices demonstrated increased proclivity for SLEs, with 40 events in tumor-bearing slices and 5 events in control slices (p-value = .0105). Observed SLEs were characterized by either low voltage fast (LVF) onset patterns or short bursts of repetitive widespread, high amplitude low frequency discharges. Seizure foci comprised areas from all three histologic regions. The onset electrode was found to be at the infiltrated margin in 50% of cases and in the peritumoral region in 36.9% of cases. These findings reveal a landscape of histopathologic and electrophysiologic alterations associated with ictogenesis and spread of tumor-associated seizures.
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Affiliation(s)
- Brian J A Gill
- Department of Neurological Surgery, Columbia University Medical Center, New York, NY, USA.
| | - Xiaoping Wu
- Department of Neurological Surgery, Columbia University Medical Center, New York, NY, USA
| | - Farhan A Khan
- Department of Neurological Surgery, Columbia University Medical Center, New York, NY, USA
| | - Alexander A Sosunov
- Department of Neurological Surgery, Columbia University Medical Center, New York, NY, USA
| | - Jyun-You Liou
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Athanassios Dovas
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Tahra L Eissa
- Department of Applied Mathematics, University of Colorado at Boulder, Boulder, CO, USA
| | - Matei A Banu
- Department of Neurological Surgery, Columbia University Medical Center, New York, NY, USA
| | - Lisa M Bateman
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Guy M McKhann
- Department of Neurological Surgery, Columbia University Medical Center, New York, NY, USA
| | - Peter Canoll
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Catherine Schevon
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
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33
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Robinson S, Courtney MJ. Spatial quantification of the synaptic activity phenotype across large populations of neurons with Markov random fields. Bioinformatics 2019; 34:3196-3204. [PMID: 29897415 DOI: 10.1093/bioinformatics/bty322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 04/25/2018] [Indexed: 11/12/2022] Open
Abstract
Motivation The collective and co-ordinated synaptic activity of large neuronal populations is relevant to neuronal development as well as a range of neurological diseases. Quantification of synaptically-mediated neuronal signalling permits further downstream analysis as well as potential application in target validation and in vitro screening assays. Our aim is to develop a phenotypic quantification for neuronal activity imaging data of large populations of neurons, in particular relating to the spatial component of the activity. Results We extend the use of Markov random field (MRF) models to achieve this aim. In particular, we consider Bayesian posterior densities of model parameters in Gaussian MRFs to directly model changes in calcium fluorescence intensity rather than using spike trains. The basis of our model is defining neuron 'neighbours' by the relative spatial positions of the neuronal somata as obtained from the image data whereas previously this has been limited to defining an artificial square grid across the field of view and spike binning. We demonstrate that our spatial phenotypic quantification is applicable for both in vitro and in vivo data consisting of thousands of neurons over hundreds of time points. We show how our approach provides insight beyond that attained by conventional spike counting and discuss how it could be used to facilitate screening assays for modifiers of disease-associated defects of communication between cells. Availability and implementation We supply the MATLAB code and data to obtain all of the results in the paper. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sean Robinson
- Department of Mathematics and Statistics, University of Turku, Turku, Finland.,Université Grenoble Alpes, CEA, INSERM, Biology of Cancer and Infection UMR S 1036, Grenoble, France
| | - Michael J Courtney
- Neuronal Signalling Lab, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.,Screening Unit, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, and Institute of Biomedicine, University of Turku, Turku, Finland.,Turku Brain and Mind Center, University of Turku and Åbo Akademi University, Turku, Finland
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34
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Marrese M, Lonardoni D, Boi F, van Hoorn H, Maccione A, Zordan S, Iannuzzi D, Berdondini L. Investigating the Effects of Mechanical Stimulation on Retinal Ganglion Cell Spontaneous Spiking Activity. Front Neurosci 2019; 13:1023. [PMID: 31611765 PMCID: PMC6776634 DOI: 10.3389/fnins.2019.01023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/09/2019] [Indexed: 01/03/2023] Open
Abstract
Mechanical forces are increasingly recognized as major regulators of several physiological processes at both the molecular and cellular level; therefore, a deep understanding of the sensing of these forces and their conversion into electrical signals are essential for studying the mechanosensitive properties of soft biological tissues. To contribute to this field, we present a dual-purpose device able to mechanically stimulate retinal tissue and to record the spiking activity of retinal ganglion cells (RGCs). This new instrument relies on combining ferrule-top micro-indentation, which provides local measurements of viscoelasticity, with high-density multi-electrode array (HD-MEAs) to simultaneously record the spontaneous activity of the retina. In this paper, we introduce this instrument, describe its technical characteristics, and present a proof-of-concept experiment that shows how RGC spiking activity of explanted mice retinas respond to mechanical micro-stimulations of their photoreceptor layer. The data suggest that, under specific conditions of indentation, the retina perceive the mechanical stimulation as modulation of the visual input, besides the longer time-scale of activation, and the increase in spiking activity is not only localized under the indentation probe, but it propagates across the retinal tissue.
