A semi-automatic approach for segmentation of three-dimensional microscopic image stacks of cardiac tissue

  • Authors:

  • Thomas Seidel;Thomas Draebing;Gunnar Seemann;Frank B. Sachse

  • Affiliations:

  • Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT;Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT;Institute of Biomedical Engineering, Karlsruhe Institute of Technology, Karlsruhe, Germany;Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT and Department of Bioengineering, University of Utah, Salt Lake City, UT

  • Venue:
  • FIMH'13 Proceedings of the 7th international conference on Functional Imaging and Modeling of the Heart
  • Year:
  • 2013

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Abstract

The segmentation of three-dimensional microscopic images of cardiac tissues provides important parameters for characterizing cardiac diseases and modeling of tissue function. Segmenting these images is, however, challenging. Currently only time-consuming manual approaches have been developed for this purpose. Here, we introduce an efficient approach for the semi-automatic segmentation (SAS) of cardiomyocytes and the extracellular space in image stacks obtained from confocal microscopy. The approach is based on a morphological watershed algorithm and iterative creation of watershed seed points on a distance map. Results of SAS were consistent with results from manual segmentation (Dice similarity coefficient: 90.8±2.6%). Cell volume was 4.6±6.5% higher in SAS cells, which mainly resulted from cell branches and membrane protrusions neglected by manual segmentation. We suggest that the novel approach constitutes an important tool for characterizing normal and diseased cardiac tissues. Furthermore, the approach is capable of providing crucial parameters for modeling of tissue structure and function.