title: ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis.
abstract: BACKGROUND
  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.
authors.forename: Teppo
authors.initials: T
authors.lastname: Annila
authors.forename: Eero
authors.initials: E
authors.lastname: Lihavainen
authors.forename: Ines J
authors.initials: IJ
authors.lastname: Marques
authors.forename: Darren R
authors.initials: DR
authors.lastname: Williams
authors.forename: Olli
authors.initials: O
authors.lastname: Yli-Harja
authors.forename: Andre
authors.initials: A
authors.lastname: Ribeiro
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D001331:Automation; D045744:Cell Line, Tumor; D004195:Disease Models, Animal; D018450:Disease Progression; D047108:Embryonic Development / Q000235:genetics; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000295:instrumentation / Q000379:methods*; D030781:Organisms, Genetically Modified / Q000196:embryology; D010190:Pancreatic Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology*; D011897:Random Allocation; D015027:Zebrafish