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Affiliation(s)
- Marica Marrese
- LaserLab, Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Davide Lonardoni
- NetS3 Laboratory, Neuroscience and Brain Technologies Department, Fondazione Istituto Italiano di Tecnologia, Genova, Italy
| | - Fabio Boi
- NetS3 Laboratory, Neuroscience and Brain Technologies Department, Fondazione Istituto Italiano di Tecnologia, Genova, Italy
| | - Hedde van Hoorn
- LaserLab, Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Alessandro Maccione
- NetS3 Laboratory, Neuroscience and Brain Technologies Department, Fondazione Istituto Italiano di Tecnologia, Genova, Italy
| | - Stefano Zordan
- NetS3 Laboratory, Neuroscience and Brain Technologies Department, Fondazione Istituto Italiano di Tecnologia, Genova, Italy
| | - Davide Iannuzzi
- LaserLab, Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Luca Berdondini
- NetS3 Laboratory, Neuroscience and Brain Technologies Department, Fondazione Istituto Italiano di Tecnologia, Genova, Italy
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35
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Tariq T, Satti MH, Kamboh HM, Saeed M, Kamboh AM. Computationally efficient fully-automatic online neural spike detection and sorting in presence of multi-unit activity for implantable circuits. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2019; 179:104986. [PMID: 31443868 DOI: 10.1016/j.cmpb.2019.104986] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/28/2019] [Accepted: 07/14/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Spike sorting is a basic step for implantable neural interfaces. With the growing number of channels, the process should be computationally efficient, automatic,robust and applicable on implantable circuits. NEW METHOD The proposed method is a combination of fully-automatic offline and online processes. It introduces a novel method for automatically determining a data-aware spike detection threshold, computationally efficient spike feature extraction, automatic optimal cluster number evaluation and verification coupled with Self-Organizing Maps to accurately determine cluster centroids. The system has the ability of unsupervised online operation after initial fully-automatic offline training. The prime focus of this paper is to fully-automate the complete spike detection and sorting pipeline, while keeping the accuracy high. RESULTS The proposed system is simulated on two well-known datasets. The automatic threshold improves detection accuracies significantly( > 15%) as compared to the most common detector. The system is able to effectively handle background multi-unit activity with improved performance. COMPARISON Most of the existing methods are not fully-automatic; they require supervision and expert intervention at various stages of the pipeline. Secondly, existing works focus on foreground neural activity. Recent research has highlighted importance of background multi-unit activity, and this work is amongst the first efforts that proposes and verifies an automatic methodology to effectively handle them as well. CONCLUSION This paper proposes a fully-automatic, computationally efficient system for spike sorting for both single-unit and multi-unit spikes. Although the scope of this work is design and verification through computer simulations, the system has been designed to be easily transferable into an integrated hardware form.
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Affiliation(s)
- Taimoor Tariq
- National University of Sciences and Technology, Islamabad, Pakistan.
