An Unsupervised Online Spike-Sorting Framework

2016 ◽  
Vol 26 (05) ◽  
pp. 1550042 ◽  
Author(s):  
Simeon Knieling ◽  
Kousik S. Sridharan ◽  
Paolo Belardinelli ◽  
Georgios Naros ◽  
Daniel Weiss ◽  
...  
Keyword(s):  
Clinical Application ◽  
Action Potentials ◽  
Scoring Systems ◽  
Spike Sorting ◽  
Microelectrode Recordings ◽  
Sorting Process ◽  
Feature Normalization ◽  
Offline Analysis ◽  
Fine Tune

Extracellular neuronal microelectrode recordings can include action potentials from multiple neurons. To separate spikes from different neurons, they can be sorted according to their shape, a procedure referred to as spike-sorting. Several algorithms have been reported to solve this task. However, when clustering outcomes are unsatisfactory, most of them are difficult to adjust to achieve the desired results. We present an online spike-sorting framework that uses feature normalization and weighting to maximize the distinctiveness between different spike shapes. Furthermore, multiple criteria are applied to either facilitate or prevent cluster fusion, thereby enabling experimenters to fine-tune the sorting process. We compare our method to established unsupervised offline (Wave_Clus (WC)) and online (OSort (OS)) algorithms by examining their performance in sorting various test datasets using two different scoring systems (AMI and the Adamos metric). Furthermore, we evaluate sorting capabilities on intra-operative recordings using established quality metrics. Compared to WC and OS, our algorithm achieved comparable or higher scores on average and produced more convincing sorting results for intra-operative datasets. Thus, the presented framework is suitable for both online and offline analysis and could substantially improve the quality of microelectrode-based data evaluation for research and clinical application.

scholarly journals Electrical Stimulus Artifact Cancellation and Neural Spike Detection on Large Multi-Electrode Arrays

2016 ◽  
Author(s):  
Gonzalo E. Mena ◽  
Lauren E. Grosberg ◽  
Sasidhar Madugula ◽  
Paweł Hottowy ◽  
Alan Litke ◽  
...  
Keyword(s):  
Electrical Stimulation ◽  
High Resolution ◽  
Action Potentials ◽  
Process Model ◽  
Error Rates ◽  
Neural Interfaces ◽  
Spike Sorting ◽  
Electrode Arrays ◽  
Retinal Prostheses ◽  
Sorting Process

AbstractSimultaneous electrical stimulation and recording using multi-electrode arrays can provide a valuable technique for studying circuit connectivity and engineering neural interfaces. However, interpreting these measurements is challenging because the spike sorting process (identifying and segregating action potentials arising from different neurons) is greatly complicated by electrical stimulation artifacts across the array, which can exhibit complex and nonlinear waveforms, and overlap temporarily with evoked spikes. Here we develop a scalable algorithm based on a structured Gaussian Process model to estimate the artifact and identify evoked spikes. The effectiveness of our methods is demonstrated in both real and simulated 512-electrode recordings in the peripheral primate retina with single-electrode and several types of multi-electrode stimulation. We establish small error rates in the identification of evoked spikes, with a computational complexity that is compatible with real-time data analysis. This technology may be helpful in the design of future high-resolution sensory prostheses based on tailored stimulation (e.g., retinal prostheses), and for closed-loop neural stimulation at a much larger scale than currently possible.Author SummarySimultaneous electrical stimulation and recording using multi-electrode arrays can provide a valuable technique for studying circuit connectivity and engineering neural interfaces. However, interpreting these recordings is challenging because the spike sorting process (identifying and segregating action potentials arising from different neurons) is largely stymied by electrical stimulation artifacts across the array, which are typically larger than the signals of interest. We develop a novel computational framework to estimate and subtract away this contaminating artifact, enabling the large-scale analysis of responses of possibly hundreds of cells to tailored stimulation. Importantly, we suggest that this technology may also be helpful for the development of future high-resolution neural prosthetic devices (e.g., retinal prostheses).

scholarly journals A low-cost computational approach to analyze spiking activity in cockroach sensory neurons

2021 ◽  
Vol 45 (1) ◽  
pp. 145-153
Author(s):  
David J. Torres ◽  
Andres Romero ◽  
Wes Colgan ◽  
Ulises M. Ricoy
Keyword(s):  
Action Potentials ◽  
Selection Criteria ◽  
Low Cost ◽  
Underrepresented Students ◽  
Spike Sorting ◽  
Interspike Intervals ◽  
Sorting Process ◽  
Rural College ◽  
Stimulation Of ◽  
Spiking Activity

