Time-Dependent Image Restoration of Low-SNR Live-Cell Ca<sup>2</sup> Fluorescence Microscopy Data

Live-cell Ca<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></in...

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Autores principales:	Lena-Marie Woelk, Sukanya A. Kannabiran , Valerie J. Brock , Christine E. Gee , Christian Lohr , Andreas H. Guse , Björn-Philipp Diercks , René Werner
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	Ca<sup>2+</sup> imaging fluorescence microscopy live-cell imaging low signal-to-noise ratio deconvolution image restoration Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/d866c1d7c1a5432ab339cbd65077aec0
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spelling	oai:doaj.org-article:d866c1d7c1a5432ab339cbd65077aec02021-11-11T17:14:30ZTime-Dependent Image Restoration of Low-SNR Live-Cell Ca<sup>2</sup> Fluorescence Microscopy Data10.3390/ijms2221117921422-00671661-6596https://doaj.org/article/d866c1d7c1a5432ab339cbd65077aec02021-10-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/21/11792https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067Live-cell Ca<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></inline-formula> fluorescence microscopy is a cornerstone of cellular signaling analysis and imaging. The demand for high spatial and temporal imaging resolution is, however, intrinsically linked to a low signal-to-noise ratio (SNR) of the acquired spatio-temporal image data, which impedes on the subsequent image analysis. Advanced deconvolution and image restoration algorithms can partly mitigate the corresponding problems but are usually defined only for <i>static</i> images. Frame-by-frame application to spatio-temporal image data neglects inter-frame contextual relationships and temporal consistency of the imaged biological processes. Here, we propose a variational approach to <i>time-dependent</i> image restoration built on entropy-based regularization specifically suited to process low- and lowest-SNR fluorescence microscopy data. The advantage of the presented approach is demonstrated by means of four datasets: synthetic data for in-depth evaluation of the algorithm behavior; two datasets acquired for analysis of initial Ca<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></inline-formula> microdomains in T-cells; finally, to illustrate the transferability of the methodical concept to different applications, one dataset depicting spontaneous Ca<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></inline-formula> signaling in jGCaMP7b-expressing astrocytes. To foster re-use and reproducibility, the source code is made publicly available.Lena-Marie WoelkSukanya A. Kannabiran Valerie J. Brock Christine E. Gee Christian Lohr Andreas H. Guse Björn-Philipp Diercks René WernerMDPI AGarticleCa<sup>2+</sup> imagingfluorescence microscopylive-cell imaginglow signal-to-noise ratiodeconvolutionimage restorationBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 11792, p 11792 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Ca<sup>2+</sup> imaging fluorescence microscopy live-cell imaging low signal-to-noise ratio deconvolution image restoration Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	Ca<sup>2+</sup> imaging fluorescence microscopy live-cell imaging low signal-to-noise ratio deconvolution image restoration Biology (General) QH301-705.5 Chemistry QD1-999 Lena-Marie Woelk Sukanya A. Kannabiran Valerie J. Brock Christine E. Gee Christian Lohr Andreas H. Guse Björn-Philipp Diercks René Werner Time-Dependent Image Restoration of Low-SNR Live-Cell Ca<sup>2</sup> Fluorescence Microscopy Data
description	Live-cell Ca<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></inline-formula> fluorescence microscopy is a cornerstone of cellular signaling analysis and imaging. The demand for high spatial and temporal imaging resolution is, however, intrinsically linked to a low signal-to-noise ratio (SNR) of the acquired spatio-temporal image data, which impedes on the subsequent image analysis. Advanced deconvolution and image restoration algorithms can partly mitigate the corresponding problems but are usually defined only for <i>static</i> images. Frame-by-frame application to spatio-temporal image data neglects inter-frame contextual relationships and temporal consistency of the imaged biological processes. Here, we propose a variational approach to <i>time-dependent</i> image restoration built on entropy-based regularization specifically suited to process low- and lowest-SNR fluorescence microscopy data. The advantage of the presented approach is demonstrated by means of four datasets: synthetic data for in-depth evaluation of the algorithm behavior; two datasets acquired for analysis of initial Ca<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></inline-formula> microdomains in T-cells; finally, to illustrate the transferability of the methodical concept to different applications, one dataset depicting spontaneous Ca<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mrow><mn>2</mn><mo>+</mo></mrow></msup></semantics></math></inline-formula> signaling in jGCaMP7b-expressing astrocytes. To foster re-use and reproducibility, the source code is made publicly available.
format	article
author	Lena-Marie Woelk Sukanya A. Kannabiran Valerie J. Brock Christine E. Gee Christian Lohr Andreas H. Guse Björn-Philipp Diercks René Werner
author_facet	Lena-Marie Woelk Sukanya A. Kannabiran Valerie J. Brock Christine E. Gee Christian Lohr Andreas H. Guse Björn-Philipp Diercks René Werner
author_sort	Lena-Marie Woelk
title	Time-Dependent Image Restoration of Low-SNR Live-Cell Ca<sup>2</sup> Fluorescence Microscopy Data
title_short	Time-Dependent Image Restoration of Low-SNR Live-Cell Ca<sup>2</sup> Fluorescence Microscopy Data
title_full	Time-Dependent Image Restoration of Low-SNR Live-Cell Ca<sup>2</sup> Fluorescence Microscopy Data
title_fullStr	Time-Dependent Image Restoration of Low-SNR Live-Cell Ca<sup>2</sup> Fluorescence Microscopy Data
title_full_unstemmed	Time-Dependent Image Restoration of Low-SNR Live-Cell Ca<sup>2</sup> Fluorescence Microscopy Data
title_sort	time-dependent image restoration of low-snr live-cell ca<sup>2</sup> fluorescence microscopy data
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/d866c1d7c1a5432ab339cbd65077aec0
work_keys_str_mv	AT lenamariewoelk timedependentimagerestorationoflowsnrlivecellcasup2supfluorescencemicroscopydata AT sukanyaakannabiran timedependentimagerestorationoflowsnrlivecellcasup2supfluorescencemicroscopydata AT valeriejbrock timedependentimagerestorationoflowsnrlivecellcasup2supfluorescencemicroscopydata AT christineegee timedependentimagerestorationoflowsnrlivecellcasup2supfluorescencemicroscopydata AT christianlohr timedependentimagerestorationoflowsnrlivecellcasup2supfluorescencemicroscopydata AT andreashguse timedependentimagerestorationoflowsnrlivecellcasup2supfluorescencemicroscopydata AT bjornphilippdiercks timedependentimagerestorationoflowsnrlivecellcasup2supfluorescencemicroscopydata AT renewerner timedependentimagerestorationoflowsnrlivecellcasup2supfluorescencemicroscopydata
_version_	1718432148282671104

Time-Dependent Image Restoration of Low-SNR Live-Cell Ca<sup>2</sup> Fluorescence Microscopy Data

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