| | - M Hashim Satti
- National University of Sciences and Technology, Islamabad, Pakistan
| | - Hamid M Kamboh
- National University of Sciences and Technology, Islamabad, Pakistan
| | - Maryam Saeed
- National University of Sciences and Technology, Islamabad, Pakistan
| | - Awais M Kamboh
- University of Jeddah, Jeddah, Saudia Arabia; National University of Sciences and Technology, Islamabad, Pakistan
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Bernert M, Yvert B. An Attention-Based Spiking Neural Network for Unsupervised Spike-Sorting. Int J Neural Syst 2019; 29:1850059. [DOI: 10.1142/s0129065718500594] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bio-inspired computing using artificial spiking neural networks promises performances outperforming currently available computational approaches. Yet, the number of applications of such networks remains limited due to the absence of generic training procedures for complex pattern recognition, which require the design of dedicated architectures for each situation. We developed a spike-timing-dependent plasticity (STDP) spiking neural network (SSN) to address spike-sorting, a central pattern recognition problem in neuroscience. This network is designed to process an extracellular neural signal in an online and unsupervised fashion. The signal stream is continuously fed to the network and processed through several layers to output spike trains matching the truth after a short learning period requiring only few data. The network features an attention mechanism to handle the scarcity of action potential occurrences in the signal, and a threshold adaptation mechanism to handle patterns with different sizes. This method outperforms two existing spike-sorting algorithms at low signal-to-noise ratio (SNR) and can be adapted to process several channels simultaneously in the case of tetrode recordings. Such attention-based STDP network applied to spike-sorting opens perspectives to embed neuromorphic processing of neural data in future brain implants.
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Affiliation(s)
- Marie Bernert
- BrainTech Laboratory U1205, INSERM, 2280 Rue de la Piscine, 38400 Saint-Martin-d’Hères, France
- BrainTech Laboratory U1205, Université Grenoble Alpes, 2280 rue de la piscine, 38400 Saint-Martin-d’Hères, France
- LETI, CEA Grenoble, 17 Rue des Martyrs, 38000 Grenoble, France
| | - Blaise Yvert
- BrainTech Laboratory U1205, INSERM, 2280 Rue de la Piscine, 38400 Saint-Martin-d’Hères, France
- BrainTech Laboratory U1205, Université Grenoble Alpes, 2280 rue de la piscine, 38400 Saint-Martin-d’Hères, France
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Active High-Density Electrode Arrays: Technology and Applications in Neuronal Cell Cultures. ADVANCES IN NEUROBIOLOGY 2019. [PMID: 31073940 DOI: 10.1007/978-3-030-11135-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Active high-density electrode arrays realized with complementary metal-oxide-semiconductor (CMOS) technology provide electrophysiological recordings from several thousands of closely spaced microelectrodes. This has drastically advanced the spatiotemporal recording resolution of conventional multielectrode arrays (MEAs). Thus, today's electrophysiology in neuronal cultures can exploit label-free electrical readouts from a large number of single neurons within the same network. This provides advanced capabilities to investigate the properties of self-assembling neuronal networks, to advance studies on neurotoxicity and neurodevelopmental alterations associated with human brain diseases, and to develop cell culture models for testing drug- or cell-based strategies for therapies.Here, after introducing the reader to this neurotechnology, we summarize the results of different recent studies demonstrating the potential of active high-density electrode arrays for experimental applications. We also discuss ongoing and possible future research directions that might allow for moving these platforms forward for screening applications.
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Pisano F, Pisanello M, De Vittorio M, Pisanello F. Single-cell micro- and nano-photonic technologies. J Neurosci Methods 2019; 325:108355. [PMID: 31319100 DOI: 10.1016/j.jneumeth.2019.108355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/02/2019] [Accepted: 07/08/2019] [Indexed: 12/15/2022]
Abstract
Since the advent of optogenetics, the technology development has focused on new methods to optically interact with single nerve cells. This gave rise to the field of photonic neural interfaces, intended as the set of technologies that can modify light radiation in either a linear or non-linear fashion to control and/or monitor cellular functions. This set includes the use of plasmonic effects, up-conversion, electron transfer and integrated light steering, with some of them already implemented in vivo. This article will review available approaches in this framework, with a particular emphasis on methods operating at the single-unit level or having the potential to reach single-cell resolution.
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Affiliation(s)
- Filippo Pisano
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Via Barsanti, 73010 Arnesano (Lecce), Italy
| | - Marco Pisanello
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Via Barsanti, 73010 Arnesano (Lecce), Italy
| | - Massimo De Vittorio
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Via Barsanti, 73010 Arnesano (Lecce), Italy; Dipartimento di Ingeneria dell'Innovazione, Università del Salento, via per Monteroni, 73100 Lecce, Italy
| | - Ferruccio Pisanello
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Via Barsanti, 73010 Arnesano (Lecce), Italy.
