scholarly journals MEArec: A Fast and Customizable Testbench Simulator for Ground-truth Extracellular Spiking Activity

2020 ◽  
Vol 19 (1) ◽  
pp. 185-204 ◽  
Author(s):  
Alessio Paolo Buccino ◽  
Gaute Tomas Einevoll
Keyword(s):  
Ground Truth ◽  
Spike Sorting ◽  
Ground Truth Data ◽  
Extracellular Signals ◽  
Software Packages ◽  
Processing Step ◽  
Important Processing ◽  
Spatio Temporal

AbstractWhen 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 , a Python-based software which permits flexible and fast simulation of extracellular recordings. 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 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.

scholarly journals MEArec: a fast and customizable testbench simulator for ground-truth extracellular spiking activity

2019 ◽  
Author(s):  
Alessio P. Buccino ◽  
Gaute T. Einevoll
Keyword(s):  
Ground Truth ◽  
Spike Sorting ◽  
Ground Truth Data ◽  
Extracellular Signals ◽  
Software Packages ◽  
Processing Step ◽  
Important Processing ◽  
Spatio Temporal

AbstractWhen 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.

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 How do spike collisions affect spike sorting performance?

2021 ◽  
Author(s):  
Samuel Garcia ◽  
Alessio Buccino ◽  
Pierre Yger
Keyword(s):  
Template Matching ◽  
Ground Truth ◽  
Spatial Density ◽  
Neuron Activity ◽  
Spike Sorting ◽  
Extracellular Signals ◽  
New Generation ◽  
Single Neuron Activity

Recently, a new generation of devices have been developed to record neural activity simultaneously from hundreds of electrodes with a very high spatial density, both for in vitro and in vivo applications. While these advances enable to record from many more cells, they also dramatically increase the amount overlapping "synchronous" spikes (colliding in space and/or in time), challenging the already complicated process of spike sorting (i.e. extracting isolated single-neuron activity from extracellular signals). In this work, we used synthetic ground-truth recordings to quantitatively benchmark the performance of state-of-the-art spike sorters focusing specifically on spike collisions. Our results show that while modern template-matching based algorithms are more accurate than density-based approaches, all methods, to some extent, failed to detect synchronous spike events of neurons with similar extracellular signals. Interestingly, the performance of the sorters is not largely affected by the the spiking activity in the recordings, with respect to average firing rates and spike-train correlation levels.

scholarly journals A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Pierre Yger ◽  
Giulia LB Spampinato ◽  
Elric Esposito ◽  
Baptiste Lefebvre ◽  
Stéphane Deny ◽  
...  
Keyword(s):  
Large Scale ◽  
Ground Truth ◽  
Multielectrode Arrays ◽  
Signal To Noise ◽  
Ground Truth Data ◽  
Sorting Problem ◽  
Expected Performance ◽  
Large Ensembles

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.

scholarly journals Development of experimental ground truth and quantification of intracranial aneurysm pulsation in a patient

2020 ◽  
Author(s):  
Axel Vanrossomme ◽  
Kamil Chodzyński ◽  
Omer Eker ◽  
Karim Zouaoui Boudjeltia
Keyword(s):  
Radiation Dose ◽  
Artery Aneurysm ◽  
Ground Truth ◽  
Anterior Communicating Artery ◽  
Ground Truth Data ◽  
Acquisition Protocol ◽  
Aneurysm Wall ◽  
Detection And Quantification

Abstract Aneurysm wall motion has been reported to be associated with rupture. However, its quantification with medical imaging is challenging and should be based on experimental ground-truth to avoid misinterpretation of results. In this work a time-resolved CT angiography (4D-CTA) acquisition protocol is proposed to detect the pulsation of intracranial aneurysms with a low radiation dose. To acquire ground-truth data, the accuracy of pulsation detection and quantification in a silicone phantom was assessed by applying pressure sinusoidal waves of increasing amplitudes. These experiments were carried out using a test bench that could reproduce pulsatile waveforms similar to those inside the internal carotid arteries of human subjects. 4D-CTA acquisition parameters (mAs, kVp) were then selected to achieve reliable pulsation detection and quantification with the lowest radiation dose achievable. The resulting acquisition protocol was then used to image an anterior communicating artery aneurysm in a human subject. Data reveals that in a simplified in vitro setting 4D-CTA allows for an effective and reproducible method to detect and quantify aneurysm pulsation with an inferior limit as low as 3 mm³ and a background noise of 0.5 to 1 mm³. Aneurysm pulsation can be detected in vivo with a radiation dose approximating 1 mSv.

scholarly journals Author response: A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo

2018 ◽  
Author(s):  
Pierre Yger ◽  
Giulia LB Spampinato ◽  
Elric Esposito ◽  
Baptiste Lefebvre ◽  
Stéphane Deny ◽  
...  
Keyword(s):  
Ground Truth ◽  
Author Response ◽  
Spike Sorting

scholarly journals Targeting of p38 Mitogen-Activated Protein Kinases to MEF2 Transcription Factors

1999 ◽  
Vol 19 (6) ◽  
pp. 4028-4038 ◽  
Author(s):  
Shen-Hsi Yang ◽  
Alex Galanis ◽  
Andrew D. Sharrocks
Keyword(s):  
Transcription Factors ◽  
Transcriptional Activation ◽  
Cellular Response ◽  
Map Kinases ◽  
Biological Response ◽  
Extracellular Signals ◽  
Extracellular Signal ◽  
Mitogen Activated Protein

