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Coupled analysis of in vitro and histology tissue samples to quantify structure-function relationship.

Acar E, Plopper GE, Yener B - PLoS ONE (2012)

Bottom Line: To the best of our knowledge, there is no prior work on a quantitative comparison of histology and in vitro samples.Features are calculated from graph theoretical representations of tissue structures and the data are analyzed in the form of matrices and higher-order tensors using matrix and tensor factorization methods, with a goal of differentiating between cancerous and healthy states of brain, breast, and bone tissues.We also show that our techniques can differentiate between the structural organization of native tissues and their corresponding in vitro engineered cell culture models.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Life Sciences, University of Copenhagen, Frederiksberg C, Denmark.

ABSTRACT
The structure/function relationship is fundamental to our understanding of biological systems at all levels, and drives most, if not all, techniques for detecting, diagnosing, and treating disease. However, at the tissue level of biological complexity we encounter a gap in the structure/function relationship: having accumulated an extraordinary amount of detailed information about biological tissues at the cellular and subcellular level, we cannot assemble it in a way that explains the correspondingly complex biological functions these structures perform. To help close this information gap we define here several quantitative temperospatial features that link tissue structure to its corresponding biological function. Both histological images of human tissue samples and fluorescence images of three-dimensional cultures of human cells are used to compare the accuracy of in vitro culture models with their corresponding human tissues. To the best of our knowledge, there is no prior work on a quantitative comparison of histology and in vitro samples. Features are calculated from graph theoretical representations of tissue structures and the data are analyzed in the form of matrices and higher-order tensors using matrix and tensor factorization methods, with a goal of differentiating between cancerous and healthy states of brain, breast, and bone tissues. We also show that our techniques can differentiate between the structural organization of native tissues and their corresponding in vitro engineered cell culture models.

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Examples of different tissue types and states as well as their representations as cell-graphs.
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pone-0032227-g001: Examples of different tissue types and states as well as their representations as cell-graphs.

Mentions: Our overall methodology used for obtaining the cell-graphs in this work can be summarized in two phases. First, we build 2D cell-graphs to represent a tissue state (Figure 1 illustrates the cell graphs for different tissue types and states). Second, the graph theoretical features of these cell-graphs are computed.


Coupled analysis of in vitro and histology tissue samples to quantify structure-function relationship.

Acar E, Plopper GE, Yener B - PLoS ONE (2012)

Examples of different tissue types and states as well as their representations as cell-graphs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3316529&req=5

pone-0032227-g001: Examples of different tissue types and states as well as their representations as cell-graphs.
Mentions: Our overall methodology used for obtaining the cell-graphs in this work can be summarized in two phases. First, we build 2D cell-graphs to represent a tissue state (Figure 1 illustrates the cell graphs for different tissue types and states). Second, the graph theoretical features of these cell-graphs are computed.

Bottom Line: To the best of our knowledge, there is no prior work on a quantitative comparison of histology and in vitro samples.Features are calculated from graph theoretical representations of tissue structures and the data are analyzed in the form of matrices and higher-order tensors using matrix and tensor factorization methods, with a goal of differentiating between cancerous and healthy states of brain, breast, and bone tissues.We also show that our techniques can differentiate between the structural organization of native tissues and their corresponding in vitro engineered cell culture models.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Life Sciences, University of Copenhagen, Frederiksberg C, Denmark.

ABSTRACT
The structure/function relationship is fundamental to our understanding of biological systems at all levels, and drives most, if not all, techniques for detecting, diagnosing, and treating disease. However, at the tissue level of biological complexity we encounter a gap in the structure/function relationship: having accumulated an extraordinary amount of detailed information about biological tissues at the cellular and subcellular level, we cannot assemble it in a way that explains the correspondingly complex biological functions these structures perform. To help close this information gap we define here several quantitative temperospatial features that link tissue structure to its corresponding biological function. Both histological images of human tissue samples and fluorescence images of three-dimensional cultures of human cells are used to compare the accuracy of in vitro culture models with their corresponding human tissues. To the best of our knowledge, there is no prior work on a quantitative comparison of histology and in vitro samples. Features are calculated from graph theoretical representations of tissue structures and the data are analyzed in the form of matrices and higher-order tensors using matrix and tensor factorization methods, with a goal of differentiating between cancerous and healthy states of brain, breast, and bone tissues. We also show that our techniques can differentiate between the structural organization of native tissues and their corresponding in vitro engineered cell culture models.

Show MeSH