scholarly journals Automatic sorting system for large calcium imaging data

2017 ◽  
Author(s):  
Takashi Takekawa ◽  
Hirotaka Asai ◽  
Noriaki Ohkawa ◽  
Masanori Nomoto ◽  
Reiko Okubo-Suzuki ◽  
...  
Keyword(s):  
Calcium Imaging ◽  
Cell Activity ◽  
Estimation Method ◽  
Matrix Decomposition ◽  
Real Data ◽  
Imaging Data ◽  
Initial State ◽  
Sorting System ◽  
The Stability ◽  
Activity Estimation

SUMMARYIt has become possible to observe neural activity in freely moving animals via calcium imaging using a microscope, which could not be observed previously. However, it remains difficult to extract the dynamics of nerve cells from the recorded imaging data. In this study, we greatly improved the stability, and robustness of the cell activity estimation method via non-negative matrix decomposition with shrinkage estimation of the baseline. In addition, by improving the initial state of the iterative algorithm using a newly proposed method to extract the shape of the cell via image processing, a solution could be obtained with a small number of iterations. These methods were applied to artificial and real data, and their effectiveness was confirmed.

scholarly journals Penalized matrix decomposition for denoising, compression, and improved demixing of functional imaging data

2018 ◽  
Author(s):  
E. Kelly Buchanan ◽  
Ian Kinsella ◽  
Ding Zhou ◽  
Rong Zhu ◽  
Pengcheng Zhou ◽  
...  
Keyword(s):  
Functional Imaging ◽  
Calcium Imaging ◽  
Matrix Decomposition ◽  
Video Data ◽  
Reproducible Research ◽  
Imaging Data ◽  
Voltage Imaging ◽  
Low Snr ◽  
Wide Range ◽  
Low Dimensional

Calcium imaging has revolutionized systems neuroscience, providing the ability to image large neural populations with single-cell resolution. The resulting datasets are quite large (with scales of TB/hour in some cases), which has presented a barrier to routine open sharing of this data, slowing progress in reproducible research. State of the art methods for analyzing this data are based on non-negative matrix factorization (NMF); these approaches solve a non-convex optimization problem, and are highly effective when good initializations are available, but can break down e.g. in low-SNR settings where common initialization approaches fail. Here we introduce an improved approach to compressing and denoising functional imaging data. The method is based on a spatially-localized penalized matrix decomposition (PMD) of the data to separate (low-dimensional) signal from (temporally-uncorrelated) noise. This approach can be applied in parallel on local spatial patches and is therefore highly scalable, does not impose non-negativity constraints or require stringent identifiability assumptions (leading to significantly more robust results compared to NMF), and estimates all parameters directly from the data, so no hand-tuning is required. We have applied the method to a wide range of functional imaging data (including one-photon, two-photon, three-photon, widefield, somatic, axonal, dendritic, calcium, and voltage imaging datasets): in all cases, we observe ~2-4x increases in SNR and compression rates of 20-300x with minimal visible loss of signal, with no adjustment of hyperparameters; this in turn facilitates the process of demixing the observed activity into contributions from individual neurons. We focus on two challenging applications: dendritic calcium imaging data and voltage imaging data in the context of optogenetic stimulation. In both cases, we show that our new approach leads to faster and much more robust extraction of activity from the video data.

scholarly journals AN EXTENSION OF THE FRI FRAMEWORK FOR CALCIUM TRANSIENT DETECTION

2015 ◽  
Author(s):  
Stephanie Reynolds ◽  
Caroline S Copeland ◽  
Simon R Schultz ◽  
Pier Luigi Dragotti
Keyword(s):  
Calcium Imaging ◽  
Real Data ◽  
Calcium Transient ◽  
High Temporal Resolution ◽  
Imaging Data ◽  
Spike Detection ◽  
Model Order ◽  
Two Photon ◽  
Calcium Indicators ◽  
Finite Rate Of Innovation

Two-photon calcium imaging of the brain allows the spatiotemporal activity of neuronal networks to be monitored at cellular resolution. In order to analyse this activity it must first be possible to detect, with high temporal resolution, spikes from the time series corresponding to single neurons. Previous work has shown that finite rate of innovation (FRI) theory can be used to reconstruct spike trains from noisy calcium imaging data. In this paper we extend the FRI framework for spike detection from calcium imaging data to encompass data generated by a larger class of calcium indicators, including the genetically encoded indicator GCaMP6s. Furthermore, we implement least squares model-order estimation and perform a noise reduction procedure ('pre-whitening') in order to increase the robustness of the algorithm. We demonstrate high spike detection performance on real data generated by GCaMP6s, detecting 90% of electrophysiologically-validated spikes.