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Mellough CB, Collin J, Queen R, Hilgen G, Dorgau B, Zerti D, Felemban M, White K, Sernagor E, Lako M. Systematic Comparison of Retinal Organoid Differentiation from Human Pluripotent Stem Cells Reveals Stage Specific, Cell Line, and Methodological Differences. Stem Cells Transl Med 2019; 8:694-706. [PMID: 30916455 PMCID: PMC6591558 DOI: 10.1002/sctm.18-0267] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/11/2019] [Indexed: 12/20/2022] Open
Abstract
A major goal in the stem cell field is to generate tissues that can be utilized as a universal tool for in vitro models of development and disease, drug development, or as a resource for patients suffering from disease or injury. Great efforts are being made to differentiate human pluripotent stem cells in vitro toward retinal tissue, which is akin to native human retina in its cytoarchitecture and function, yet the numerous existing retinal induction protocols remain variable in their efficiency and do not routinely produce morphologically or functionally mature photoreceptors. Herein, we determine the impact that the method of embryoid body (EB) formation and maintenance as well as cell line background has on retinal organoid differentiation from human embryonic stem cells and human induced pluripotent stem cells. Our data indicate that cell line-specific differences dominate the variables that underline the differentiation efficiency in the early stages of differentiation. In contrast, the EB generation method and maintenance conditions determine the later differentiation and maturation of retinal organoids. Of the latter, the mechanical method of EB generation under static conditions, accompanied by media supplementation with Y27632 for the first 48 hours of differentiation, results in the most consistent formation of laminated retinal neuroepithelium containing mature and electrophysiologically responsive photoreceptors. Collectively, our data provide substantive evidence for stage-specific differences in the ability to give rise to laminated retinae, which is determined by cell line-specific differences in the early stages of differentiation and EB generation/organoid maintenance methods at later stages.
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Affiliation(s)
- Carla B. Mellough
- Institute of Genetic MedicineNewcastle UniversityNewcastleUnited Kingdom
- Centre for Ophthalmology and Visual ScienceLions Eye Institute, University of Western AustraliaPerthWestern AustraliaAustralia
| | - Joseph Collin
- Institute of Genetic MedicineNewcastle UniversityNewcastleUnited Kingdom
| | - Rachel Queen
- Institute of Genetic MedicineNewcastle UniversityNewcastleUnited Kingdom
| | - Gerrit Hilgen
- Institute of NeuroscienceNewcastle UniversityNewcastleUnited Kingdom
| | - Birthe Dorgau
- Institute of Genetic MedicineNewcastle UniversityNewcastleUnited Kingdom
| | - Darin Zerti
- Institute of Genetic MedicineNewcastle UniversityNewcastleUnited Kingdom
| | - Majed Felemban
- Institute of Genetic MedicineNewcastle UniversityNewcastleUnited Kingdom
| | - Kathryn White
- EM Research ServicesNewcastle UniversityNewcastleUnited Kingdom
| | - Evelyne Sernagor
- Institute of NeuroscienceNewcastle UniversityNewcastleUnited Kingdom
| | - Majlinda Lako
- Institute of Genetic MedicineNewcastle UniversityNewcastleUnited Kingdom
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Abstract
The shape of extracellularly recorded action potentials is a product of several variables, such as the biophysical and anatomical properties of the neuron and the relative position of the electrode. This allows isolating spikes of different neurons recorded in the same channel into clusters based on waveform features. However, correctly classifying spike waveforms into their underlying neuronal sources remains a challenge. This process, called spike sorting, typically consists of two steps: (1) extracting relevant waveform features (e.g., height, width), and (2) clustering them into non-overlapping groups believed to correspond to different neurons. In this study, we explored the performance of Gaussian mixture models (GMMs) in these two steps. We extracted relevant features using a combination of common techniques (e.g., principal components, wavelets) and GMM fitting parameters (e.g., Gaussian distances). Then, we developed an approach to perform unsupervised clustering using GMMs, estimating cluster properties in a data-driven way. We found the proposed GMM-based framework outperforms previously established methods in simulated and real extracellular recordings. We also discuss potentially better techniques for feature extraction than the widely used principal components. Finally, we provide a friendly graphical user interface to run our algorithm, which allows manual adjustments.
