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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

Extracted landmarks. The outline of the reference fish is shown as a solid line while the outline of the target fish is shown by a dashed line. Empty circles indicate the landmarks in the reference fish, while full circles indicate the landmarks in the target fish. The dotted lines indicate the correspondence between landmarks in the two fish.
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Figure 4: Extracted landmarks. The outline of the reference fish is shown as a solid line while the outline of the target fish is shown by a dashed line. Empty circles indicate the landmarks in the reference fish, while full circles indicate the landmarks in the target fish. The dotted lines indicate the correspondence between landmarks in the two fish.

Mentions: Next, we use the outline to obtain landmarks automatically for both reference and non-reference fish. Once the head and tail are located, we generate new landmarks by moving along the contour and placing landmarks between them. These are introduced as follows. In general, they are equally spaced. However, in two regions, the tail and the yolk, they are not added, as these regions differ significantly in shape from one embryo to the next. The direct correspondence between landmarks of reference and non-reference fish is obtained by generating an equal amount of landmarks for both fish. The result of placing landmarks and the correspondence between reference and non-reference fish is illustrated in Figure 4. To support this process, ZebIAT has a user interface to add, remove or modify landmarks. This can be of use particularly in registering internal organs or regions of interest.


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)

Extracted landmarks. The outline of the reference fish is shown as a solid line while the outline of the target fish is shown by a dashed line. Empty circles indicate the landmarks in the reference fish, while full circles indicate the landmarks in the target fish. The dotted lines indicate the correspondence between landmarks in the two fish.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Extracted landmarks. The outline of the reference fish is shown as a solid line while the outline of the target fish is shown by a dashed line. Empty circles indicate the landmarks in the reference fish, while full circles indicate the landmarks in the target fish. The dotted lines indicate the correspondence between landmarks in the two fish.
Mentions: Next, we use the outline to obtain landmarks automatically for both reference and non-reference fish. Once the head and tail are located, we generate new landmarks by moving along the contour and placing landmarks between them. These are introduced as follows. In general, they are equally spaced. However, in two regions, the tail and the yolk, they are not added, as these regions differ significantly in shape from one embryo to the next. The direct correspondence between landmarks of reference and non-reference fish is obtained by generating an equal amount of landmarks for both fish. The result of placing landmarks and the correspondence between reference and non-reference fish is illustrated in Figure 4. To support this process, ZebIAT has a user interface to add, remove or modify landmarks. This can be of use particularly in registering internal organs or regions of interest.

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