BIOMEDICAL IMAGING GROUP (BIG)
Laboratoire d'imagerie biomédicale (LIB)

DiversePathsJ: Diverse Shortest Paths for Bioimage Analysis

V. Uhlmann, C. Haubold, F.A. Hamprecht, M. Unser

Bioinformatics, vol. 34, no. 3, pp. 538–540, February 1, 2018.

Motivation: We introduce a formulation for the general task of finding diverse shortest paths between two end-points. Our approach is not linked to a specific biological problem and can be applied to a large variety of images thanks to its generic implementation as a user-friendly ImageJ/Fiji plugin. It relies on the introduction of additional layers in a Viterbi path graph, which requires slight modifications to the standard Viterbi algorithm rules. This layered graph construction allows for the specification of various constraints imposing diversity between solutions.

Results: The software allows obtaining a collection of diverse shortest paths under some user-defined constraints through a convenient and user-friendly interface. It can be used alone or be integrated into larger image analysis pipelines.

Availability and implementation: http://bigwww.epfl.ch/algorithms/diversepathsj/

Contact: michael.unser@epfl.ch or fred.hamprecht@iwr.uni-heidelberg.de

Supplementary information: Supplementary data are available at Bioinformatics online. 

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AUTHOR="Uhlmann, V. and Haubold, C. and Hamprecht, F.A. and Unser, M.",
TITLE="{DiversePathsJ}: {D}iverse Shortest Paths for Bioimage Analysis",
JOURNAL="Bioinformatics",
YEAR="2018",
volume="34",
number="3",
pages="538--540",
month="February 1,",
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