Limits...
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.

Show MeSH

Related in: MedlinePlus

Area of the cancer spots per organ, normalized by the area of the organ. Top: Fish at 1 dpi, bottom: Fish at 2 dpi.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3750475&req=5

Figure 7: Area of the cancer spots per organ, normalized by the area of the organ. Top: Fish at 1 dpi, bottom: Fish at 2 dpi.

Mentions: Finally, to demonstrate the utility of ZebIAT in extracting biologically relevant information from the images, we show in Figure 7, for the two first days post-injection, the mean fraction of the area of each organ that exhibited cancer spots in the embryos examined. Note that we sub-divided the ventral and dorsal regions into smaller sub-regions. By comparing the top and bottom images, it is possible to see the utility of ZebIAT in studying cancer progression, both in individuals, as well as when averaged over many individuals. For example, from this particular comparison we observe an increase of the areas with cancer cells with time in both the ventral region and yolk. It is also visible a decrease of these cells in, e.g., the otic vesicle, which demonstrates that they migrate throughout the body [1]. Using ZebIAT, not only could one obtain a quantified assessment of this process, but one could also execute a comparative analysis of this process, e.g., for different cancer cells.


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)

Area of the cancer spots per organ, normalized by the area of the organ. Top: Fish at 1 dpi, bottom: Fish at 2 dpi.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Area of the cancer spots per organ, normalized by the area of the organ. Top: Fish at 1 dpi, bottom: Fish at 2 dpi.
Mentions: Finally, to demonstrate the utility of ZebIAT in extracting biologically relevant information from the images, we show in Figure 7, for the two first days post-injection, the mean fraction of the area of each organ that exhibited cancer spots in the embryos examined. Note that we sub-divided the ventral and dorsal regions into smaller sub-regions. By comparing the top and bottom images, it is possible to see the utility of ZebIAT in studying cancer progression, both in individuals, as well as when averaged over many individuals. For example, from this particular comparison we observe an increase of the areas with cancer cells with time in both the ventral region and yolk. It is also visible a decrease of these cells in, e.g., the otic vesicle, which demonstrates that they migrate throughout the body [1]. Using ZebIAT, not only could one obtain a quantified assessment of this process, but one could also execute a comparative analysis of this process, e.g., for different cancer cells.

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