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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

Registration procedure. Top: Reference fish with 1 day after injection of cancer cells. Middle: Fish to be registered. Bottom: Registered fish. For illustration purposes, the images are presented with inverted grayscale values.
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Figure 5: Registration procedure. Top: Reference fish with 1 day after injection of cancer cells. Middle: Fish to be registered. Bottom: Registered fish. For illustration purposes, the images are presented with inverted grayscale values.

Mentions: Images of the reference fish, followed by the target fish, before and after the registration are shown in Figure 5. Also visible is the mask of the reference fish over the target fish, before and after registration. We used 20 landmarks, 17 selected automatically and 3 added manually.


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)

Registration procedure. Top: Reference fish with 1 day after injection of cancer cells. Middle: Fish to be registered. Bottom: Registered fish. For illustration purposes, the images are presented with inverted grayscale values.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Registration procedure. Top: Reference fish with 1 day after injection of cancer cells. Middle: Fish to be registered. Bottom: Registered fish. For illustration purposes, the images are presented with inverted grayscale values.
Mentions: Images of the reference fish, followed by the target fish, before and after the registration are shown in Figure 5. Also visible is the mask of the reference fish over the target fish, before and after registration. We used 20 landmarks, 17 selected automatically and 3 added manually.

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