Undergraduates use a spike sorting routine developed in Octave to analyze the spiking activity generated from mechanical stimulation of spines of cockroach legs with the inexpensive SpikerBox amplifier and the free software Audacity. Students learn the procedures involved in handling the cockroaches and recording extracellular action potentials (spikes) with the SpikerBox apparatus as well as the importance of spike sorting for analysis in neuroscience. The spike sorting process requires students to choose the spike threshold and spike selection criteria and interact with the clustering process that forms the groups of similar spikes. Once the spike groups are identified, interspike intervals and neuron firing frequencies can be calculated and analyzed. A classic neurophysiology lab exercise is thus adapted to be interdisciplinary for underrepresented students in a small rural college.

scholarly journals Extracellular detection of neuronal coupling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Elmer Guzman ◽  
Zhuowei Cheng ◽  
Paul K. Hansma ◽  
Kenneth R. Tovar ◽  
Linda R. Petzold ◽  
...  
Keyword(s):  
Action Potentials ◽  
Microelectrode Arrays ◽  
Short Latency ◽  
Spike Sorting ◽  
Neuronal Connectivity ◽  
Direct Stimulation ◽  
Multiple Electrodes

AbstractWe developed a method to non-invasively detect synaptic relationships among neurons from in vitro networks. Our method uses microelectrode arrays on which neurons are cultured and from which propagation of extracellular action potentials (eAPs) in single axons are recorded at multiple electrodes. Detecting eAP propagation bypasses ambiguity introduced by spike sorting. Our methods identify short latency spiking relationships between neurons with properties expected of synaptically coupled neurons, namely they were recapitulated by direct stimulation and were sensitive to changing the number of active synaptic sites. Our methods enabled us to assemble a functional subset of neuronal connectivity in our cultures.

scholarly journals The evaluation of malignant astrocytoma score (MAS)

2013 ◽  
Vol 70 (5) ◽  
pp. 452-456
Author(s):  
Zeljko Kojadinovic ◽  
Petar Vulekovic ◽  
Djordje Jajic ◽  
Tomislav Cigic ◽  
Vladimir Papic ◽  
...  
Keyword(s):  
Performance Status ◽  
Radiation Therapy Oncology Group ◽  
Scoring Systems ◽  
Hospital Treatment ◽  
Malignant Astrocytoma ◽  
Or Groups ◽  
The Mean ◽  
The Moment ◽  
Astrocytoma Grade Iii

Background/Aim. At the moment there are few scoring systems for malignant astrocytoma but they are not widely accepted. The aim of this study was to evaluate malignant astrocytoma score (MAS) on a new group of patients with malignant astrocytoma, to compare MAS with other prognostic tools and to describe the use of MAS in everyday practice in neurooncology. Methods. The study was performed on 124 patients with supratentorial malignant astrocytoma grade III or IV. They were operated on and subsequently irradiated with 50-60 Gy. Results. The mean age of the patients was 57.3 years. The mean Karnofski performance status (KPS) of the functional inpairment was 54. The removal of the tumor > 90% was done in 59.7% of patients. The mean survival was 9.1 months, and 27.4% of patients had a 12-month survival. The area under receiver operating characteristic (ROC) curve (AUC) of the MAS for predicting 6-, 12- and 18-month survival was 0.754, 0.783 and 0.882, respectively. We compared the MAS with the two mostly cited scoring systems. The AUC for the same prediction for medical research council (MRC) was 0.601, 0.693, 0.772 respectively. For the Radiation Therapy Oncology Group (RTOG) the AUC was 0.732, 0.765, 0.827, respectively. Conclusion. MAS represents a useful scoring system for determining illness severity and prognosis in patients with malignant supratentorial astrocytoma. It can be helpful in comparing single patients or groups of patients, as well as results of different treatments and in controlling the quality of hospital treatment and so on.

scholarly journals Assessing the Quality of Patient Information for Cholesteatoma on the Video Sharing Platform YouTube

2021 ◽  
Author(s):  
Rithvik Reddy ◽  
Horace Cheng ◽  
Nicholas Jufas ◽  
Nirmal Patel
Keyword(s):  
Video Quality ◽  
Scoring Systems ◽  
Poor Quality ◽  
Cross Sectional Survey ◽  
Kappa Score ◽  
Good Reliability ◽  
Cross Sectional ◽  
Youtube Videos ◽  
Scoring Tool

