scholarly journals Spike Detection Using FRI Methods and Protein Calcium Sensors: Performance Analysis and Comparisons

2015 ◽  
Author(s):  
Stephanie Reynolds ◽  
Jon Onativia ◽  
Caroline S Copeland ◽  
Simon R Schultz ◽  
Pier Luigi Dragotti
Keyword(s):  
Calcium Imaging ◽  
High Performance ◽  
Surrogate Data ◽  
Synthetic Dyes ◽  
Imaging Data ◽  
Spike Detection ◽  
Calcium Sensors ◽  
New Family ◽  
Calcium Indicator ◽  
Finite Rate Of Innovation

Fast and accurate detection of action potentials from neurophysiological data is key to the study of information processing in the nervous system. Previous work has shown that finite rate of innovation (FRI) theory can be used to successfully reconstruct spike trains from noisy calcium imaging data. This is due to the fact that calcium imaging data can be modeled as streams of decaying exponentials which are a subclass of FRI signals. Recent progress in the development of genetically encoded calcium indicators (GECIs) has produced protein calcium sensors that exceed the sensitivity of the synthetic dyes traditionally used in calcium imaging experiments. In this paper, we compare the suitability for spike detection of the kinetics of a new family of GECIs (the GCaMP6 family) with the synthetic dye Oregon Green BAPTA-1. We demonstrate the high performance of the FRI algorithm on surrogate data for each calcium indicator and we calculate the Crame ́r-Rao lower bound on the uncertainty of the position of a detected spike in calcium imaging data for each calcium indicator.

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 CaImAn an open source tool for scalable calcium imaging data analysis

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Andrea Giovannucci ◽  
Johannes Friedrich ◽  
Pat Gunn ◽  
Jérémie Kalfon ◽  
Brandon L Brown ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Calcium Imaging ◽  
High Performance ◽  
Human Performance ◽  
Streaming Data ◽  
Imaging Data ◽  
Two Photon ◽  
Real Time Analysis

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. We present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good scalability on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected and combined a corpus of manual annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.

scholarly journals CalmAn: An open source tool for scalable Calcium Imaging data Analysis

2018 ◽  
Author(s):  
Andrea Giovannucci ◽  
Johannes Friedrich ◽  
Pat Gunn ◽  
Jérémie Kalfon ◽  
Sue Ann Koay ◽  
...  
Keyword(s):  
Data Analysis ◽  
Open Source ◽  
Calcium Imaging ◽  
High Performance ◽  
Human Performance ◽  
Ground Truth ◽  
Streaming Data ◽  
Imaging Data ◽  
Two Photon

AbstractAdvances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months. Here we present CaImAn, an open-source library for calcium imaging data analysis. CaImAn provides automatic and scalable methods to address problems common to pre-processing, including motion correction, neural activity identification, and registration across different sessions of data collection. It does this while requiring minimal user intervention, with good performance on computers ranging from laptops to high-performance computing clusters. CaImAn is suitable for two-photon and one-photon imaging, and also enables real-time analysis on streaming data. To benchmark the performance of CaImAn we collected a corpus of ground truth annotations from multiple labelers on nine mouse two-photon datasets. We demonstrate that CaImAn achieves near-human performance in detecting locations of active neurons.

A new family of fluorescent calcium indicators designed to resist leakage or for measuring calcium near membranes

1994 ◽  
Vol 52 ◽  
pp. 168-169
Author(s):  
Martin Poenie ◽  
Akwasi Minta ◽  
Charles Vorndran
Keyword(s):  
Metal Binding ◽  
Acetoxymethyl Ester ◽  
Binding Properties ◽  
Fura 2 ◽  
New Family ◽  
Anion Transporter ◽  
Calcium Indicator ◽  
Calcium Indicators ◽  
High Calcium ◽  
Intracellular Compartmentalization

The use of fura-2 as an intracellular calcium indicator is complicated by problems of rapid dye leakage and intracellular compartmentalization which is due to a probenecid sensitive anion transporter. In addition there is increasing evidence for localized microdomains of high calcium signals which may not be faithfully reported by fura-2.We have developed a new family of fura-2 analogs aimed at addressing some of these problems. These new indicators are based on a modified bapta which can be readily derivatized to produce fura-2 analogs with a variety of new properties. The modifications do not affect the chromophore and have little impact on the spectral and metal binding properties of the indicator. One of these new derivatives known as FPE3 is a zwitterionic analog of fura-2 that can be loaded into cells as an acetoxymethyl ester and whose retention in cells is much improved. The improved retention of FPE3 is important for both cuvettebased measurements of cell suspensions and for calcium imaging.

Co-planar two-dimensional Metal-Insulator-Semiconductor Capacitor: Numerical study of the device electrostatics.

