TiQuant: software for tissue analysis, quantification and surface reconstruction

Friebel, Adrian; Neitsch, Johannes; Johann, Tim; Hammad, Seddik; Hengstler, Jan G.; Drasdo, Dirk; Hoehme, Stefan

doi:10.1093/bioinformatics/btv346

Cited by 33 publications

(37 citation statements)

References 7 publications

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“…Apart from a detailed characterization of spheroids, our image analysis also results in a reduction of large images to simple lists. The number of extracted nuclei features goes well beyond those available in most existing programs2141424344. The output comprises measurements obtained from the segmentation extended by features obtained from graph and topological analysis.…”

Section: Discussionmentioning

confidence: 99%

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids

Schmitz¹,

Fischer²,

Mattheyer³

et al. 2017

Sci Rep

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Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid’s size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 105 to 1 × 106 cells/mm3. Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.

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Section: Discussionmentioning

confidence: 99%

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids

Schmitz¹,

Fischer²,

Mattheyer³

et al. 2017

Sci Rep

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show abstract

“…15), with cell numbers starting from few and ranging up to 10 6 [83,150]. Refined image analysis techniques and available software increasingly permit a quantitative analysis of tissues in 3D at micro-meter resolution [38,151]. The data infered can subsequently be transfered into modeling software such as CellSys [150], to simulate the tissue organization process of interest as demonstrated for the example of the regenerating liver (Fig.…”

Section: Achievements Limitations and Practical Usementioning

confidence: 99%

Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results

et al. 2015

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In this paper we present an overview of agentbased models that are used to simulate mechanical and physiological phenomena in cells and tissues, and we discuss underlying concepts, limitations, and future perspectives of these models. As the interest in cell and tissue mechanics increase, agent-based models are becoming more common the modeling community. We overview the physical aspects, complexity, shortcomings, and capabilities of the major agent-based model categories: lattice-based models (cellular automata, lattice gas cellular automata, cellular Potts models), off-lattice models (center-based models, deformable cell models, vertex models), and hybrid discrete-continuum models. In this way, we hope to assist future researchers in choosing a model for the phenomenon they want to model and understand. The article also contains some novel results.

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“…The 3D reconstructions of the lobe-specific vascular trees were individually skeletonized and converted to graphs using dedicated software [18], which was developed based on TiQuant [20,21]. By applying a diameter-defined top-down ordering algorithm presented earlier in [18], we were able to classify the trees according to their branching topology and extract morphological features (radius, length and number of vessels).…”

Section: ) Data Analysismentioning

confidence: 99%

Closed-Loop Lumped Parameter Modeling of Hemodynamics During Cirrhogenesis in Rats

Audebert

Peeters

Segers

et al. 2018

IEEE Trans. Biomed. Eng.

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TiQuant: software for tissue analysis, quantification and surface reconstruction

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 33 publications

References 7 publications

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids

Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids

Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results

Closed-Loop Lumped Parameter Modeling of Hemodynamics During Cirrhogenesis in Rats

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