scholarly journals HTsort: Enabling Fast and Accurate Spike Sorting on Multi-Electrode Arrays

2021 ◽  
Vol 15 ◽  
Author(s):  
Keming Chen ◽  
Yangtao Jiang ◽  
Zhanxiong Wu ◽  
Nenggan Zheng ◽  
Haochuan Wang ◽  
...  
Keyword(s):  
Classification Accuracy ◽  
Template Matching ◽  
Spatial Information ◽  
Spatial Clustering ◽  
Divide And Conquer ◽  
Spike Sorting ◽  
Electrode Arrays ◽  
Clustering Method ◽  
Threshold Detection ◽  
Time Consumption

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.

scholarly journals Spike sorting of synchronous spikes from local neuron ensembles

2015 ◽  
Vol 114 (4) ◽  
pp. 2535-2549 ◽  
Author(s):  
Felix Franke ◽  
Robert Pröpper ◽  
Henrik Alle ◽  
Philipp Meier ◽  
Jörg R. P. Geiger ◽  
...  
Keyword(s):  
Cortical Neurons ◽  
Template Matching ◽  
Spatial Information ◽  
Simulated Data ◽  
Error Rates ◽  
Dimensional Structure ◽  
Spike Sorting ◽  
Spike Discharge

Synchronous spike discharge of cortical neurons is thought to be a fingerprint of neuronal cooperativity. Because neighboring neurons are more densely connected to one another than neurons that are located further apart, near-synchronous spike discharge can be expected to be prevalent and it might provide an important basis for cortical computations. Using microelectrodes to record local groups of neurons does not allow for the reliable separation of synchronous spikes from different cells, because available spike sorting algorithms cannot correctly resolve the temporally overlapping waveforms. We show that high spike sorting performance of in vivo recordings, including overlapping spikes, can be achieved with a recently developed filter-based template matching procedure. Using tetrodes with a three-dimensional structure, we demonstrate with simulated data and ground truth in vitro data, obtained by dual intracellular recording of two neurons located next to a tetrode, that the spike sorting of synchronous spikes can be as successful as the spike sorting of nonoverlapping spikes and that the spatial information provided by multielectrodes greatly reduces the error rates. We apply the method to tetrode recordings from the prefrontal cortex of behaving primates, and we show that overlapping spikes can be identified and assigned to individual neurons to study synchronous activity in local groups of neurons.

scholarly journals Fast and accurate spike sorting in vitro and in vivo for up to thousands of electrodes

2016 ◽  
Author(s):  
Pierre Yger ◽  
Giulia L.B. Spampinato ◽  
Elric Esposito ◽  
Baptiste Lefebvre ◽  
Stéphane Deny ◽  
...  
Keyword(s):  
Template Matching ◽  
Large Scale ◽  
Ground Truth ◽  
Spike Sorting ◽  
Electrode Arrays ◽  
Ground Truth Data ◽  
Sorting Problem ◽  
Large Populations

AbstractUnderstanding how assemblies of neurons encode information requires recording large populations of cells in the brain. In recent years, multi-electrode arrays and large silicon probes have been developed to record simultaneously from hundreds or thousands of electrodes packed with a high density. However, these new devices challenge the classical way to do spike sorting. Here we developed a new method to solve these issues, based on a highly automated algorithm to extract spikes from extracellular data, and show that this algorithm reached near optimal performance both in vitro and in vivo. The algorithm is composed of two main steps: 1) a “template-finding” phase to extract the cell templates, i.e. the pattern of activity evoked over many electrodes when one neuron fires an action potential; 2) a “template-matching” phase where the templates were matched to the raw data to find the location of the spikes. The manual intervention by the user was reduced to the minimal, and the time spent on manual curation did not scale with the number of electrodes. We tested our algorithm with large-scale data from in vitro and in vivo recordings, from 32 to 4225 electrodes. We performed simultaneous extracellular and patch recordings to obtain “ground truth” data, i.e. cases where the solution to the sorting problem is at least partially known. The performance of our algorithm was always close to the best expected performance. We thus provide a general solution to sort spikes from large-scale extracellular recordings.

scholarly journals Applicability Evaluation of Several Spatial Clustering Methods in Spatiotemporal Data Mining of Floating Car Trajectory

2021 ◽  
Vol 10 (3) ◽  
pp. 161
Author(s):  
Hao-xuan Chen ◽  
Fei Tao ◽  
Pei-long Ma ◽  
Li-na Gao ◽  
Tong Zhou
Keyword(s):  
Spatial Analysis ◽  
Spatial Clustering ◽  
Heat Index ◽  
Operating Efficiency ◽  
Clustering Methods ◽  
Clustering Method ◽  
Trajectory Mining ◽  
Density Peaks ◽  
Analysis Methods ◽  
Taxi Trajectory