scholarly journals ABLE: an Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data

2017 ◽  
Author(s):  
Stephanie Reynolds ◽  
Therese Abrahamsson ◽  
Renaud Schuck ◽  
P. Jesper Sjöström ◽  
Simon R. Schultz ◽  
...  
Keyword(s):  
Level Set ◽  
Calcium Imaging ◽  
Cell Shape ◽  
Active Contours ◽  
Real Data ◽  
Imaging Data ◽  
Similar Time ◽  
Two Photon

AbstractWe present an algorithm for detecting the location of cells from two-photon calcium imaging data. In our framework, multiple coupled active contours evolve, guided by a model-based cost function, to identify cell boundaries. An active contour seeks to partition a local region into two subregions, a cell interior and ex-terior, in which all pixels have maximally ‘similar’ time courses. This simple, local model allows contours to be evolved predominantly independently. When contours are sufficiently close, their evolution is coupled, in a manner that permits overlap. We illustrate the ability of the proposed method to demix overlapping cells on real data. The proposed framework is flexible, incorporating no prior information regarding a cell’s morphology or stereotypical temporal activity, which enables the detection of cells with diverse properties. We demonstrate algorithm performance on a challenging mouse in vitro dataset, containing synchronously spiking cells, and a manually labelled mouse in vivo dataset, on which ABLE achieves a 67.5% success rate.Significance statementTwo-photon calcium imaging enables the study of brain activity during learning and behaviour at single-cell resolution. To decode neuronal spiking activity from the data, algorithms are first required to detect the location of cells in the video. It is still common for scientists to perform this task manually, as the heterogeneity in cell shape and frequency of cellular overlap impede automatic segmentation algorithms. We developed a versatile algorithm based on a popular image segmentation approach (the Level Set Method) and demonstrated its capability to overcome these challenges. We include no assumptions on cell shape or stereotypical temporal activity. This lends our framework the flexibility to be applied to new datasets with minimal adjustment.

scholarly journals Estimation of fractional cycle bias for GPS/BDS-2/Galileo based on international GNSS monitoring and assessment system observations using the uncombined PPP model

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Jin Wang ◽  
Qin Zhang ◽  
Guanwen Huang
Keyword(s):  
Estimation Method ◽  
Satellite Orbit ◽  
Satellite System ◽  
Assessment System ◽  
Navigation Satellite ◽  
Dual Frequency ◽  
Fractional Cycle Bias ◽  
The Stability ◽  
High Consistency ◽  
Global Navigation Satellite

AbstractThe Fractional Cycle Bias (FCB) product is crucial for the Ambiguity Resolution (AR) in Precise Point Positioning (PPP). Different from the traditional method using the ionospheric-free ambiguity which is formed by the Wide Lane (WL) and Narrow Lane (NL) combinations, the uncombined PPP model is flexible and effective to generate the FCB products. This study presents the FCB estimation method based on the multi-Global Navigation Satellite System (GNSS) precise satellite orbit and clock corrections from the international GNSS Monitoring and Assessment System (iGMAS) observations using the uncombined PPP model. The dual-frequency raw ambiguities are combined by the integer coefficients (4,− 3) and (1,− 1) to directly estimate the FCBs. The details of FCB estimation are described with the Global Positioning System (GPS), BeiDou-2 Navigation Satellite System (BDS-2) and Galileo Navigation Satellite System (Galileo). For the estimated FCBs, the Root Mean Squares (RMSs) of the posterior residuals are smaller than 0.1 cycles, which indicates a high consistency for the float ambiguities. The stability of the WL FCBs series is better than 0.02 cycles for the three GNSS systems, while the STandard Deviation (STD) of the NL FCBs for BDS-2 is larger than 0.139 cycles. The combined FCBs have better stability than the raw series. With the multi-GNSS FCB products, the PPP AR for GPS/BDS-2/Galileo is demonstrated using the raw observations. For hourly static positioning results, the performance of the PPP AR with the three-system observations is improved by 42.6%, but only 13.1% for kinematic positioning results. The results indicate that precise and reliable positioning can be achieved with the PPP AR of GPS/BDS-2/Galileo, supported by multi-GNSS satellite orbit, clock, and FCB products based on iGMAS.

scholarly journals An Initial Value Estimation Method for the Kalman and Extended Kalman Filters in Underground Metal Detection

