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DiversePathsJ: diverse shortest paths for bioimage analysis

Uhlmann, Virginie ; Haubold, Carsten ; Hamprecht, Fred A. ; Unser, Michael ; Murphy, Robert ; Murphy, Robert

In: Bioinformatics, 2018, vol. 34, no. 3, p. 538-540

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    Titre
    • DiversePathsJ: diverse shortest paths for bioimage analysis
    Auteur
    • Uhlmann, Virginie. École polytechnique fédérale de Lausanne (EPFL), Biomedical Imaging Group, Lausanne, Switzerland
    • Haubold, Carsten. Heidelberg University, Interdisziplinären Zentrums für Wissenschaftliches Rechnen/Heidelberg Collaboratory for Image Processing (IWR/HCI), Heidelberg, Germany
    • Hamprecht, Fred A.. Heidelberg University, Interdisziplinären Zentrums für Wissenschaftliches Rechnen/Heidelberg Collaboratory for Image Processing (IWR/HCI), Heidelberg, Germany
    • Unser, Michael. École polytechnique fédérale de Lausanne (EPFL), Biomedical Imaging Group, Lausanne, Switzerland
    • Murphy, Robert. École polytechnique fédérale de Lausanne (EPFL), Biomedical Imaging Group, Lausanne, Switzerland
    • Murphy, Robert. École polytechnique fédérale de Lausanne (EPFL), Biomedical Imaging Group, Lausanne, Switzerland
    Type de document
    • Postprint
    Identifiant OAI-PMH
    • oai:doc.rero.ch:331356
    Summary
    Abstract 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 Supplementary information Supplementary data are available at Bioinformatics online.