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Shape Decomposition Algorithms for Laser Capture Microdissection

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

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Leonie Selbach
  • Department of Computer Science and Center for Protein Diagnostics, Ruhr University Bochum, Germany
Tobias Kowalski
  • Department of Biophysics and Center for Protein Diagnostics, Ruhr University Bochum, Germany
Klaus Gerwert
  • Department of Biophysics and Center for Protein Diagnostics, Ruhr University Bochum, Germany
Maike Buchin
  • Department of Computer Science, Ruhr University Bochum, Germany
Axel Mosig
  • Department of Biophysics and Center for Protein Diagnostics, Ruhr University Bochum, Germany

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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)
https://doi.org/10.4230/LIPIcs.WABI.2020.13

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.

Subject Classification

ACM Subject Classification
  • Applied computing → Bioinformatics
  • Theory of computation → Computational geometry
  • Theory of computation → Dynamic programming
Keywords
  • Laser capture microdissection
  • shape decomposition
  • skeletonization

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References

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