2019 ◽  
Vol 9 (19) ◽  
pp. 4113 ◽  
Author(s):  
Yadong Wan ◽  
Zhen Wang ◽  
Peng Wang ◽  
Zhiyang Liu ◽  
Na Li ◽  
...  
Keyword(s):  
Kalman Filter ◽  
Estimation Method ◽  
Detection Methods ◽  
Polarizability Tensor ◽  
Filter Method ◽  
Excellent Performance ◽  
Initial Value ◽  
Initial State ◽  
Metal Detection ◽  
Value Estimation

As an underground metal detection technology, the electromagnetic induction (EMI) method is widely used in many cases. Therefore, the EMI detection algorithms with excellent performance are worth studying. One of the EMI detection methods in the underground metal detection is the filter method, which first obtains the secondary magnetic field data and then uses the Kalman filter (KF) and the extended Kalman filter (EKF) to estimate the parameters of metal targets. However, the traditional KF methods used in the underground metal detection have an unsatisfactory performance of the convergence as the algorithms are given a random or a fixed initial value. Here, an initial state estimation algorithm for the underground metal detection is proposed. The initial state of the target’s horizontal position is estimated by the first order central moments of the secondary field strength map. In addition, the initial state of the target’s depth is estimated by the full width at half maximum (FWHM) method. In addition, the initial state of the magnetic polarizability tensor is estimated by the least squares method. Then, these initial states are used as the initial values for KF and EKF. Finally, the position, posture and polarizability of the target are recursively calculated. A simulation platform for the underground metal detection is built in this paper. The simulation results show that the initial value estimation method proposed for the filtering algorithm has an excellent performance in the underground metal detection.

scholarly journals A multidimensional generalized many-facet Rasch model for rubric-based performance assessment

2021 ◽  
Author(s):  
Masaki Uto
Keyword(s):  
Performance Assessment ◽  
Rasch Model ◽  
Measurement Accuracy ◽  
Estimation Method ◽  
Real Data ◽  
Monte Carlo Algorithm ◽  
Irt Model ◽  
Irt Models ◽  
Proposed Model ◽  
Problem Item

AbstractPerformance assessment, in which human raters assess examinee performance in a practical task, often involves the use of a scoring rubric consisting of multiple evaluation items to increase the objectivity of evaluation. However, even when using a rubric, assigned scores are known to depend on characteristics of the rubric’s evaluation items and the raters, thus decreasing ability measurement accuracy. To resolve this problem, item response theory (IRT) models that can estimate examinee ability while considering the effects of these characteristics have been proposed. These IRT models assume unidimensionality, meaning that a rubric measures one latent ability. In practice, however, this assumption might not be satisfied because a rubric’s evaluation items are often designed to measure multiple sub-abilities that constitute a targeted ability. To address this issue, this study proposes a multidimensional IRT model for rubric-based performance assessment. Specifically, the proposed model is formulated as a multidimensional extension of a generalized many-facet Rasch model. Moreover, a No-U-Turn variant of the Hamiltonian Markov chain Monte Carlo algorithm is adopted as a parameter estimation method for the proposed model. The proposed model is useful not only for improving the ability measurement accuracy, but also for detailed analysis of rubric quality and rubric construct validity. The study demonstrates the effectiveness of the proposed model through simulation experiments and application to real data.

scholarly journals The Weibull Birnbaum-Saunders Distribution And Its Applications

2020 ◽  
Vol 9 (1) ◽  
pp. 61-81
Author(s):  
Lazhar BENKHELIFA
Keyword(s):  
Maximum Likelihood ◽  
Estimation Method ◽  
Likelihood Estimation ◽  
Real Data ◽  
Reliability Estimation ◽  
Maximum Likelihood Estimates ◽  
Model Parameters ◽  
Data Sets ◽  
Proposed Model ◽  
Modeling Data

A new lifetime model, with four positive parameters, called the Weibull Birnbaum-Saunders distribution is proposed. The proposed model extends the Birnbaum-Saunders distribution and provides great flexibility in modeling data in practice. Some mathematical properties of the new distribution are obtained including expansions for the cumulative and density functions, moments, generating function, mean deviations, order statistics and reliability. Estimation of the model parameters is carried out by the maximum likelihood estimation method. A simulation study is presented to show the performance of the maximum likelihood estimates of the model parameters. The flexibility of the new model is examined by applying it to two real data sets.

scholarly journals Jewel: A Novel Method for Joint Estimation of Gaussian Graphical Models

