scholarly journals Unsupervised Spike Sorting for Large-Scale, High-Density Multielectrode Arrays

Cell Reports ◽  
2017 ◽  
Vol 18 (10) ◽  
pp. 2521-2532 ◽  
Author(s):  
Gerrit Hilgen ◽  
Martino Sorbaro ◽  
Sahar Pirmoradian ◽  
Jens-Oliver Muthmann ◽  
Ibolya Edit Kepiro ◽  
...  
Keyword(s):  
Large Scale ◽  
High Density ◽  
Spike Sorting ◽  
Multielectrode Arrays

scholarly journals Unsupervised spike sorting for large scale, high density multielectrode arrays

2016 ◽  
Author(s):  
Gerrit Hilgen ◽  
Martino Sorbaro ◽  
Sahar Pirmoradian ◽  
Jens-Oliver Muthmann ◽  
Ibolya E. Kepiro ◽  
...  
Keyword(s):  
Large Scale ◽  
High Density ◽  
Spike Sorting ◽  
Multielectrode Arrays ◽  
Anatomical Imaging ◽  
Multiple Electrodes ◽  
Spike Shape ◽  
Low Dimensional ◽  
Dense Sampling ◽  
Better Than

AbstractA new method for automated spike sorting for recordings with high density, large scale multielectrode arrays is presented. Exploiting the dense sampling of single neurons by multiple electrodes, we obtain an efficient, low-dimensional representation of detected spikes consisting of estimated spatial spike locations and dominant spike shape features, which enables fast and reliable clustering into single units. Millions of events can be sorted in minutes, and the method is parallelized and scales better than quadratically with the number of detected spikes. We demonstrate this method using recordings with a 4,096 channel array, and present validation based on anatomical imaging, optogenetic stimulation and model-based quality control. A comparison with semi-automated, shape-based spike sorting exposes significant limitations of conventional methods. Our analysis shows that it is feasible to reliably isolate the activity of hundreds to thousands of neurons in a single recording, and that dense, multi-channel probes substantially aid reliable spike sorting.

scholarly journals Implantable computer-controlled adaptive multielectrode positioning system

2018 ◽  
Vol 119 (4) ◽  
pp. 1471-1484 ◽  
Author(s):  
E. Ferrea ◽  
L. Suriya-Arunroj ◽  
D. Hoehl ◽  
U. Thomas ◽  
A. Gail
Keyword(s):  
Cerebral Cortex ◽  
Large Scale ◽  
Nonhuman Primates ◽  
Tissue Response ◽  
High Signal ◽  
Signal Quality ◽  
Positioning System ◽  
Multielectrode Arrays ◽  
User Friendliness ◽  
Computer Controlled

Acute neuronal recordings performed with metal microelectrodes in nonhuman primates allow investigating the neural substrate of complex cognitive behaviors. Yet the daily reinsertion and positioning of the electrodes prevents recording from many neurons simultaneously, limiting the suitability of these types of recordings for brain-computer interface applications or for large-scale population statistical methods on a trial-by-trial basis. In contrast, chronically implanted multielectrode arrays offer the opportunity to record from many neurons simultaneously, but immovable electrodes prevent optimization of the signal during and after implantation and cause the tissue response to progressively impair the transduced signal quality, thereby limiting the number of different neurons that can be recorded over the lifetime of the implant. Semichronically implanted matrices of electrodes, instead, allow individually movable electrodes in depth and achieve higher channel count compared with acute methods, hence partially overcoming these limitations. Existing semichronic systems with higher channel count lack computerized control of electrode movements, leading to limited user-friendliness and uncertainty in depth positioning. Here we demonstrate a chronically implantable adaptive multielectrode positioning system with detachable drive for computerized depth adjustment of individual electrodes over several millimeters. This semichronic 16-channel system is designed to optimize the simultaneous yield of units in an extended period following implantation since the electrodes can be independently depth adjusted with minimal effort and their signal quality continuously assessed. Importantly, the electrode array is designed to remain within a chronic recording chamber for a prolonged time or can be used for acute recordings with high signal-to-noise ratio in the cerebral cortex of nonhuman primates. NEW & NOTEWORTHY We present a 16-channel motorized, semichronic multielectrode array with individually depth-adjustable electrodes to record in the cerebral cortex of nonhuman primates. Compared with fixed-geometry arrays, this system allows repeated reestablishing of single neuron isolation. Compared with manually adjustable arrays it benefits from computer-controlled positioning. Compared with motorized semichronic systems it allows higher channel counts due to a robotic single actuator approach. Overall the system is designed to optimize the simultaneous yield of units over the course of implantation.

