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DOI: 10.4230/LIPIcs.WABI.2020.13

Shape Decomposition Algorithms for Laser Capture Microdissection

Authors: Leonie Selbach, Tobias Kowalski, Klaus Gerwert, Maike Buchin, and Axel Mosig

Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)

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.

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Leonie Selbach, Tobias Kowalski, Klaus Gerwert, Maike Buchin, and Axel Mosig. Shape Decomposition Algorithms for Laser Capture Microdissection. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 13:1-13:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{selbach_et_al:LIPIcs.WABI.2020.13,
  author =	{Selbach, Leonie and Kowalski, Tobias and Gerwert, Klaus and Buchin, Maike and Mosig, Axel},
  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 =	{Kingsford, Carl and Pisanti, Nadia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.13},
  URN =		{urn:nbn:de:0030-drops-128020},
  doi =		{10.4230/LIPIcs.WABI.2020.13},
  annote =	{Keywords: Laser capture microdissection, shape decomposition, skeletonization}
}

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Shape Decomposition Algorithms for Laser Capture Microdissection

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