ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis
| Autor: | Andre S. Ribeiro, Olli Yli-Harja, Darren R. Williams, Eero Lihavainen, Ines J. Marques, Teppo Annila |
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| Přispěvatelé: | Finlands Akademi (Finlandia), Emil Aaltonen Foundation, Finnish Funding Agency for Technology and Innovation |
| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Xenotransplantation
medicine.medical_treatment Cancer metastasis Embryonic Development Image processing Bioinformatics Biochemistry Metastasis Automated data Animals Genetically Modified Automation Random Allocation Structural Biology Cell Line Tumor medicine Image Processing Computer-Assisted Animals Humans Molecular Biology Zebrafish Developmental stage biology Organisms Genetically Modified Applied Mathematics Research biology.organism_classification medicine.disease Computer Science Applications Pancreatic Neoplasms Disease Models Animal Zebrafish embryo Disease Progression |
| Zdroj: | BMC Bioinformatics Repisalud Instituto de Salud Carlos III (ISCIII) |
| ISSN: | 1471-2105 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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