Objectives: The objective of this study is to assess quality of the most popular cholesteatoma videos on YouTube using recognized scoring systems and to determine if video quality metrics correlated with video popularity based on likes and views Design: Cross sectional survey of available data Setting: Metadata acquisition using YouTube searches using Australian IP addresses Participants: Three independent neuro-otologists partaking in scoring videos Main outcome measures: Each video was viewed and scored by three independent assessors using both a novel tool to score the usefulness of the video as well as the validated DISCERN scoring tool. Popularity metrics were analyzed and compared to video popularity. Results: A total of 90 YouTube videos were analyzed with an average 55,292 views per video with an average of 271 likes and 22 dislikes. The inter-rater correlation was moderate with Fleiss-kappa score 0.42 [P < 0.01] using a novel scoring tool for cholesteatoma and inter-rater correlation coefficient was 0.78 [95% CI = 0.58 - 0.90] indicating good reliability for DISCERN scores. The overall video quality was poor with higher DISCERN scores found in videos uploaded from Academic Institutions. Conclusions: Informative video quality on YouTube on cholesteatoma is overall of poor quality. Videos with unclassified sources or more dislikes correlated poorly with video quality. Given the increase in patients turning to the internet for information regarding their health conditions, otology and otolaryngology societies should be encouraged to publish high quality YouTube videos on cholesteatoma and other ear conditions.

scholarly journals Performance of colposcopic scoring by modified International Federation of Cervical Pathology and Colposcopy terminology for diagnosing cervical intraepithelial neoplasia in a low-resource setting

2019 ◽  
Vol 08 (04) ◽  
pp. 218-220 ◽  
Author(s):  
Prabhakaran Nair Rema ◽  
Aleyamma Mathew ◽  
Shaji Thomas
Keyword(s):  
Cervical Intraepithelial Neoplasia ◽  
Scoring Systems ◽  
Intraepithelial Neoplasia ◽  
International Federation ◽  
Screening Tests ◽  
Substantial Agreement ◽  
Low Resource ◽  
Resource Setting ◽  
Low Resource Setting

Abstract Introduction: Colposcopy is a tool to evaluate women with cervical pre-cancer and cancer. To interpret the colposcopic findings, various scoring systems are used but with inter observer variations. To improve the quality of colposcopy, International Federation of Cervical Pathology and Colposcopy (IFCPC) has introduced a colposcopic nomenclature in 2011. Colposcopic scoring helps to select patients who need treatment for cervical intraepithelial neoplasia. Aim of the Study: The study aimed to evaluate the agreement between colposcopic diagnosis with the modified IFCPC terminology and cervical pathology in patients with abnormal screening tests and to assess the utility of this colposcopic scoring system in low resource settings. Methodology: Patients with abnormal screening tests who underwent colposcopic assessment in the department of Gynaecological oncology were included in the study. Colposcopic scoring was done by the modified IFCPC nomenclature. The results were compared with cytology and the final histopathology. Results: 56 patients were included in the study. The colposcopic scoring when compared to histopathology showed agreement in 65.7% which indicated the agreement was substantial and was statistically significant (P = 0.0001). With cytology the colposcopic score showed agreement in 35.6% indicating a fair agreement and this was also statistically significant (P = 0.001). Conclusion: Colposcopic scoring by modified IFCPC 2011 criteria showed substantial agreement with cervical histopathology. Compared to traditional methods, 2011 international terminology of colposcopy could improve colposcopic accuracy.

scholarly journals Assessing the practice of written referrals to neuroradiology and how this process can be improved and standardised

BJPsych Open ◽  
2021 ◽  
Vol 7 (S1) ◽  
pp. S181-S182
Author(s):  
Fraser Currie ◽  
Rashi Negi ◽  
Hari Shanmugaratnam
Keyword(s):  
Quality Improvement ◽  
Scoring Systems ◽  
Quality Improvement Project ◽  
Cortical Atrophy ◽  
Secondary Outcome ◽  
Quality Improvement Initiative ◽  
Exclusion Criteria ◽  
Quality Of Information ◽  
Improvement Project