Mathematics ◽  
2021 ◽  
Vol 9 (17) ◽  
pp. 2105
Author(s):  
Claudia Angelini ◽  
Daniela De De Canditiis ◽  
Anna Plaksienko
Keyword(s):  
Graphical Models ◽  
Regulatory Networks ◽  
Regularization Parameter ◽  
Estimation Method ◽  
Real Data ◽  
Penalized Regression ◽  
Joint Estimation ◽  
Gaussian Graphical Models ◽  
Lasso Penalty ◽  
Independence Structure

In this paper, we consider the problem of estimating multiple Gaussian Graphical Models from high-dimensional datasets. We assume that these datasets are sampled from different distributions with the same conditional independence structure, but not the same precision matrix. We propose jewel, a joint data estimation method that uses a node-wise penalized regression approach. In particular, jewel uses a group Lasso penalty to simultaneously guarantee the resulting adjacency matrix’s symmetry and the graphs’ joint learning. We solve the minimization problem using the group descend algorithm and propose two procedures for estimating the regularization parameter. Furthermore, we establish the estimator’s consistency property. Finally, we illustrate our estimator’s performance through simulated and real data examples on gene regulatory networks.

scholarly journals On the potential of variational calibration for a fully distributed hydrological model: application on a Mediterranean catchment

2019 ◽  
Author(s):  
Maxime Jay-Allemand ◽  
Pierre Javelle ◽  
Igor Gejadze ◽  
Patrick Arnaud ◽  
Pierre-Olivier Malaterre ◽  
...  
Keyword(s):  
Hydrological Model ◽  
Weather Forecasting ◽  
Flash Flood ◽  
Estimation Method ◽  
Distributed Hydrological Model ◽  
Initial State ◽  
Ungauged Catchments ◽  
Temporal Dimension ◽  
Radar Rainfall ◽  
Additional Constraints

Abstract. Flash flood alerts in metropolitan France are provided by SCHAPI (Service Central Hydrométéorologique et d’Appui à la Prévision des Inondations) through the Vigicrues Flash service, which is designed to work in ungauged catchments. The AIGA method implemented in Vigicrues Flash is designed for flood forecasting on small- and medium-scale watersheds. It is based on a distributed hydrological model accounting for spatial variability of the rainfall and the catchment properties, based on the radar rainfall observation inputs. Calibration of distributed parameters describing these properties with high resolution is difficult, both technically (in terms of the estimation method), and because of the identifiability issues. Indeed, the number of parameters to be calibrated is much greater than the number of spatial locations where the discharge observations are usually available. However, the flood propagation is a dynamic process, so observations have also a temporal dimension. This must be larger enough to comprise a representative set of events. In order to fully benefit from using the AIGA method, we consider its hydrological model (GRD) in combination with the variational estimation (data assimilation) method. In this method, the optimal set of parameters is found by minimizing the objective function which includes the misfit between the observed and predicted values and some additional constraints. The minimization process requires the gradient of the cost function with respect to all control parameters, which is efficiently computed using the adjoint model. The variational estimation method is scalable, fast converging, and offers a convenient framework for introducing additional constraints relevant to hydrology. It can be used both for calibrating the parameters and estimating the initial state of the hydrological system for short range forecasting (in a manner used in weather forecasting). The study area is the Gardon d’Anduze watershed where four gauging stations are available. In numerical experiments, the benefits of using the distributed against the uniform calibration are analysed in terms of the model predictive performance. Distributed calibration shows encouraging results with better model prediction at gauged and ungauged locations.

scholarly journals The Role of lncRNAs in Regulating the Intestinal Mucosal Mechanical Barrier

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Shanshan Chen ◽  
Chi Zhang ◽  
Beihui He ◽  
Ruonan He ◽  
Li Xu ◽  
...  
Keyword(s):  
Gene Transcription ◽  
Pathogenic Bacteria ◽  
Inflammatory Diseases ◽  
Cell Activity ◽  
Chromatin Regulation ◽  
Intestinal Diseases ◽  
Intestinal Environment ◽  
The Stability ◽  
Mechanical Barrier

lncRNA is a transcript that is more than 200 bp in length. Currently, evidence has shown that lncRNA is of great significance in cell activity, involved in epigenetics, gene transcription, chromatin regulation, etc. The existence of an intestinal mucosal mechanical barrier hinders the invasion of pathogenic bacteria and toxins, maintaining the stability of the intestinal environment. Serious destruction or dysfunction of the mechanical barrier often leads to intestinal diseases. This review first summarizes the ability of lncRNAs to regulate the intestinal mucosal mechanical barrier. We then discussed how lncRNAs participate in various intestinal diseases by regulating the intestinal mucosal mechanical barrier. Finally, we envision its potential as a new marker for diagnosing and treating intestinal inflammatory diseases.

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