ZFIN ID: ZDB-PUB-140127-2
ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis
Annila, T., Lihavainen, E., Marques, I.J., Williams, D.R., Yli-Harja, O., and Ribeiro, A.
Date: 2013
Source: BMC Bioinformatics   14(10): S5 (Journal)
Registered Authors: Marques, Ines
Keywords: none
MeSH Terms:
  • Animals
  • Animals, Genetically Modified
  • Automation
  • Cell Line, Tumor
  • Disease Models, Animal
  • Disease Progression
  • Embryonic Development/genetics
  • Humans
  • Image Processing, Computer-Assisted/instrumentation
  • Image Processing, Computer-Assisted/methods*
  • Organisms, Genetically Modified/embryology
  • Pancreatic Neoplasms/diagnosis*
  • Pancreatic Neoplasms/genetics
  • Pancreatic Neoplasms/pathology*
  • Random Allocation
  • Zebrafish
PubMed: 24267347 Full text @ BMC Bioinformatics


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.


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.


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.


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.