Annila, TeppoLihavainen, EeroMarques, Ines JoaoWilliams, Darren RYli-Harja, OlliRibeiro, Andre2019-09-252019-09-252013-08BMC Bioinformatics. 2013; 14(Suppl 10):S51471-2105http://hdl.handle.net/20.500.12105/8376BACKGROUND: Zebrafish embryos have recently been established as a xenotransplantation model of the metastatic behaviour of primary human tumours. Current tools for automated data extraction from the microscope images are restrictive concerning the developmental stage of the embryos, usually require laborious manual image preprocessing, and, in general, cannot characterize the metastasis as a function of the internal organs. METHODS: We present a tool, ZebIAT, that allows both automatic or semi-automatic registration of the outer contour and inner organs of zebrafish embryos. ZebIAT provides a registration at different stages of development and an automatic analysis of cancer metastasis per organ, thus allowing to study cancer progression. The semi-automation relies on a graphical user interface. RESULTS: We quantified the performance of the registration method, and found it to be accurate, except in some of the smallest organs. Our results show that the accuracy of registering small organs can be improved by introducing few manual corrections. We also demonstrate the applicability of the tool to studies of cancer progression. CONCLUSIONS: ZebIAT offers major improvement relative to previous tools by allowing for an analysis on a per-organ or region basis. It should be of use in high-throughput studies of cancer metastasis in zebrafish embryos.engVoRhttp://creativecommons.org/licenses/by/4.0/AnimalsAnimals, Genetically ModifiedAutomationCell Line, TumorDisease Models, AnimalDisease ProgressionEmbryonic DevelopmentHumansImage Processing, Computer-AssistedOrganisms, Genetically ModifiedPancreatic NeoplasmsRandom AllocationZebrafishAtribución 4.0 Internacional2426734714 Suppl 10Suppl 10S510.1186/1471-2105-14-S10-S51471-2105BMC bioinformaticsopen access