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41
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Dorgau B, Felemban M, Hilgen G, Kiening M, Zerti D, Hunt NC, Doherty M, Whitfield P, Hallam D, White K, Ding Y, Krasnogor N, Al-Aama J, Asfour HZ, Sernagor E, Lako M. Decellularised extracellular matrix-derived peptides from neural retina and retinal pigment epithelium enhance the expression of synaptic markers and light responsiveness of human pluripotent stem cell derived retinal organoids. Biomaterials 2019; 199:63-75. [PMID: 30738336 DOI: 10.1016/j.biomaterials.2019.01.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/11/2019] [Accepted: 01/20/2019] [Indexed: 12/13/2022]
Abstract
Tissue specific extracellular matrices (ECM) provide structural support and enable access to molecular signals and metabolites, which are essential for directing stem cell renewal and differentiation. To mimic this phenomenon in vitro, tissue decellularisation approaches have been developed, resulting in the generation of natural ECM scaffolds that have comparable physical and biochemical properties of the natural tissues and are currently gaining traction in tissue engineering and regenerative therapies due to the ease of standardised production, and constant availability. In this manuscript we report the successful generation of decellularised ECM-derived peptides from neural retina (decel NR) and retinal pigment epithelium (decel RPE), and their impact on differentiation of human pluripotent stem cells (hPSCs) to retinal organoids. We show that culture media supplementation with decel RPE and RPE-conditioned media (CM RPE) significantly increases the generation of rod photoreceptors, whilst addition of decel NR and decel RPE significantly enhances ribbon synapse marker expression and the light responsiveness of retinal organoids. Photoreceptor maturation, formation of correct synapses between retinal cells and recording of robust light responses from hPSC-derived retinal organoids remain unresolved challenges for the field of regenerative medicine. Enhanced rod photoreceptor differentiation, synaptogenesis and light response in response to addition of decellularised matrices from RPE and neural retina as shown herein provide a novel and substantial advance in generation of retinal organoids for drug screening, tissue engineering and regenerative medicine.
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Affiliation(s)
- Birthe Dorgau
- Institute of Genetic Medicine, Newcastle University, UK
| | | | | | | | - Darin Zerti
- Institute of Genetic Medicine, Newcastle University, UK
| | | | | | | | - Dean Hallam
- Institute of Genetic Medicine, Newcastle University, UK
| | | | - Yuchun Ding
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, UK
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex Biosystems (ICOS) Research Group, Newcastle University, UK
| | - Jumana Al-Aama
- Department of Genetic Medicine and Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Faculty of Medicine, King Abdulaziz University, Saudi Arabia
| | - Hani Z Asfour
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Princess Al-Jawhara Center of Excellence in Research o Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, UK.
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Scaling Spike Detection and Sorting for Next-Generation Electrophysiology. ADVANCES IN NEUROBIOLOGY 2019; 22:171-184. [PMID: 31073936 DOI: 10.1007/978-3-030-11135-9_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Reliable spike detection and sorting, the process of assigning each detected spike to its originating neuron, are essential steps in the analysis of extracellular electrical recordings from neurons. The volume and complexity of the data from recently developed large-scale, high-density microelectrode arrays and probes, which allow recording from thousands of channels simultaneously, substantially complicate this task conceptually and computationally. This chapter provides a summary and discussion of recently developed methods to tackle these challenges and discusses the important aspect of algorithm validation, and assessment of detection and sorting quality.
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43
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Jouty J, Hilgen G, Sernagor E, Hennig MH. Non-parametric Physiological Classification of Retinal Ganglion Cells in the Mouse Retina. Front Cell Neurosci 2018; 12:481. [PMID: 30581379 PMCID: PMC6292960 DOI: 10.3389/fncel.2018.00481] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/26/2018] [Indexed: 11/27/2022] Open
Abstract
Retinal ganglion cells, the sole output neurons of the retina, exhibit surprising diversity. A recent study reported over 30 distinct types in the mouse retina, indicating that the processing of visual information is highly parallelised in the brain. The advent of high density multi-electrode arrays now enables recording from many hundreds to thousands of neurons from a single retina. Here we describe a method for the automatic classification of large-scale retinal recordings using a simple stimulus paradigm and a spike train distance measure as a clustering metric. We evaluate our approach using synthetic spike trains, and demonstrate that major known cell types are identified in high-density recording sessions from the mouse retina with around 1,000 retinal ganglion cells. A comparison across different retinas reveals substantial variability between preparations, suggesting pooling data across retinas should be approached with caution. As a parameter-free method, our approach is broadly applicable for cellular physiological classification in all sensory modalities.
