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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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Detalles Bibliográficos
Autores principales: Uhlmann, Virginie, Haubold, Carsten, Hamprecht, Fred A, Unser, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860364/
https://www.ncbi.nlm.nih.gov/pubmed/29029024
http://dx.doi.org/10.1093/bioinformatics/btx621
Descripción
Sumario: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.