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

Annila T, Lihavainen E, Marques IJ, Williams DR, Yli-Harja O, Ribeiro A - BMC Bioinformatics (2013)

Bottom Line: 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.ZebIAT offers major improvement relative to previous tools by allowing for an analysis on a per-organ or region basis.

View Article: PubMed Central - HTML - PubMed

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.

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Related in: MedlinePlus

Example of a reference embryo, with organs marked. For easier visualization, only the borders of the masks of the organs are shown.
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Figure 1: Example of a reference embryo, with organs marked. For easier visualization, only the borders of the masks of the organs are shown.

Mentions: At this stage, one image has to be selected as the 'reference embryo'. In this image, the user manually marks the organs or other areas of interest (see User's Manual). We advise the use of different reference images for each stage of development given the rapid morphological changes. As an example, we show in (Figure 1) an example mask with several organs and areas of interest selected. ZebIAT already contains a predefined mask for each of four development stages (days 1 to 4). If the ventral and dorsal caudal regions are marked, ZebIAT has an additional option of dividing them into smaller regions. Once this procedure is complete, other fish can be automatically registered to the reference fish, and the inner organs located.


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

Annila T, Lihavainen E, Marques IJ, Williams DR, Yli-Harja O, Ribeiro A - BMC Bioinformatics (2013)

Example of a reference embryo, with organs marked. For easier visualization, only the borders of the masks of the organs are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750475&req=5

Figure 1: Example of a reference embryo, with organs marked. For easier visualization, only the borders of the masks of the organs are shown.
Mentions: At this stage, one image has to be selected as the 'reference embryo'. In this image, the user manually marks the organs or other areas of interest (see User's Manual). We advise the use of different reference images for each stage of development given the rapid morphological changes. As an example, we show in (Figure 1) an example mask with several organs and areas of interest selected. ZebIAT already contains a predefined mask for each of four development stages (days 1 to 4). If the ventral and dorsal caudal regions are marked, ZebIAT has an additional option of dividing them into smaller regions. Once this procedure is complete, other fish can be automatically registered to the reference fish, and the inner organs located.

Bottom Line: 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.ZebIAT offers major improvement relative to previous tools by allowing for an analysis on a per-organ or region basis.

View Article: PubMed Central - HTML - PubMed

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.

Show MeSH
Related in: MedlinePlus