Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking

Abstract Ca2+ imaging is a widely used microscopy technique to simultaneously study cellular activity in multiple cells. The desired information consists of cell-specific time series of pixel intensity values, in which the fluorescence intensity represents cellular activity. For static scenes, cellu...

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Autores principales:	Youcef Kazwiny, João Pedrosa, Zhiqing Zhang, Werend Boesmans, Jan D’hooge, Pieter Vanden Berghe
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fd3ae19f54fb4275bf5d7fe9b454d594
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spelling	oai:doaj.org-article:fd3ae19f54fb4275bf5d7fe9b454d5942021-12-02T14:49:25ZExtracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking10.1038/s41598-021-90448-42045-2322https://doaj.org/article/fd3ae19f54fb4275bf5d7fe9b454d5942021-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-90448-4https://doaj.org/toc/2045-2322Abstract Ca2+ imaging is a widely used microscopy technique to simultaneously study cellular activity in multiple cells. The desired information consists of cell-specific time series of pixel intensity values, in which the fluorescence intensity represents cellular activity. For static scenes, cellular signal extraction is straightforward, however multiple analysis challenges are present in recordings of contractile tissues, like those of the enteric nervous system (ENS). This layer of critical neurons, embedded within the muscle layers of the gut wall, shows optical overlap between neighboring neurons, intensity changes due to cell activity, and constant movement. These challenges reduce the applicability of classical segmentation techniques and traditional stack alignment and regions-of-interest (ROIs) selection workflows. Therefore, a signal extraction method capable of dealing with moving cells and is insensitive to large intensity changes in consecutive frames is needed. Here we propose a b-spline active contour method to delineate and track neuronal cell bodies based on local and global energy terms. We develop both a single as well as a double-contour approach. The latter takes advantage of the appearance of GCaMP expressing cells, and tracks the nucleus’ boundaries together with the cytoplasmic contour, providing a stable delineation of neighboring, overlapping cells despite movement and intensity changes. The tracked contours can also serve as landmarks to relocate additional and manually-selected ROIs. This improves the total yield of efficacious cell tracking and allows signal extraction from other cell compartments like neuronal processes. Compared to manual delineation and other segmentation methods, the proposed method can track cells during large tissue deformations and high-intensity changes such as during neuronal firing events, while preserving the shape of the extracted Ca2+ signal. The analysis package represents a significant improvement to available Ca2+ imaging analysis workflows for ENS recordings and other systems where movement challenges traditional Ca2+ signal extraction workflows.Youcef KazwinyJoão PedrosaZhiqing ZhangWerend BoesmansJan D’hoogePieter Vanden BergheNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Youcef Kazwiny João Pedrosa Zhiqing Zhang Werend Boesmans Jan D’hooge Pieter Vanden Berghe Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking
description	Abstract Ca2+ imaging is a widely used microscopy technique to simultaneously study cellular activity in multiple cells. The desired information consists of cell-specific time series of pixel intensity values, in which the fluorescence intensity represents cellular activity. For static scenes, cellular signal extraction is straightforward, however multiple analysis challenges are present in recordings of contractile tissues, like those of the enteric nervous system (ENS). This layer of critical neurons, embedded within the muscle layers of the gut wall, shows optical overlap between neighboring neurons, intensity changes due to cell activity, and constant movement. These challenges reduce the applicability of classical segmentation techniques and traditional stack alignment and regions-of-interest (ROIs) selection workflows. Therefore, a signal extraction method capable of dealing with moving cells and is insensitive to large intensity changes in consecutive frames is needed. Here we propose a b-spline active contour method to delineate and track neuronal cell bodies based on local and global energy terms. We develop both a single as well as a double-contour approach. The latter takes advantage of the appearance of GCaMP expressing cells, and tracks the nucleus’ boundaries together with the cytoplasmic contour, providing a stable delineation of neighboring, overlapping cells despite movement and intensity changes. The tracked contours can also serve as landmarks to relocate additional and manually-selected ROIs. This improves the total yield of efficacious cell tracking and allows signal extraction from other cell compartments like neuronal processes. Compared to manual delineation and other segmentation methods, the proposed method can track cells during large tissue deformations and high-intensity changes such as during neuronal firing events, while preserving the shape of the extracted Ca2+ signal. The analysis package represents a significant improvement to available Ca2+ imaging analysis workflows for ENS recordings and other systems where movement challenges traditional Ca2+ signal extraction workflows.
format	article
author	Youcef Kazwiny João Pedrosa Zhiqing Zhang Werend Boesmans Jan D’hooge Pieter Vanden Berghe
author_facet	Youcef Kazwiny João Pedrosa Zhiqing Zhang Werend Boesmans Jan D’hooge Pieter Vanden Berghe
author_sort	Youcef Kazwiny
title	Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking
title_short	Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking
title_full	Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking
title_fullStr	Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking
title_full_unstemmed	Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking
title_sort	extracting neuronal activity signals from microscopy recordings of contractile tissue using b-spline explicit active surfaces (beas) cell tracking
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/fd3ae19f54fb4275bf5d7fe9b454d594
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Extracting neuronal activity signals from microscopy recordings of contractile tissue using B-spline Explicit Active Surfaces (BEAS) cell tracking

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