scholarly journals A finite rate of innovation algorithm for fast and accurate spike detection from two-photon calcium imaging

2013 ◽  
Vol 10 (4) ◽  
pp. 046017 ◽  
Author(s):  
Jon Oñativia ◽  
Simon R Schultz ◽  
Pier Luigi Dragotti
Keyword(s):  
Calcium Imaging ◽  
Spike Detection ◽  
Finite Rate ◽  
Two Photon ◽  
Finite Rate Of Innovation

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 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 Two-photon calcium imaging during fictive navigation in virtual environments

2013 ◽  
Vol 7 ◽  
Author(s):  
Misha B. Ahrens ◽  
Kuo Hua Huang ◽  
Sujatha Narayan ◽  
Brett D. Mensh ◽  
Florian Engert
Keyword(s):  
Virtual Environments ◽  
Calcium Imaging ◽  
Two Photon

scholarly journals Functional Microarchitecture of the Mouse Dorsal Inferior Colliculus Revealed through In Vivo Two-Photon Calcium Imaging

2015 ◽  
Vol 35 (31) ◽  
pp. 10927-10939 ◽  
Author(s):  
O. Barnstedt ◽  
P. Keating ◽  
Y. Weissenberger ◽  
A. J. King ◽  
J. C. Dahmen
Keyword(s):  
Inferior Colliculus ◽  
Calcium Imaging ◽  
Two Photon
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