Large‐scale high‐density culture of hepatocytes in a liver microsystem with mimicked sinusoid blood flow

2018 ◽  
Vol 12 (12) ◽  
pp. 2266-2276
Author(s):  
Jing Liu ◽  
Chengpan Li ◽  
Shaohui Cheng ◽  
Shengnan Ya ◽  
Dayong Gao ◽  
...  
Keyword(s):  
Blood Flow ◽  
Large Scale ◽  
High Density ◽  
High Density Culture ◽  
Culture Of Hepatocytes

scholarly journals YAP Promotes Cell Proliferation and Stemness Maintenance of Porcine Muscle Stem Cells under High-Density Condition

Cells ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 3069
Author(s):  
Zheng Liu ◽  
Ling Lin ◽  
Haozhe Zhu ◽  
Zhongyuan Wu ◽  
Xi Ding ◽  
...  
Keyword(s):  
Stem Cells ◽  
Cell Proliferation ◽  
Large Scale ◽  
High Density ◽  
Meat Production ◽  
Density Condition ◽  
High Density Culture ◽  
Differentiation Potential ◽  
Muscle Stem Cells ◽  
Cultured Meat

Muscle stem cells (MuSCs) isolated ex vivo are essential original cells to produce cultured meat. Currently, one of the main obstacles for cultured meat production derives from the limited capacity of large-scale amplification of MuSCs, especially under high-density culture condition. Here, we show that at higher cell densities, proliferation and differentiation capacities of porcine MuSCs are impaired. We investigate the roles of Hippo-YAP signaling, which is important regulators in response to cell contact inhibition. Interestingly, abundant but not functional YAP proteins are accumulated in MuSCs seeded at high density. When treated with lysophosphatidic acid (LPA), the activator of YAP, porcine MuSCs exhibit increased proliferation and elevated differentiation potential compared with control cells. Moreover, constitutively active YAP with deactivated phosphorylation sites, but not intact YAP, promotes cell proliferation and stemness maintenance of MuSCs. Together, we reveal a potential molecular target that enables massive MuSCs expansion for large-scale cultured meat production under high-density condition.

scholarly journals Enhancing Form-Based Code: A parametric approach to urban volumetric morphology in high density cities

2021 ◽  
Author(s):  
◽  
Yingyi Zhang
Keyword(s):  
Hong Kong ◽  
Large Scale ◽  
Positive Impact ◽  
High Density ◽  
Original Form ◽  
Human Society ◽  
Parametric Modelling ◽  
Physical Form ◽  
Urban Regulation ◽  
Modelling System

<p>Parametric tools have been broadly implemented in Architecture, Engineering and Construction (AEC) industry. Recently, an increasing volume of research finds that parametric tools also have the capability to facilitate large-scale planning and urban design. Much of this research, however, focuses on parametric representation or environment simulation. There is insufficient research about using parametric tools to enhance urban regulation. Parametric tools can provide smart design procedures by integrating strategies, solutions and expressions in one system. They may allow alternative approaches to urban regulation that conventional tools do not process.  This research aims to create a parametric modelling system to aid urban regulation. The system offers a visualised coding interface to manipulate parameters and achieve interactive performance feedback at the early stage of urban regulation. Form-Based Code uses the modelling system in this research. It generates a specific morphology by controlling physical form with less focus on land use. With the rise of New Urbanism, Form-Based Code has been used in various American regulation projects. This research extends the application of Form-Based Code, adopting it for urban-peripheral environments outside of the USA. High-density cities where provide the volumetric morphology context is important for this work. Tsim Sha Tsui area of Hong Kong works as an experimental site.  The feasibility of parametric urban regulation is examined by developing a parametric modelling system for Form-Based Code in Hong Kong. Understanding the site’s form characteristics, the transect matrix of Form-Based Code is expanded by incorporating multi-layered zone types and regulating plans. Embedding the zones into parametric modelling software Rhinoceros 3D and Grasshopper 3D, a regenerative prototype works to create real-time scenarios responding to parameters, rules and geometry constraints. The results of parametric urban regulation are evaluated by both Form-Based Code standards and local urban regulation standards to assess its feasibility in context.  This research demonstrates that the parametric modelling system for Form-Based Code has both technological and implemental potential to work as an alternative approach to urban regulation, especially in complex developments. Form complexity is a reflection of sophisticated human-society systems and the sequential evolution of a dynamic morphology. Form-Based Code is enhanced by the parametric modelling system to describe and regulate form complexity in a logical manner. Additionally, although parametric Form-Based Code processing is based on the original Form-Based Code, it is not limited to that. Describing urban regulation with visualised models bridges specialists and the public in community demonstrations and code assembling. The parametric modelling system has a positive impact on resolving challenges, predicting outcomes, and applying urban regulation innovation to the volumetric morphology of high-density cities in Asia.</p>

