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Ratsnake: a versatile image annotation tool with application to computer-aided diagnosis.

Iakovidis DK, Goudas T, Smailis C, Maglogiannis I - ScientificWorldJournal (2014)

Bottom Line: In this paper we present Ratsnake, a publicly available generic image annotation tool providing annotation efficiency, semantic awareness, versatility, and extensibility, features that can be exploited to transform it into an effective CAD system.However a tool for detecting and quantifying the disease is not yet available.The experimental evaluation of the proposed application of Ratsnake demonstrates its efficiency and effectiveness and promises its wide applicability across a variety of medical imaging domains.

View Article: PubMed Central - PubMed

Affiliation: Department of Informatics and Computer Technology, Technological Educational Institute of Lamia, 35100 Lamia, Greece.

ABSTRACT
Image segmentation and annotation are key components of image-based medical computer-aided diagnosis (CAD) systems. In this paper we present Ratsnake, a publicly available generic image annotation tool providing annotation efficiency, semantic awareness, versatility, and extensibility, features that can be exploited to transform it into an effective CAD system. In order to demonstrate this unique capability, we present its novel application for the evaluation and quantification of salient objects and structures of interest in kidney biopsy images. Accurate annotation identifying and quantifying such structures in microscopy images can provide an estimation of pathogenesis in obstructive nephropathy, which is a rather common disease with severe implication in children and infants. However a tool for detecting and quantifying the disease is not yet available. A machine learning-based approach, which utilizes prior domain knowledge and textural image features, is considered for the generation of an image force field customizing the presented tool for automatic evaluation of kidney biopsy images. The experimental evaluation of the proposed application of Ratsnake demonstrates its efficiency and effectiveness and promises its wide applicability across a variety of medical imaging domains.

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Related in: MedlinePlus

A snapshot of Ratsnake's GUI. It displays the annotated kidney biopsy image of Figure 1(b). The user may click on the annotation names (labels) on the right and display the respective ROI. The labels used are semantic identifiers from the gene ontology [41]. Only the currently selected annotation can be displayed at a time, as a layer over the image to which it belongs. The dialog box is the result of the menu option Measurement→Area Measurement, which is used to measure the area of the current ROI. The panel on the left controls the parameters of the snake.
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fig4: A snapshot of Ratsnake's GUI. It displays the annotated kidney biopsy image of Figure 1(b). The user may click on the annotation names (labels) on the right and display the respective ROI. The labels used are semantic identifiers from the gene ontology [41]. Only the currently selected annotation can be displayed at a time, as a layer over the image to which it belongs. The dialog box is the result of the menu option Measurement→Area Measurement, which is used to measure the area of the current ROI. The panel on the left controls the parameters of the snake.

Mentions: The described methodology has been implemented in Java and has been integrated in Ratsnake as a custom coded plugin. The processes related to the kidney biopsy image analysis have been implemented as a web service communicating with the plugin. A snapshot of Ratsnake's GUI is illustrated in Figure 4. The effect of the force field generated by the plugin, as well as the values of the rest of the parameters of the snake (see (1)), is controlled by the settings panel. The functionality of Ratsnake from the user's viewpoint for the particular application can be summarized into the following steps.


Ratsnake: a versatile image annotation tool with application to computer-aided diagnosis.

Iakovidis DK, Goudas T, Smailis C, Maglogiannis I - ScientificWorldJournal (2014)

A snapshot of Ratsnake's GUI. It displays the annotated kidney biopsy image of Figure 1(b). The user may click on the annotation names (labels) on the right and display the respective ROI. The labels used are semantic identifiers from the gene ontology [41]. Only the currently selected annotation can be displayed at a time, as a layer over the image to which it belongs. The dialog box is the result of the menu option Measurement→Area Measurement, which is used to measure the area of the current ROI. The panel on the left controls the parameters of the snake.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3926425&req=5

fig4: A snapshot of Ratsnake's GUI. It displays the annotated kidney biopsy image of Figure 1(b). The user may click on the annotation names (labels) on the right and display the respective ROI. The labels used are semantic identifiers from the gene ontology [41]. Only the currently selected annotation can be displayed at a time, as a layer over the image to which it belongs. The dialog box is the result of the menu option Measurement→Area Measurement, which is used to measure the area of the current ROI. The panel on the left controls the parameters of the snake.
Mentions: The described methodology has been implemented in Java and has been integrated in Ratsnake as a custom coded plugin. The processes related to the kidney biopsy image analysis have been implemented as a web service communicating with the plugin. A snapshot of Ratsnake's GUI is illustrated in Figure 4. The effect of the force field generated by the plugin, as well as the values of the rest of the parameters of the snake (see (1)), is controlled by the settings panel. The functionality of Ratsnake from the user's viewpoint for the particular application can be summarized into the following steps.

Bottom Line: In this paper we present Ratsnake, a publicly available generic image annotation tool providing annotation efficiency, semantic awareness, versatility, and extensibility, features that can be exploited to transform it into an effective CAD system.However a tool for detecting and quantifying the disease is not yet available.The experimental evaluation of the proposed application of Ratsnake demonstrates its efficiency and effectiveness and promises its wide applicability across a variety of medical imaging domains.

View Article: PubMed Central - PubMed

Affiliation: Department of Informatics and Computer Technology, Technological Educational Institute of Lamia, 35100 Lamia, Greece.

ABSTRACT
Image segmentation and annotation are key components of image-based medical computer-aided diagnosis (CAD) systems. In this paper we present Ratsnake, a publicly available generic image annotation tool providing annotation efficiency, semantic awareness, versatility, and extensibility, features that can be exploited to transform it into an effective CAD system. In order to demonstrate this unique capability, we present its novel application for the evaluation and quantification of salient objects and structures of interest in kidney biopsy images. Accurate annotation identifying and quantifying such structures in microscopy images can provide an estimation of pathogenesis in obstructive nephropathy, which is a rather common disease with severe implication in children and infants. However a tool for detecting and quantifying the disease is not yet available. A machine learning-based approach, which utilizes prior domain knowledge and textural image features, is considered for the generation of an image force field customizing the presented tool for automatic evaluation of kidney biopsy images. The experimental evaluation of the proposed application of Ratsnake demonstrates its efficiency and effectiveness and promises its wide applicability across a variety of medical imaging domains.

Show MeSH
Related in: MedlinePlus