ABSTRACT Mitogen-activated protein (MAP) kinase-mediated signalling to the nucleus is an important event in the conversion of extracellular signals into a cellular response. However, the existence of multiple MAP kinases which phosphorylate similar phosphoacceptor motifs poses a problem in maintaining substrate specificity and hence the correct biological response. Both the extracellular signal-regulated kinase (ERK) and c-Jun NH2-terminal kinase (JNK) subfamilies of MAP kinases use a second specificity determinant and require docking to their transcription factor substrates to achieve maximal substrate activation. In this study, we demonstrate that among the different MAP kinases, the MADS-box transcription factors MEF2A and MEF2C are preferentially phosphorylated and activated by the p38 subfamily members p38α and p38β2. The efficiency of phosphorylation in vitro and transcriptional activation in vivo of MEF2A and MEF2C by these p38 subtypes requires the presence of a kinase docking domain (D-domain). Furthermore, the D-domain from MEF2A is sufficient to confer p38 responsiveness on different transcription factors, and reciprocal effects are observed upon the introduction of alternative D-domains into MEF2A. These results therefore contribute to our understanding of signalling to MEF2 transcription factors and demonstrate that the requirement for substrate binding by MAP kinases is an important facet of three different subclasses of MAP kinases (ERK, JNK, and p38).

scholarly journals Adhesion molecules during somitogenesis in the avian embryo.

1987 ◽  
Vol 104 (5) ◽  
pp. 1361-1374 ◽  
Author(s):  
J L Duband ◽  
S Dufour ◽  
K Hatta ◽  
M Takeichi ◽  
G M Edelman ◽  
...  
Keyword(s):  
Adhesion Molecules ◽  
Tissue Remodeling ◽  
Cell Aggregation ◽  
Avian Embryo ◽  
Primary Role ◽  
Calcium Dependent ◽  
Tissue Dissociation ◽  
Spatio Temporal

In avian embryos, somites constitute the morphological unit of the metameric pattern. Somites are epithelia formed from a mesenchyme, the segmental plate, and are subsequently reorganized into dermatome, myotome, and sclerotome. In this study, we used somitogenesis as a basis to examine tissue remodeling during early vertebrate morphogenesis. Particular emphasis was put on the distribution and possible complementary roles of adhesion-promoting molecules, neural cell adhesion molecule (N-CAM), N-cadherin, fibronectin, and laminin. Both segmental plate and somitic cells exhibited in vitro calcium-dependent and calcium-independent systems of cell aggregation that could be inhibited respectively by anti-N-cadherin and anti-N-CAM antibodies. In vivo, the spatio-temporal expression of N-cadherin was closely associated with both the formation and local disruption of the somites. In contrast, changes in the prevalence of N-CAM did not strictly accompany the remodeling of the somitic epithelium into dermamyotome and sclerotome. It was also observed that fibronectin and laminin were reorganized secondarily in the extracellular spaces after CAM-mediated contacts were modulated. In an in vitro culture system of somites, N-cadherin was lost on individual cells released from somite explants and was reexpressed when these cells reached confluence and established intercellular contacts. In an assay of tissue dissociation in vitro, antibodies to N-cadherin or medium devoid of calcium strongly and reversibly dissociated explants of segmental plates and somites. Antibodies to N-CAM exhibited a smaller disrupting effect only on segmental plate explants. In contrast, antibodies to fibronectin and laminin did not perturb the cohesion of cells within the explants. These results emphasize the possible role of cell surface modulation of CAMs during the formation and remodeling of some transient embryonic epithelia. It is suggested that N-cadherin plays a major role in the control of tissue remodeling, a process in which N-CAM is also involved but to a lesser extent. The substratum adhesion molecules, fibronectin and laminin, do not appear to play a primary role in the regulation of these processes but may participate in cell positioning and in the stabilization of the epithelial structures.

scholarly journals Polyacrylamide Bead Sensors for in vivo Quantification of Cell-Scale Stress in Zebrafish Development

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
N. Träber ◽  
K. Uhlmann ◽  
S. Girardo ◽  
G. Kesavan ◽  
K. Wagner ◽  
...  
Keyword(s):  
Computational Analysis ◽  
Tissue Level ◽  
Quantitative Investigation ◽  
Pulsatile Pressure ◽  
Spatio Temporal ◽  
Stress Sensing ◽  
Living Organisms ◽  
Insight Into

AbstractMechanical stress exerted and experienced by cells during tissue morphogenesis and organ formation plays an important role in embryonic development. While techniques to quantify mechanical stresses in vitro are available, few methods exist for studying stresses in living organisms. Here, we describe and characterize cell-like polyacrylamide (PAAm) bead sensors with well-defined elastic properties and size for in vivo quantification of cell-scale stresses. The beads were injected into developing zebrafish embryos and their deformations were computationally analyzed to delineate spatio-temporal local acting stresses. With this computational analysis-based cell-scale stress sensing (COMPAX) we are able to detect pulsatile pressure propagation in the developing neural rod potentially originating from polarized midline cell divisions and continuous tissue flow. COMPAX is expected to provide novel spatio-temporal insight into developmental processes at the local tissue level and to facilitate quantitative investigation and a better understanding of morphogenetic processes.

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