This article is part of the supplement: Selected articles from the 10th International Workshop on Computational Systems Biology (WCSB) 2013: Bioinformatics

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ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis

Teppo Annila1, Eero Lihavainen1, Ines J Marques2, Darren R Williams3, Olli Yli-Harja1 and Andre Ribeiro1*

Author affiliations

1 Department of Signal Processing, Tampere University of Technology, Tampere, 33720, Finland

2 Cardiovascular Development and Repair, Centro Nacional de Investigacoes Cardiovasculares, Madrid, 28029, Spain

3 New Drug Targets Laboratory, School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 500-712, Republic of Korea

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Citation and License

BMC Bioinformatics 2013, 14(Suppl 10):S5  doi:10.1186/1471-2105-14-S10-S5

Published: 12 August 2013



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.