Spatial analysis is an important means of mining floating car trajectory information, and clustering method and density analysis are common methods among them. The choice of the clustering method affects the accuracy and time efficiency of the analysis results. Therefore, clarifying the principles and characteristics of each method is the primary prerequisite for problem solving. Taking four representative spatial analysis methods—KMeans, Density-Based Spatial Clustering of Applications with Noise (DBSCAN), Clustering by Fast Search and Find of Density Peaks (CFSFDP), and Kernel Density Estimation (KDE)—as examples, combined with the hotspot spatiotemporal mining problem of taxi trajectory, through quantitative analysis and experimental verification, it is found that DBSCAN and KDE algorithms have strong hotspot discovery capabilities, but the heat regions’ shape of DBSCAN is found to be relatively more robust. DBSCAN and CFSFDP can achieve high spatial accuracy in calculating the entrance and exit position of a Point of Interest (POI). KDE and DBSCAN are more suitable for the classification of heat index. When the dataset scale is similar, KMeans has the highest operating efficiency, while CFSFDP and KDE are inferior. This paper resolves to a certain extent the lack of scientific basis for selecting spatial analysis methods in current research. The conclusions drawn in this paper can provide technical support and act as a reference for the selection of methods to solve the taxi trajectory mining problem.

scholarly journals Random Forest with Adaptive Local Template for Pedestrian Detection

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Tao Xiang ◽  
Tao Li ◽  
Mao Ye ◽  
Zijian Liu
Keyword(s):  
Computer Vision ◽  
Random Forest ◽  
Classification Accuracy ◽  
Template Matching ◽  
Detection Method ◽  
State Of The Art ◽  
Pedestrian Detection ◽  
Sliding Window ◽  
Experimental Results ◽  
Training Samples

Pedestrian detection with large intraclass variations is still a challenging task in computer vision. In this paper, we propose a novel pedestrian detection method based on Random Forest. Firstly, we generate a few local templates with different sizes and different locations in positive exemplars. Then, the Random Forest is built whose splitting functions are optimized by maximizing class purity of matching the local templates to the training samples, respectively. To improve the classification accuracy, we adopt a boosting-like algorithm to update the weights of the training samples in a layer-wise fashion. During detection, the trained Random Forest will vote the category when a sliding window is input. Our contributions are the splitting functions based on local template matching with adaptive size and location and iteratively weight updating method. We evaluate the proposed method on 2 well-known challenging datasets: TUD pedestrians and INRIA pedestrians. The experimental results demonstrate that our method achieves state-of-the-art or competitive performance.

scholarly journals Comparison of LSS-IV and LISS-III+LISS-IV merged data for classification of crops

2014 ◽  
Vol II-8 ◽  
pp. 101-105 ◽  
Author(s):  
R. Hebbar ◽  
M. V. R. Sesha Sai
Keyword(s):  
Image Quality ◽  
Data Fusion ◽  
Classification Accuracy ◽  
Spatial Information ◽  
Principal Component ◽  
Pass Filter ◽  
Simultaneous Acquisition ◽  
Liss Iii ◽  
Image Quality Index ◽  
Selection Of

Resourcesat-1 satellite with its unique capability of simultaneous acquisition of multispectral images at different spatial resolutions (AWiFS, LISS-III and LISS-IV MX / Mono) has immense potential for crop inventory. The present study was carried for selection of suitable LISS-IV MX band for data fusion and its evaluation for delineation different crops in a multi-cropped area. Image fusion techniques namely intensity hue saturation (IHS), principal component analysis (PCA), brovey, high pass filter (HPF) and wavelet methods were used for merging LISS-III and LISS-IV Mono data. The merged products were evaluated visually and through universal image quality index, ERGAS and classification accuracy. The study revealed that red band of LISS-IV MX data was found to be optimal band for merging with LISS-III data in terms of maintaining both spectral and spatial information and thus, closely matching with multispectral LISS-IVMX data. Among the five data fusion techniques, wavelet method was found to be superior in retaining image quality and higher classification accuracy compared to commonly used methods of IHS, PCA and Brovey. The study indicated that LISS-IV data in mono mode with wider swath of 70 km could be exploited in place of 24km LISS-IVMX data by selection of appropriate fusion techniques by acquiring monochromatic data in the red band.

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.

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