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Affiliation(s)
- Jonathan Jouty
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Gerrit Hilgen
- Institute of Neuroscience, Newcastle University, Newcastle, United Kingdom
| | - Evelyne Sernagor
- Institute of Neuroscience, Newcastle University, Newcastle, United Kingdom
| | - Matthias H Hennig
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
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Ghahari A, Kumar SR, Badea TC. Identification of Retinal Ganglion Cell Firing Patterns Using Clustering Analysis Supplied with Failure Diagnosis. Int J Neural Syst 2018; 28:1850008. [PMID: 29631502 PMCID: PMC6160263 DOI: 10.1142/s0129065718500089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An important goal in visual neuroscience is to understand how neuronal population coding in vertebrate retina mediates the broad range of visual functions. Microelectrode arrays interface on isolated retina registers a collective measure of the spiking dynamics of retinal ganglion cells (RGCs) by probing them simultaneously and in large numbers. The recorded data stream is then processed to identify spike trains of individual RGCs by efficient and scalable spike detection and sorting routines. Most spike sorting software packages, available either commercially or as freeware, combine automated steps with judgment calls by the investigator to verify the quality of sorted spikes. This work focused on sorting spikes of RGCs into clusters using an integrated analytical platform for the data recorded during visual stimulation of wild-type mice retinas with whole field stimuli. After spike train detection, we projected each spike onto two feature spaces: a parametric space and a principal components space. We then applied clustering algorithms to sort spikes into separate clusters. To eliminate the need for human intervention, the initial clustering results were submitted to diagnostic tests that evaluated the results to detect the sources of failure in cluster assignment. This failure diagnosis formed a decision logic for diagnosable electrodes to enhance the clustering quality iteratively through rerunning the clustering algorithms. The new clustering results showed that the spike sorting accuracy was improved. Subsequently, the number of active RGCs during each whole field stimulation was found, and the light responsiveness of each RGC was identified. Our approach led to error-resilient spike sorting in both feature extraction methods; however, using parametric features led to less erroneous spike sorting compared to principal components, particularly for low signal-to-noise ratios. As our approach is reliable for retinal signal processing in response to simple visual stimuli, it could be applied to the evaluation of disrupted physiological signaling in retinal neurodegenerative diseases.
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Affiliation(s)
- Alireza Ghahari
- 1 Retinal Circuit Development and Genetics Unit, National Eye Institute, 6 Center Drive, Bethesda, MD 20892, USA
| | - Sumit R Kumar
- 1 Retinal Circuit Development and Genetics Unit, National Eye Institute, 6 Center Drive, Bethesda, MD 20892, USA
| | - Tudor C Badea
- 1 Retinal Circuit Development and Genetics Unit, National Eye Institute, 6 Center Drive, Bethesda, MD 20892, USA
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45
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Hallam D, Hilgen G, Dorgau B, Zhu L, Yu M, Bojic S, Hewitt P, Schmitt M, Uteng M, Kustermann S, Steel D, Nicholds M, Thomas R, Treumann A, Porter A, Sernagor E, Armstrong L, Lako M. Human-Induced Pluripotent Stem Cells Generate Light Responsive Retinal Organoids with Variable and Nutrient-Dependent Efficiency. Stem Cells 2018; 36:1535-1551. [PMID: 30004612 PMCID: PMC6392112 DOI: 10.1002/stem.2883] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/17/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
Abstract
The availability of in vitro models of the human retina in which to perform pharmacological and toxicological studies is an urgent and unmet need. An essential step for developing in vitro models of human retina is the ability to generate laminated, physiologically functional, and light-responsive retinal organoids from renewable and patient specific sources. We investigated five different human-induced pluripotent stem cell (iPSC) lines and showed a significant variability in their efficiency to generate retinal organoids. Despite this variability, by month 5 of differentiation, all iPSC-derived retinal organoids were able to generate light responses, albeit immature, comparable to the earliest light responses recorded from the neonatal mouse retina, close to the period of eye opening. All iPSC-derived retinal organoids exhibited at this time a well-formed outer nuclear like layer containing photoreceptors with inner segments, connecting cilium, and outer like segments. The differentiation process was highly dependent on seeding cell density and nutrient availability determined by factorial experimental design. We adopted the differentiation protocol to a multiwell plate format, which enhanced generation of retinal organoids with retinal-pigmented epithelium (RPE) and improved ganglion cell development and the response to physiological stimuli. We tested the response of iPSC-derived retinal organoids to Moxifloxacin and showed that similarly to in vivo adult mouse retina, the primary affected cell types were photoreceptors. Together our data indicate that light responsive retinal organoids derived from carefully selected and differentiation efficient iPSC lines can be generated at the scale needed for pharmacology and drug screening purposes. Stem Cells 2018;36:1535-1551.
