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DiversePathsJ: diverse shortest paths for bioimage analysis

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...

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Hauptverfasser: Uhlmann, Virginie (VerfasserIn) , Haubold, Carsten (VerfasserIn) , Hamprecht, Fred (VerfasserIn)
Dokumenttyp: Article (Journal)
Sprache:Englisch
Veröffentlicht: 2018
In: Bioinformatics
Year: 2017, Jahrgang: 34, Heft: 3, Pages: 538-540
ISSN:1367-4811
DOI:10.1093/bioinformatics/btx621
Online-Zugang:Verlag, Volltext: http://dx.doi.org/10.1093/bioinformatics/btx621
Verlag, Volltext: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860364/
Volltext
Verfasserangaben:Virginie Uhlmann, Carsten Haubold, Fred A Hamprecht and Michael Unser

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520 |a 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: are available at Bioinformatics online. 
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