Creation of Three-Dimensional Liver Tissue Models from Experimental Images for Systems Medicine

Methods Mol Biol. 2017;1506:319-362. doi: 10.1007/978-1-4939-6506-9_22.


In this chapter, we illustrate how three-dimensional liver tissue models can be created from experimental image modalities by utilizing a well-established processing chain of experiments, microscopic imaging, image processing, image analysis and model construction. We describe how key features of liver tissue architecture are quantified and translated into model parameterizations, and show how a systematic iteration of experiments and model simulations often leads to a better understanding of biological phenomena in systems biology and systems medicine.

Keywords: 2D/3D microscopy; Confocal scanning microscopy; Hepatocyte transplantation; Liver architecture; Liver tissue model; Spatiotemporal model; Systems biology; Systems medicine; TiQuant software.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Fluorescent Dyes / chemistry
  • Imaging, Three-Dimensional / methods*
  • Immunohistochemistry / instrumentation
  • Immunohistochemistry / methods
  • Liver / anatomy & histology
  • Liver / diagnostic imaging*
  • Liver / pathology
  • Mice
  • Mice, Knockout
  • Microscopy, Confocal / instrumentation
  • Microscopy, Confocal / methods*
  • Models, Biological*
  • Quality Control
  • Software
  • Staining and Labeling / instrumentation
  • Staining and Labeling / methods*
  • Swine


  • Fluorescent Dyes