AimsThis quality improvement project aims to improve the quality of information provided in the referrals from the older adult psychiatry department to radiology when requesting neuroradiological imaging.The secondary outcome aims to standardise information on the referral proforma. We hypothesise that this improved referral proforma will lead to improved quality of reporting from the radiology department, which will form the second stage of this quality improvement project.A further area of interest of this exercise is to establish whether standardised radiological scoring systems are requested in the referral, as these can be utilised as a means to standardise reported information.MethodRetrospective electronic case analysis was performed on 50 consecutive radiology referrals for a period of 3 months from November 2019 to January 2020. Data were obtained from generic MRI and CT referral proforma and entered into a specifically designed data collection tool. Recorded were patient demographics, provisional diagnosis, modality of imaging, use of ACE-III cognitive score, radiological scoring systems, and inclusion and exclusion criteria.ResultResults from 50 referrals have shown: 60% were male, 40% female. Average patient age of 74, ranging from 49 to 95. 58% were referred for CT head with 42% for MRI head. More than half of referrals quoted the ACE-III score. 26% of referrals stated exclusion criteria such as space occupying lesions, haemorrhages or infarcts. 10% of referrals requested specific neuro-radiological scoring scales. Specific scales which were requested included GCA (global cortical atrophy), MTA scale (medial temporal atrophy), Koedam scale (evidence of parietal atrophy) and Fazekas (evidence of vascular changes). Only 80% of referrals included the patients GP details on the referral form.Conclusion1. This quality improvement initiative has highlighted that the current level of information in referring patient to radiology is variable and dependent on the referrer.2. All referrals should state exclusion criteria as per the NICE guidelines on neuroimaging in diagnosis of dementia.3. Preliminary evidence suggests that requesting specific radiological rating scales could improve the quality of information received in the imaging report. The second part of this quality improvement initiative will aim to explore the impact of requesting these scales routinely.

scholarly journals P126 An analysis of the quality and readability of online information for osteoarthritis

Rheumatology ◽  
2020 ◽  
Vol 59 (Supplement_2) ◽  
Author(s):  
Kieran Murray ◽  
Timothy Murray ◽  
Candice Low ◽  
Anna O'Rourke ◽  
Douglas J Veale
Keyword(s):  
Grade Level ◽  
English Language ◽  
Assessment Tool ◽  
Scoring Systems ◽  
Online Information ◽  
Flesch Reading Ease ◽  
12Th Grade ◽  
8Th Grade ◽  
Ease Score

Abstract Background Osteoarthritis is the most common cause of disability in people over 65 years old. The readability of of online osteoarthritis information has never been assessed. A 2003 study found the quality of online osteoarthritis information to be poor. This study reviews the quality of online information regarding osteoarthritis in 2018 using three validated scoring systems. Readability is reviewed for the first time, again using three validated tools. Methods The term osteoarthritis was searched across the three most popular English language search engines. The first 25 pages from each search engine were analysed. Duplicate pages, websites featuring paid advertisements, inaccessible pages (behind a pay wall, not available for geographical reasons) and non-text pages were excluded. Readability was measured using Flesch Reading Ease Score (FRES), Flesch-Kincaid Grade Level (FKGL) and Gunning-Fog Index (GFI). Website quality was scored using the the Journal of the American Medical Association (JAMA) benchmark criteria and DISCERN criteria. Presence or absence of HONcode certification, age of content, content producer and author characteristics were noted. Results 37 unique websites were suitable for analysis. Readability varied by assessment tool from 8th to 12th grade level. This compares with the recommended 7- 8th grade level. One (2.7%) website met all four JAMA Criteria. Mean DISCERN quality of information for OA websites was “fair”, comparing favourably with the “poor” grading of a 2003 study. HONCode endorsed websites (43.2%) were of a statistically significantly higher quality. Conclusion Quality of online health information for OA is “fair”. 2.7% of websites met JAMA benchmark criteria for quality. Readability was equal to or more difficult than recommendations. HONcode certification was indicative of higher quality, but not readability. Disclosures K. Murray None. T. Murray None. C. Low None. A. O'Rourke None. D.J. Veale None.

Data Driven Symbiotic Machine Learning for the Identification of Motion-Based Action Potentials

2019 ◽  
Vol 7 (1) ◽  
pp. 61-79
Author(s):  
Volkhard Klinger
Keyword(s):  
Peripheral Nerves ◽  
Action Potentials ◽  
Data Driven ◽  
Identification System ◽  
Biological Processes ◽  
Movement Trajectories ◽  
Identification Method ◽  
Closed Loop Identification ◽  
And Control

Understanding and modelling technical and biological processes is one of the basic prerequisites for the management and control of such processes. With the help of identification, the interdependencies of such processes can be deciphered and thus a model can be achieved. The verification of the models enables the quality of the models to be assessed. This article focuses on the identification and verification of motion and sensory feedback-based action potentials in peripheral nerves. Based on the acquisition of action potentials, the identification process correlates physiological and motion-based parameters to match movement trajectories and the corresponding action potentials. After a brief description of a prototype of a biosignal acquisition and identification system, this article introduces a new identification method, the symbiotic cycle, based on the well-known term symbiotic simulation. As an example, this article presents a data-driven method to create a human readable model without using presampled data. The closed-loop identification method is integrated into this symbiotic cycle.

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