Integrated Cells and Collagen Fibers Spatial Image Analysis

Modern technologies designed for tissue structure visualization like brightfield microscopy, fluorescent microscopy, mass cytometry imaging (MCI) and mass spectrometry imaging (MSI) provide large amounts of quantitative and spatial information about cells and tissue structures like vessels, bronchio...

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Autores principales:	Georgii Vasiukov, Tatiana Novitskaya, Maria-Fernanda Senosain, Alex Camai, Anna Menshikh, Pierre Massion, Andries Zijlstra, Sergey Novitskiy
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	image analysis ECM–extracellular matrix spatial analysis fibers image processing collagen fiber (CF) Computer applications to medicine. Medical informatics R858-859.7
Acceso en línea:	https://doaj.org/article/29041d8a47c14a7fbda334f76f3e2568
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id	oai:doaj.org-article:29041d8a47c14a7fbda334f76f3e2568
record_format	dspace
spelling	oai:doaj.org-article:29041d8a47c14a7fbda334f76f3e25682021-11-08T05:32:26ZIntegrated Cells and Collagen Fibers Spatial Image Analysis2673-764710.3389/fbinf.2021.758775https://doaj.org/article/29041d8a47c14a7fbda334f76f3e25682021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fbinf.2021.758775/fullhttps://doaj.org/toc/2673-7647Modern technologies designed for tissue structure visualization like brightfield microscopy, fluorescent microscopy, mass cytometry imaging (MCI) and mass spectrometry imaging (MSI) provide large amounts of quantitative and spatial information about cells and tissue structures like vessels, bronchioles etc. Many published reports have demonstrated that the structural features of cells and extracellular matrix (ECM) and their interactions strongly predict disease development and progression. Computational image analysis methods in combination with spatial analysis and machine learning can reveal novel structural patterns in normal and diseased tissue. Here, we have developed a Python package designed for integrated analysis of cells and ECM in a spatially dependent manner. The package performs segmentation, labeling and feature analysis of ECM fibers, combines this information with pre-generated single-cell based datasets and realizes cell-cell and cell-fiber spatial analysis. To demonstrate performance and compatibility of our computational tool, we integrated it with a pipeline designed for cell segmentation, classification, and feature analysis in the KNIME analytical platform. For validation, we used a set of mouse mammary gland tumors and human lung adenocarcinoma tissue samples stained for multiple cellular markers and collagen as the main ECM protein. The developed package provides sufficient performance and precision to be used as a novel method to investigate cell-ECM relationships in the tissue, as well as detect structural patterns correlated with specific disease outcomes.Georgii VasiukovTatiana NovitskayaMaria-Fernanda SenosainAlex CamaiAnna MenshikhPierre MassionAndries ZijlstraSergey NovitskiyFrontiers Media S.A.articleimage analysisECM–extracellular matrixspatial analysisfibersimage processingcollagen fiber (CF)Computer applications to medicine. Medical informaticsR858-859.7ENFrontiers in Bioinformatics, Vol 1 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	image analysis ECM–extracellular matrix spatial analysis fibers image processing collagen fiber (CF) Computer applications to medicine. Medical informatics R858-859.7
spellingShingle	image analysis ECM–extracellular matrix spatial analysis fibers image processing collagen fiber (CF) Computer applications to medicine. Medical informatics R858-859.7 Georgii Vasiukov Tatiana Novitskaya Maria-Fernanda Senosain Alex Camai Anna Menshikh Pierre Massion Andries Zijlstra Sergey Novitskiy Integrated Cells and Collagen Fibers Spatial Image Analysis
description	Modern technologies designed for tissue structure visualization like brightfield microscopy, fluorescent microscopy, mass cytometry imaging (MCI) and mass spectrometry imaging (MSI) provide large amounts of quantitative and spatial information about cells and tissue structures like vessels, bronchioles etc. Many published reports have demonstrated that the structural features of cells and extracellular matrix (ECM) and their interactions strongly predict disease development and progression. Computational image analysis methods in combination with spatial analysis and machine learning can reveal novel structural patterns in normal and diseased tissue. Here, we have developed a Python package designed for integrated analysis of cells and ECM in a spatially dependent manner. The package performs segmentation, labeling and feature analysis of ECM fibers, combines this information with pre-generated single-cell based datasets and realizes cell-cell and cell-fiber spatial analysis. To demonstrate performance and compatibility of our computational tool, we integrated it with a pipeline designed for cell segmentation, classification, and feature analysis in the KNIME analytical platform. For validation, we used a set of mouse mammary gland tumors and human lung adenocarcinoma tissue samples stained for multiple cellular markers and collagen as the main ECM protein. The developed package provides sufficient performance and precision to be used as a novel method to investigate cell-ECM relationships in the tissue, as well as detect structural patterns correlated with specific disease outcomes.
format	article
author	Georgii Vasiukov Tatiana Novitskaya Maria-Fernanda Senosain Alex Camai Anna Menshikh Pierre Massion Andries Zijlstra Sergey Novitskiy
author_facet	Georgii Vasiukov Tatiana Novitskaya Maria-Fernanda Senosain Alex Camai Anna Menshikh Pierre Massion Andries Zijlstra Sergey Novitskiy
author_sort	Georgii Vasiukov
title	Integrated Cells and Collagen Fibers Spatial Image Analysis
title_short	Integrated Cells and Collagen Fibers Spatial Image Analysis
title_full	Integrated Cells and Collagen Fibers Spatial Image Analysis
title_fullStr	Integrated Cells and Collagen Fibers Spatial Image Analysis
title_full_unstemmed	Integrated Cells and Collagen Fibers Spatial Image Analysis
title_sort	integrated cells and collagen fibers spatial image analysis
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/29041d8a47c14a7fbda334f76f3e2568
work_keys_str_mv	AT georgiivasiukov integratedcellsandcollagenfibersspatialimageanalysis AT tatiananovitskaya integratedcellsandcollagenfibersspatialimageanalysis AT mariafernandasenosain integratedcellsandcollagenfibersspatialimageanalysis AT alexcamai integratedcellsandcollagenfibersspatialimageanalysis AT annamenshikh integratedcellsandcollagenfibersspatialimageanalysis AT pierremassion integratedcellsandcollagenfibersspatialimageanalysis AT andrieszijlstra integratedcellsandcollagenfibersspatialimageanalysis AT sergeynovitskiy integratedcellsandcollagenfibersspatialimageanalysis
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Integrated Cells and Collagen Fibers Spatial Image Analysis

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