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Affiliation(s)
- Dean Hallam
- Newcastle University, Institute for Genetic Medicine, Newcastle upon Tyne, UK
| | - Gerrit Hilgen
- Newcastle University, Institute of Neuroscience, Newcastle upon Tyne, UK
| | - Birthe Dorgau
- Newcastle University, Institute for Genetic Medicine, Newcastle upon Tyne, UK
| | - Lili Zhu
- Newcastle University, Institute for Genetic Medicine, Newcastle upon Tyne, UK
| | - Min Yu
- Newcastle University, Institute for Genetic Medicine, Newcastle upon Tyne, UK
| | - Sanja Bojic
- Newcastle University, Institute for Genetic Medicine, Newcastle upon Tyne, UK
| | | | | | | | - Stefan Kustermann
- F. Hoffmann-La Roche Ltd, University of Tübingen, Basel, Switzerland
| | - David Steel
- Newcastle University, Institute for Genetic Medicine, Newcastle upon Tyne, UK
| | | | - Robert Thomas
- Centre for Biological Engineering, Loughborough University, Loughborough, UK
| | - Achim Treumann
- Newcastle University, Newcastle University Protein and Proteome Analysis, Newcastle upon Tyne, UK
| | - Andrew Porter
- Newcastle University, Newcastle University Protein and Proteome Analysis, Newcastle upon Tyne, UK
| | - Evelyne Sernagor
- Newcastle University, Institute of Neuroscience, Newcastle upon Tyne, UK
| | - Lyle Armstrong
- Newcastle University, Institute for Genetic Medicine, Newcastle upon Tyne, UK.,Newcells Biotech, Newcastle upon Tyne, UK
| | - Majlinda Lako
- Newcastle University, Institute for Genetic Medicine, Newcastle upon Tyne, UK
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Weisenburger S, Vaziri A. A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity. Annu Rev Neurosci 2018; 41:431-452. [PMID: 29709208 PMCID: PMC6037565 DOI: 10.1146/annurev-neuro-072116-031458] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mammalian brain is a densely interconnected network that consists of millions to billions of neurons. Decoding how information is represented and processed by this neural circuitry requires the ability to capture and manipulate the dynamics of large populations at high speed and high resolution over a large area of the brain. Although the use of optical approaches by the neuroscience community has rapidly increased over the past two decades, most microscopy approaches are unable to record the activity of all neurons comprising a functional network across the mammalian brain at relevant temporal and spatial resolutions. In this review, we survey the recent development in optical technologies for Ca2+ imaging in this regard and provide an overview of the strengths and limitations of each modality and its potential for scalability. We provide guidance from the perspective of a biological user driven by the typical biological applications and sample conditions. We also discuss the potential for future advances and synergies that could be obtained through hybrid approaches or other modalities.
