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3D visualization, skeletonization and branching analysis of blood vessels in angiogenesis

Angiogenesis is the process of new blood vessels growing from existing vasculature. Visualizing them as a three-dimensional (3D) model is a challenging, yet relevant, task as it would be of great help to researchers, pathologists, and medical doctors. A branching analysis on the 3D model would furth...

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Main Authors: Ramakrishnan, Vignesh (Author) , Schönmehl, Rebecca (Author) , Artinger, Annalena (Author) , Winter, Lina (Author) , Böck, Hendrik (Author) , Schreml, Stephan (Author) , Gürtler, Florian (Author) , Daza Barragán, Jimmy Andres (Author) , Schmitt, Volker H. (Author) , Mamilos, Andreas (Author) , Arbelaez, Pablo (Author) , Teufel, Andreas (Author) , Niedermair, Tanja (Author) , Topolcan, Ondrej (Author) , Karlíková, Marie (Author) , Sossalla, Samuel (Author) , Wiedenroth, Christoph B. (Author) , Rupp, Markus (Author) , Brochhausen, Christoph (Author)
Format: Article (Journal)
Language:English
Published: 23 April 2023
In: International journal of molecular sciences
Year: 2023, Volume: 24, Issue: 9, Pages: 1-14
ISSN:1422-0067
DOI:10.3390/ijms24097714
Online Access:Verlag, kostenfrei, Volltext: https://doi.org/10.3390/ijms24097714
Verlag, kostenfrei, Volltext: https://www.mdpi.com/1422-0067/24/9/7714
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Author Notes:Vignesh Ramakrishnan, Rebecca Schönmehl, Annalena Artinger, Lina Winter, Hendrik Böck, Stephan Schreml, Florian Gürtler, Jimmy Daza, Volker H. Schmitt, Andreas Mamilos, Pablo Arbelaez, Andreas Teufel, Tanja Niedermair, Ondrej Topolcan, Marie Karlíková, Samuel Sossalla, Christoph B. Wiedenroth, Markus Rupp and Christoph Brochhausen
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Summary:Angiogenesis is the process of new blood vessels growing from existing vasculature. Visualizing them as a three-dimensional (3D) model is a challenging, yet relevant, task as it would be of great help to researchers, pathologists, and medical doctors. A branching analysis on the 3D model would further facilitate research and diagnostic purposes. In this paper, a pipeline of vision algorithms is elaborated to visualize and analyze blood vessels in 3D from formalin-fixed paraffin-embedded (FFPE) granulation tissue sections with two different staining methods. First, a U-net neural network is used to segment blood vessels from the tissues. Second, image registration is used to align the consecutive images. Coarse registration using an image-intensity optimization technique, followed by finetuning using a neural network based on Spatial Transformers, results in an excellent alignment of images. Lastly, the corresponding segmented masks depicting the blood vessels are aligned and interpolated using the results of the image registration, resulting in a visualized 3D model. Additionally, a skeletonization algorithm is used to analyze the branching characteristics of the 3D vascular model. In summary, computer vision and deep learning is used to reconstruct, visualize and analyze a 3D vascular model from a set of parallel tissue samples. Our technique opens innovative perspectives in the pathophysiological understanding of vascular morphogenesis under different pathophysiological conditions and its potential diagnostic role.
Item Description:Gesehen am 26.03.2024
Physical Description:Online Resource
ISSN:1422-0067
DOI:10.3390/ijms24097714

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