CO2 in large-scale and high-density CHO cell perfusion culture

1996 ◽  
Vol 22 (1-3) ◽  
pp. 65-78 ◽  
Author(s):  
David R. Gray ◽  
Su Chen ◽  
William Howarth ◽  
Duane Inlow ◽  
Brian L. Maiorella
Keyword(s):  
Large Scale ◽  
Perfusion Culture ◽  
High Density ◽  
Cho Cell

scholarly journals YASS: Yet Another Spike Sorter

2017 ◽  
Author(s):  
JinHyung Lee ◽  
David Carlson ◽  
Hooshmand Shokri ◽  
Weichi Yao ◽  
Georges Goetz ◽  
...  
Keyword(s):  
Dirichlet Process ◽  
Large Scale ◽  
Matching Pursuit ◽  
Spike Sorting ◽  
Dirichlet Process Mixture ◽  
Electrode Arrays ◽  
Neural Signals ◽  
Model Framework ◽  
Multi Stage ◽  
Computational Bottleneck

AbstractSpike sorting is a critical first step in extracting neural signals from large-scale electrophysiological data. This manuscript describes an efficient, reliable pipeline for spike sorting on dense multi-electrode arrays (MEAs), where neural signals appear across many electrodes and spike sorting currently represents a major computational bottleneck. We present several new techniques that make dense MEA spike sorting more robust and scalable. Our pipeline is based on an efficient multi-stage “triage-then-cluster-then-pursuit” approach that initially extracts only clean, high-quality waveforms from the electrophysiological time series by temporarily skipping noisy or “collided” events (representing two neurons firing synchronously). This is accomplished by developing a neural network detection method followed by efficient outlier triaging. The clean waveforms are then used to infer the set of neural spike waveform templates through nonparametric Bayesian clustering. Our clustering approach adapts a “coreset” approach for data reduction and uses efficient inference methods in a Dirichlet process mixture model framework to dramatically improve the scalability and reliability of the entire pipeline. The “triaged” waveforms are then finally recovered with matching-pursuit deconvolution techniques. The proposed methods improve on the state-of-the-art in terms of accuracy and stability on both real and biophysically-realistic simulated MEA data. Furthermore, the proposed pipeline is efficient, learning templates and clustering much faster than real-time for a ≃ 500-electrode dataset, using primarily a single CPU core.

A High Density WSN Cluster Positioning Approach

2021 ◽  
Vol 12 (2) ◽  
pp. 1-17
Author(s):  
Qinqing Kang
Keyword(s):  
Large Scale ◽  
Attenuation Factor ◽  
Cluster Head ◽  
High Density ◽  
Wireless Sensor ◽  
Programming Algorithm ◽  
Localization Algorithm ◽  
Network Applications ◽  
Topology Information ◽  
Cluster Location

Node self-positioning is one of the supporting technologies for wireless sensor network applications. In this paper, a clustering localization algorithm is proposed for large-scale high-density wireless sensor networks. Firstly, the potential of the node is defined as the basis for the election of the cluster head. The distance between the nodes in the network is calculated indirectly by the relationship between the received signal strength and the communication radius. The topology information in each cluster is saved by the cluster head, and the linear programming method is used in the cluster head to implement the cluster internal relative positioning. Then, from the sink node, the inter-cluster location fusion is gradually implemented, and finally the absolute positioning of the whole network is realized. Compared with the centralized convex programming algorithm, the proposed algorithm has low computational complexity, small traffic, high positioning accuracy, and does not need to know the signal attenuation factor in the environment in advance, and there is anti-noise ability.

scholarly journals N-body Simulations of Galaxy Formation

1988 ◽  
Vol 130 ◽  
pp. 259-271
Author(s):  
Carlos S. Frenk
Keyword(s):  
Dark Matter ◽  
Galaxy Formation ◽  
Large Scale ◽  
Cold Dark Matter ◽  
Large Scale Structure ◽  
High Density ◽  
Galactic Halos ◽  
Body Techniques ◽  
Massive Halos ◽  
The Universe

Modern N-body techniques allow the study of galaxy formation in the wider context of the formation of large-scale structure in the Universe. The results of such a study within the cold dark matter cosmogony are described. Dark galactic halos form at relatively recent epochs. Their properties and abundance are similar to those inferred for the halos of real galaxies. Massive halos tend to form preferentially in high density regions and as a result the galaxies that form within them are significantly more clustered than the underlying mass. This natural bias may be strong enough to reconcile the observed clustering of galaxies with the assumption that Ω = 1.

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