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Affiliation(s)
- Siegfried Weisenburger
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, New York 10065, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, New York 10065, USA
- Kavli Neural Systems Institute, The Rockefeller University, New York, New York 10065, USA
- Research Institute of Molecular Pathology, 1030 Vienna, Austria;
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Steinmetz NA, Koch C, Harris KD, Carandini M. Challenges and opportunities for large-scale electrophysiology with Neuropixels probes. Curr Opin Neurobiol 2018; 50:92-100. [PMID: 29444488 PMCID: PMC5999351 DOI: 10.1016/j.conb.2018.01.009] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/15/2017] [Accepted: 01/17/2018] [Indexed: 12/27/2022]
Abstract
Electrophysiological methods are the gold standard in neuroscience because they reveal the activity of individual neurons at high temporal resolution and in arbitrary brain locations. Microelectrode arrays based on complementary metal-oxide semiconductor (CMOS) technology, such as Neuropixels probes, look set to transform these methods. Neuropixels probes provide ∼1000 recording sites on an extremely narrow shank, with on-board amplification, digitization, and multiplexing. They deliver low-noise recordings from hundreds of neurons, providing a step change in the type of data available to neuroscientists. Here we discuss the opportunities afforded by these probes for large-scale electrophysiology, the challenges associated with data processing and anatomical localization, and avenues for further improvements of the technology.
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Affiliation(s)
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA, United States
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Yger P, Spampinato GLB, Esposito E, Lefebvre B, Deny S, Gardella C, Stimberg M, Jetter F, Zeck G, Picaud S, Duebel J, Marre O. A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo. eLife 2018; 7:e34518. [PMID: 29557782 PMCID: PMC5897014 DOI: 10.7554/elife.34518] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/19/2018] [Indexed: 01/03/2023] Open
Abstract
In recent years, multielectrode arrays and large silicon probes have been developed to record simultaneously between hundreds and thousands of electrodes packed with a high density. However, they require novel methods to extract the spiking activity of large ensembles of neurons. Here, we developed a new toolbox to sort spikes from these large-scale extracellular data. To validate our method, we performed simultaneous extracellular and loose patch recordings in rodents to obtain 'ground truth' data, where the solution to this sorting problem is known for one cell. The performance of our algorithm was always close to the best expected performance, over a broad range of signal-to-noise ratios, in vitro and in vivo. The algorithm is entirely parallelized and has been successfully tested on recordings with up to 4225 electrodes. Our toolbox thus offers a generic solution to sort accurately spikes for up to thousands of electrodes.
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Affiliation(s)
- Pierre Yger
- Institut de la Vision, INSERM UMRS 968, UPMC UM 80ParisFrance
| | | | - Elric Esposito
- Institut de la Vision, INSERM UMRS 968, UPMC UM 80ParisFrance
| | | | - Stéphane Deny
- Institut de la Vision, INSERM UMRS 968, UPMC UM 80ParisFrance
| | - Christophe Gardella
- Institut de la Vision, INSERM UMRS 968, UPMC UM 80ParisFrance
- Laboratoire de Physique Statistique, CNRS, ENS, UPMC, 75005ParisFrance
| | - Marcel Stimberg
- Institut de la Vision, INSERM UMRS 968, UPMC UM 80ParisFrance
| | | | | | - Serge Picaud
- Institut de la Vision, INSERM UMRS 968, UPMC UM 80ParisFrance
| | - Jens Duebel
- Institut de la Vision, INSERM UMRS 968, UPMC UM 80ParisFrance
| | - Olivier Marre
- Institut de la Vision, INSERM UMRS 968, UPMC UM 80ParisFrance
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Large scale matching of function to the genetic identity of retinal ganglion cells. Sci Rep 2017; 7:15395. [PMID: 29133846 PMCID: PMC5684394 DOI: 10.1038/s41598-017-15741-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023] Open
Abstract
Understanding the role of neurons in encoding and transmitting information is a major goal in neuroscience. This requires insight on the data-rich neuronal spiking patterns combined, ideally, with morphology and genetic identity. Electrophysiologists have long experienced the trade-offs between anatomically-accurate single-cell recording techniques and high-density multi-cellular recording methods with poor anatomical correlations. In this study, we present a novel technique that combines large-scale micro-electrode array recordings with genetic identification and the anatomical location of the retinal ganglion cell soma. This was obtained through optogenetic stimulation and subsequent confocal imaging of genetically targeted retinal ganglion cell sub-populations in the mouse. With the many molecular options available for optogenetic gene expression, we view this method as a versatile tool for matching function to genetic classifications, which can be extended to include morphological information if the density of labelled cells is at the correct level.
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