2017 ◽  
Author(s):  
Varun Bheemireddy
Keyword(s):  
Space Charge ◽  
High Performance ◽  
Numerical Study ◽  
2D Materials ◽  
Space Charge Density ◽  
Two Dimensional ◽  
Short Channel ◽  
Metal Insulator ◽  
Metal Insulator Semiconductor ◽  
New Family

The two-dimensional(2D) materials are highly promising candidates to realise elegant and e cient transistor. In the present letter, we conjecture a novel co-planar metal-insulator-semiconductor(MIS) device(capacitor) completely based on lateral 2D materials architecture and perform numerical study of the capacitor with a particular emphasis on its di erences with the conventional 3D MIS electrostatics. The space-charge density features a long charge-tail extending into the bulk of the semiconductor as opposed to the rapid decay in 3D capacitor. Equivalently, total space-charge and semiconductor capacitance densities are atleast an order of magnitude more in 2D semiconductor. In contrast to the bulk capacitor, expansion of maximum depletion width in 2D semiconductor is observed with increasing doping concentration due to lower electrostatic screening. The heuristic approach of performance analysis(2D vs 3D) for digital-logic transistor suggest higher ON-OFF current ratio in the long-channel limit even without third dimension and considerable room to maximise the performance of short-channel transistor. The present results could potentially trigger the exploration of new family of co-planar at transistors that could play a signi significant role in the future low-power and/or high performance electronics.<br>

scholarly journals Simple HPLC-PDA Analysis to Determine Illegal Synthetic Dyes in Herbal Medicines

2021 ◽  
Vol 11 (14) ◽  
pp. 6641
Author(s):  
Kyung-Yuk Ko ◽  
Eun-Young Choi ◽  
Se-Hee Jeong ◽  
Sohwa Kim ◽  
Choon-Kil Lee ◽  
...  
Keyword(s):  
High Performance ◽  
Hplc Analysis ◽  
Ammonium Acetate ◽  
Herbal Medicines ◽  
Positive Sample ◽  
Array Detector ◽  
Synthetic Dyes ◽  
Sunset Yellow ◽  
Herbal Medication ◽  
Relative Standard

Various synthetic dyes are artificially added to herbal medicines for the purpose of visual attraction. In order to monitor the illegal usage of synthetic dyes in herbal medication, a rapid and straightforward analysis method to determine synthetic dyes is required. The study aimed to develop and validate a high-performance liquid chromatography (HPLC) analysis to determine ten synthetic dyes in Hawthorn fruit, Cornus fruit, and Schisandra fruit. Ten synthetic dyes such as Tartrazine, Sunset yellow, Metanil yellow, Auramine O, Amaranth, Orange II, Acid red 73, Amaranth, New Coccine, Azorubine, and Erythrosine B, were extracted using 50 mM ammonium acetate in 70% MeOH; then separated by gradient elution with a mobile phase consisting of acetonitrile and 50 mM ammonium acetate in distilled water using a photodiode array detector (PDA) at 428 nm or 500 nm. In addition, this study established the LC-MS/MS method to confirm the existence of synthetic dyes in the positive sample solution. The HPLC analysis had good linearity (r2 > 0.999). The recoveries of this method ranged from 74.6~132.1%, and the relative standard deviation (RSD) values were less than 6.9%. Most of the samples fulfilled the acceptance criteria of the AOAC guideline. This study demonstrates that the HPLC analysis can be applied to determine ten synthetic dyes in herbal medication.

scholarly journals Automated cellular structure extraction in biological images with applications to calcium imaging data

2018 ◽  
Author(s):  
Gal Mishne ◽  
Ronald R. Coifman ◽  
Maria Lavzin ◽  
Jackie Schiller
Keyword(s):  
Calcium Imaging ◽  
Image Plane ◽  
Cellular Level ◽  
Full Potential ◽  
Imaging Data ◽  
Image Domain ◽  
Biological Images ◽  
Large Populations ◽  
In Vivo Calcium Imaging

AbstractRecent advances in experimental methods in neuroscience enable measuring in-vivo activity of large populations of neurons at cellular level resolution. To leverage the full potential of these complex datasets and analyze the dynamics of individual neurons, it is essential to extract high-resolution regions of interest, while addressing demixing of overlapping spatial components and denoising of the temporal signal of each neuron. In this paper, we propose a data-driven solution to these challenges, by representing the spatiotemporal volume as a graph in the image plane. Based on the spectral embedding of this graph calculated across trials, we propose a new clustering method, Local Selective Spectral Clustering, capable of handling overlapping clusters and disregarding clutter. We also present a new nonlinear mapping which recovers the structural map of the neurons and dendrites, and global video denoising. We demonstrate our approach on in-vivo calcium imaging of neurons and apical dendrites, automatically extracting complex structures in the image domain, and denoising and demixing their time-traces.

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