Visualization and analysis of 3D-connectivity at cell resolution | TU Wien

Information

Publication Type: Master Thesis
Workgroup(s)/Project(s): not specified
Date: 2025
TU Wien Library: AC17473350
Open Access: yes
First Supervisor: Renata Georgia Raidou
Pages: 123
Keywords: Visualization, 3D Reconstruction, Connectivity, Cellular Neighborhoods, Functional Tissue Units, Glomeruli, Nerves, PanIN, Melanoma

Abstract

With the advancement of imaging technologies, the mapping of the human body at continually increasing resolution becomes possible. Multiple research programs have achieved the imaging of various functional tissue units at cell resolution and even the imaging of single-cells in a combined effort to map out the human body and its disease states. Novel contributions to these programs open up a multitude of avenues to explore the functional complexity and disease progression of organs in even more detail. A vital part of this exploration is the analysis of connectivity between the functional tissue units or single-cells, as they are believed to communicate through diverse channels. This thesis presents two independent tools that empower researchers to improve their connectivity analysis workflows. Firstly, an installable Python tool that generates surface meshes and a connectivity abstraction in the form of a network from segmented volumetric data. In the course of this, a method for suggesting the connectivity of incomplete tubular meshes is proposed. Secondly, an interactive web-based visualization tool that improves connectivity analysis by synchronizing a three-dimensional spatial view with two network views that incorporate the connectivity abstraction. The applicability of both tools is tested and showcased with data from three distinct fields by analyzing the connectivity between glomeruli and nerves in the kidney, the connectivity of intraepitheliel lesions in pancreatic ducts with the surrounding nervous system, and the connectivity between single-cells of a melanoma.

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thesis

Weblinks

BibTeX

@mastersthesis{beinder-2025-vao,
  title =      "Visualization and analysis of 3D-connectivity at cell
               resolution",
  author =     "Benjamin Beinder",
  year =       "2025",
  abstract =   "With the advancement of imaging technologies, the mapping of
               the human body at continually increasing resolution becomes
               possible. Multiple research programs have achieved the
               imaging of various functional tissue units at cell
               resolution and even the imaging of single-cells in a
               combined effort to map out the human body and its disease
               states. Novel contributions to these programs open up a
               multitude of avenues to explore the functional complexity
               and disease progression of organs in even more detail. A
               vital part of this exploration is the analysis of
               connectivity between the functional tissue units or
               single-cells, as they are believed to communicate through
               diverse channels. This thesis presents two independent tools
               that empower researchers to improve their connectivity
               analysis workflows. Firstly, an installable Python tool that
               generates surface meshes and a connectivity abstraction in
               the form of a network from segmented volumetric data. In the
               course of this, a method for suggesting the connectivity of
               incomplete tubular meshes is proposed. Secondly, an
               interactive web-based visualization tool that improves
               connectivity analysis by synchronizing a three-dimensional
               spatial view with two network views that incorporate the
               connectivity abstraction. The applicability of both tools is
               tested and showcased with data from three distinct fields by
               analyzing the connectivity between glomeruli and nerves in
               the kidney, the connectivity of intraepitheliel lesions in
               pancreatic ducts with the surrounding nervous system, and
               the connectivity between single-cells of a melanoma.",
  pages =      "123",
  address =    "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria",
  school =     "Research Unit of Computer Graphics, Institute of Visual
               Computing and Human-Centered Technology, Faculty of
               Informatics, TU Wien",
  keywords =   "Visualization, 3D Reconstruction, Connectivity, Cellular
               Neighborhoods, Functional Tissue Units, Glomeruli, Nerves,
               PanIN, Melanoma",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2025/beinder-2025-vao/",
}