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DiversePathsJ: Diverse Shortest Paths for Bioimage Analysis

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

Bioinformatics, in press.

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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, fred.hamprecht@iwr.uni-heidelberg.de

Supplementary information: Supplementary material is available at Bioinformatics online.

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