License: Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2020.13
URN: urn:nbn:de:0030-drops-128020
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2020/12802/
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Selbach, Leonie ; Kowalski, Tobias ; Gerwert, Klaus ; Buchin, Maike ; Mosig, Axel

Shape Decomposition Algorithms for Laser Capture Microdissection

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LIPIcs-WABI-2020-13.pdf (1 MB)

Abstract

In the context of biomarker discovery and molecular characterization of diseases, laser capture microdissection is a highly effective approach to extract disease-specific regions from complex, heterogeneous tissue samples. These regions have to be decomposed into feasible fragments as they have to satisfy certain constraints in size and morphology for the extraction to be successful. We model this problem of constrained shape decomposition as the computation of optimal feasible decompositions of simple polygons. We use a skeleton-based approach and present an algorithmic framework that allows the implementation of various feasibility criteria as well as optimization goals. Motivated by our application, we consider different constraints and examine the resulting fragmentations. Furthermore, we apply our method to lung tissue samples and show its advantages in comparison to a heuristic decomposition approach.

BibTeX - Entry

@InProceedings{selbach_et_al:LIPIcs:2020:12802,
  author =	{Leonie Selbach and Tobias Kowalski and Klaus Gerwert and Maike Buchin and Axel Mosig},
  title =	{{Shape Decomposition Algorithms for Laser Capture Microdissection}},
  booktitle =	{20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
  pages =	{13:1--13:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-161-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{172},
  editor =	{Carl Kingsford and Nadia Pisanti},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/opus/volltexte/2020/12802},
  URN =		{urn:nbn:de:0030-drops-128020},
  doi =		{10.4230/LIPIcs.WABI.2020.13},
  annote =	{Keywords: Laser capture microdissection, shape decomposition, skeletonization}
}

Keywords: Laser capture microdissection, shape decomposition, skeletonization
Collection: 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
Issue Date: 2020
Date of publication: 25.08.2020

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