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PeakCaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening

BACKGROUND: Intracellular calcium is an important ion involved in the regulation and modulation of many neuronal functions. From regulating cell cycle and proliferation to initiating signaling cascades and regulating presynaptic neurotransmitter release, the concentration and timing of calcium activ...

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Autores principales: Artimovich, Elena, Jackson, Russell K., Kilander, Michaela B. C., Lin, Yu-Chih, Nestor, Michael W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5644055/
https://www.ncbi.nlm.nih.gov/pubmed/29037171
http://dx.doi.org/10.1186/s12868-017-0391-y
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author Artimovich, Elena
Jackson, Russell K.
Kilander, Michaela B. C.
Lin, Yu-Chih
Nestor, Michael W.
author_facet Artimovich, Elena
Jackson, Russell K.
Kilander, Michaela B. C.
Lin, Yu-Chih
Nestor, Michael W.
author_sort Artimovich, Elena
collection PubMed
description BACKGROUND: Intracellular calcium is an important ion involved in the regulation and modulation of many neuronal functions. From regulating cell cycle and proliferation to initiating signaling cascades and regulating presynaptic neurotransmitter release, the concentration and timing of calcium activity governs the function and fate of neurons. Changes in calcium transients can be used in high-throughput screening applications as a basic measure of neuronal maturity, especially in developing or immature neuronal cultures derived from stem cells. RESULTS: Using human induced pluripotent stem cell derived neurons and dissociated mouse cortical neurons combined with the calcium indicator Fluo-4, we demonstrate that PeakCaller reduces type I and type II error in automated peak calling when compared to the oft-used PeakFinder algorithm under both basal and pharmacologically induced conditions. CONCLUSION: Here we describe PeakCaller, a novel MATLAB script and graphical user interface for the quantification of intracellular calcium transients in neuronal cultures. PeakCaller allows the user to set peak parameters and smoothing algorithms to best fit their data set. This new analysis script will allow for automation of calcium measurements and is a powerful software tool for researchers interested in high-throughput measurements of intracellular calcium.
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spelling pubmed-56440552017-10-18 PeakCaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening Artimovich, Elena Jackson, Russell K. Kilander, Michaela B. C. Lin, Yu-Chih Nestor, Michael W. BMC Neurosci Software BACKGROUND: Intracellular calcium is an important ion involved in the regulation and modulation of many neuronal functions. From regulating cell cycle and proliferation to initiating signaling cascades and regulating presynaptic neurotransmitter release, the concentration and timing of calcium activity governs the function and fate of neurons. Changes in calcium transients can be used in high-throughput screening applications as a basic measure of neuronal maturity, especially in developing or immature neuronal cultures derived from stem cells. RESULTS: Using human induced pluripotent stem cell derived neurons and dissociated mouse cortical neurons combined with the calcium indicator Fluo-4, we demonstrate that PeakCaller reduces type I and type II error in automated peak calling when compared to the oft-used PeakFinder algorithm under both basal and pharmacologically induced conditions. CONCLUSION: Here we describe PeakCaller, a novel MATLAB script and graphical user interface for the quantification of intracellular calcium transients in neuronal cultures. PeakCaller allows the user to set peak parameters and smoothing algorithms to best fit their data set. This new analysis script will allow for automation of calcium measurements and is a powerful software tool for researchers interested in high-throughput measurements of intracellular calcium. BioMed Central 2017-10-16 /pmc/articles/PMC5644055/ /pubmed/29037171 http://dx.doi.org/10.1186/s12868-017-0391-y Text en © The Author(s) 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Artimovich, Elena
Jackson, Russell K.
Kilander, Michaela B. C.
Lin, Yu-Chih
Nestor, Michael W.
PeakCaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening
title PeakCaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening
title_full PeakCaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening
title_fullStr PeakCaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening
title_full_unstemmed PeakCaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening
title_short PeakCaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening
title_sort peakcaller: an automated graphical interface for the quantification of intracellular calcium obtained by high-content screening
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5644055/
https://www.ncbi.nlm.nih.gov/pubmed/29037171
http://dx.doi.org/10.1186/s12868-017-0391-y
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