Begonia—A Two-Photon Imaging Analysis Pipeline for Astrocytic Ca2+ Signals
Imaging the intact brain of awake behaving mice without the dampening effects of anesthesia, has revealed an exceedingly rich repertoire of astrocytic Ca2+ signals. Analyzing and interpreting such complex signals pose many challenges. Traditional analyses of fluorescent changes typically rely on man...
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doaj-18660baa31d04df0abe332f3ac0f13aa2021-05-20T04:38:16ZengFrontiers Media S.A.Frontiers in Cellular Neuroscience1662-51022021-05-011510.3389/fncel.2021.681066681066Begonia—A Two-Photon Imaging Analysis Pipeline for Astrocytic Ca2+ SignalsDaniel M. Bjørnstad0Knut S. Åbjørsbråten1Eivind Hennestad2Céline Cunen3Gudmund Horn Hermansen4Laura Bojarskaite5Laura Bojarskaite6Klas H. Pettersen7Klas H. Pettersen8Koen Vervaeke9Rune Enger10GliaLab at the Letten Centre, Division of Anatomy, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, NorwayGliaLab at the Letten Centre, Division of Anatomy, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, NorwayLab for Neural Computation, Division of Physiology, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, NorwayStatistics and Data Science Group, Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, NorwayStatistics and Data Science Group, Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, NorwayGliaLab at the Letten Centre, Division of Anatomy, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, NorwayDepartment of Neurology, Oslo University Hospital, Rikshospitalet, Oslo, NorwayGliaLab at the Letten Centre, Division of Anatomy, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, NorwayNORA—Norwegian Artificial Intelligence Research Consortium, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, NorwayLab for Neural Computation, Division of Physiology, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, NorwayGliaLab at the Letten Centre, Division of Anatomy, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, NorwayImaging the intact brain of awake behaving mice without the dampening effects of anesthesia, has revealed an exceedingly rich repertoire of astrocytic Ca2+ signals. Analyzing and interpreting such complex signals pose many challenges. Traditional analyses of fluorescent changes typically rely on manually outlined static region-of-interests, but such analyses fail to capture the intricate spatiotemporal patterns of astrocytic Ca2+ dynamics. Moreover, all astrocytic Ca2+ imaging data obtained from awake behaving mice need to be interpreted in light of the complex behavioral patterns of the animal. Hence processing multimodal data, including animal behavior metrics, stimulation timings, and electrophysiological signals is needed to interpret astrocytic Ca2+ signals. Managing and incorporating these data types into a coherent analysis pipeline is challenging and time-consuming, especially if research protocols change or new data types are added. Here, we introduce Begonia, a MATLAB-based data management and analysis toolbox tailored for the analyses of astrocytic Ca2+ signals in conjunction with behavioral data. The analysis suite includes an automatic, event-based algorithm with few input parameters that can capture a high level of spatiotemporal complexity of astrocytic Ca2+ signals. The toolbox enables the experimentalist to quantify astrocytic Ca2+ signals in a precise and unbiased way and combine them with other types of time series data.https://www.frontiersin.org/articles/10.3389/fncel.2021.681066/fulltwo-photon (2P)image analysiscalcium imagingROA analysisastrocyte |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Daniel M. Bjørnstad Knut S. Åbjørsbråten Eivind Hennestad Céline Cunen Gudmund Horn Hermansen Laura Bojarskaite Laura Bojarskaite Klas H. Pettersen Klas H. Pettersen Koen Vervaeke Rune Enger |
spellingShingle |
Daniel M. Bjørnstad Knut S. Åbjørsbråten Eivind Hennestad Céline Cunen Gudmund Horn Hermansen Laura Bojarskaite Laura Bojarskaite Klas H. Pettersen Klas H. Pettersen Koen Vervaeke Rune Enger Begonia—A Two-Photon Imaging Analysis Pipeline for Astrocytic Ca2+ Signals Frontiers in Cellular Neuroscience two-photon (2P) image analysis calcium imaging ROA analysis astrocyte |
author_facet |
Daniel M. Bjørnstad Knut S. Åbjørsbråten Eivind Hennestad Céline Cunen Gudmund Horn Hermansen Laura Bojarskaite Laura Bojarskaite Klas H. Pettersen Klas H. Pettersen Koen Vervaeke Rune Enger |
author_sort |
Daniel M. Bjørnstad |
title |
Begonia—A Two-Photon Imaging Analysis Pipeline for Astrocytic Ca2+ Signals |
title_short |
Begonia—A Two-Photon Imaging Analysis Pipeline for Astrocytic Ca2+ Signals |
title_full |
Begonia—A Two-Photon Imaging Analysis Pipeline for Astrocytic Ca2+ Signals |
title_fullStr |
Begonia—A Two-Photon Imaging Analysis Pipeline for Astrocytic Ca2+ Signals |
title_full_unstemmed |
Begonia—A Two-Photon Imaging Analysis Pipeline for Astrocytic Ca2+ Signals |
title_sort |
begonia—a two-photon imaging analysis pipeline for astrocytic ca2+ signals |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Cellular Neuroscience |
issn |
1662-5102 |
publishDate |
2021-05-01 |
description |
Imaging the intact brain of awake behaving mice without the dampening effects of anesthesia, has revealed an exceedingly rich repertoire of astrocytic Ca2+ signals. Analyzing and interpreting such complex signals pose many challenges. Traditional analyses of fluorescent changes typically rely on manually outlined static region-of-interests, but such analyses fail to capture the intricate spatiotemporal patterns of astrocytic Ca2+ dynamics. Moreover, all astrocytic Ca2+ imaging data obtained from awake behaving mice need to be interpreted in light of the complex behavioral patterns of the animal. Hence processing multimodal data, including animal behavior metrics, stimulation timings, and electrophysiological signals is needed to interpret astrocytic Ca2+ signals. Managing and incorporating these data types into a coherent analysis pipeline is challenging and time-consuming, especially if research protocols change or new data types are added. Here, we introduce Begonia, a MATLAB-based data management and analysis toolbox tailored for the analyses of astrocytic Ca2+ signals in conjunction with behavioral data. The analysis suite includes an automatic, event-based algorithm with few input parameters that can capture a high level of spatiotemporal complexity of astrocytic Ca2+ signals. The toolbox enables the experimentalist to quantify astrocytic Ca2+ signals in a precise and unbiased way and combine them with other types of time series data. |
topic |
two-photon (2P) image analysis calcium imaging ROA analysis astrocyte |
url |
https://www.frontiersin.org/articles/10.3389/fncel.2021.681066/full |
work_keys_str_mv |
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