Ontologies for Liver Diseases Representation: A Systematic Literature Review.

Ontology, as a useful knowledge engineering technique, has been widely used for reducing ambiguity and helping with information sharing. It is considered originally to be clear, comprehensive, and with well-defined format. It characterizes several domains purposes description through structured and formalized languages. In various areas of research, it has become a significant way to realize successful and powerful accomplishments. Actually, medical ontologies were turned into an efficient application in medical domains. They also become a relevant approach to process large medical data volumes. Consequently, they are behaving as a support decision system in some cases. Also, they ensure diagnosis process acceleration and assistance. Additionally, they have been integrated especially to represent human healthcare concepts. For that reason, plenty of research works applied ontologies to design and treat liver diseases. In this article, we present a general overview of medical ontologies to stand for this type of disease. We expose and discuss these works in details by a complete comparison. Also, we show their performance to arrange clinical data and extract results.

Ontology-Based Approach for Liver Cancer Diagnosis and Treatment.

Liver cancer is the third deadliest cancer in the world. It characterizes a malignant tumor that develops through liver cells. The hepatocellular carcinoma (HCC) is one of these tumors. Hepatic primary cancer is the leading cause of cancer deaths. This article deals with the diagnostic process of liver cancers. In order to analyze a large mass of medical data, ontologies are effective; they are efficient to improve medical image analysis used to detect different tumors and other liver lesions. We are interested in the HCC. Hence, the main purpose of this paper is to offer a new ontology-based approach modeling HCC tumors by focusing on two major aspects: the first focuses on tumor detection in medical imaging, and the second focuses on its staging by applying different classification systems. We implemented our approach in Java using Jena API. Also, we developed a prototype OntHCC by the use of semantic aspects and reasoning rules to validate our work. To show the efficiency of our work, we tested the proposed approach on real datasets. The obtained results have showed a reliable system with high accuracies of recall (76%), precision (85%), and F-measure (80%).

How anatomical impairments found on CT affect perfusion percentage assessed by SPECT/CT scan?

AIM: CT images can identify structural and opacity alterations of the lungs while nuclear medicine's lung perfusion studies show the homogeneity (or lack of) of blood perfusion on the organ. Therefore, the use of SPECT/CT in lung perfusion scintigraphies can help physicians to assess anatomical and functional alterations of the lungs and to differentiate between acute and chronic disease. OBJECTIVE: To develop a computer-aided methodology to quantify the total global perfusion of the lungs via SPECT/CT images and to compare these results with parenchymal alterations obtained in CT images. METHODS: 39 perfusion SPECT/CT images collected retrospectively from the Nuclear Medicine Facility of Botucatu Medical School's Clinics Hospital in São Paulo, Brazil, were analyzed. Anatomical lung impairments (emphysema, collapsed and infiltrated tissue) and the functional percentage of the lungs (blood perfusion) were quantified from CT and SPECT images, with the aid of the free, open-source software 3D Slicer. The results obtained with 3D Slicer (3D-TGP) were also compared to the total global perfusion of each patient's found on their medical report, obtained from visual inspection of planar images (2D-TGP). RESULTS: This research developed a novel and practical methodology for obtaining lungs' total global perfusion from SPECT/CT images in a semiautomatic manner. 3D-TGP versus 2D-TGP showed a bias of 7% with a variation up to 67% between the two methods. Perfusion percentage showed a weak positive correlation with infiltration (p = 0.0070 and ρ = 0.43) and collapsed parenchyma (p = 0.040 and ρ = 0.33). CONCLUSIONS: This research brings meaningful contributions to the scientific community because it used a free open-source software to quantify the lungs blood perfusion via SPECT/CT images and pointed that the relationship between parenchyma alterations and the organ's perfusion capability might not be so direct, given compensatory mechanisms.

Smoothed Shock Filtering: Algorithm and Applications.

This article presents the smoothed shock filter, which iteratively produces local segmentations in image's inflection zones with smoothed morphological operators (dilations, erosions). Hence, it enhances contours by creating smoothed ruptures, while preserving homogeneous regions. After describing the algorithm, we show that it is a robust approach for denoising, compared to related works. Then, we expose how we exploited this filter as a pre-processing step in different image analysis tasks (medical image segmentation, fMRI, and texture classification). By means of its ability to enhance important patterns in images, the smoothed shock filter has a real positive impact upon such applications, for which we would like to explore it more in the future.

Automatic segmentation methods for liver and hepatic vessels from CT and MRI volumes, applied to the Couinaud scheme.

BACKGROUND: Proper segmentation of the liver from medical images is critical for computer-assisted diagnosis, therapy and surgical planning. Knowledge of its vascular structure allows division of the liver into eight functionally independent segments, each with its own vascular inflow, known as the Couinaud scheme. Couinaud's description is the most widely used classification, since it is well-suited for surgery and accurate for the localization of lesions. However, automatic segmentation of the liver and its vascular structure to construct the Couinaud scheme remains a challenging task. METHODS: We present a complete framework to obtain Couinaud's classification in three main steps; first, we propose a model-based liver segmentation, then a vascular segmentation based on a skeleton process, and finally, the construction of the eight independent liver segments. Our algorithms are automatic and allow 3D visualizations. RESULTS: We validate these algorithms on various databases with different imaging modalities (Magnetic Resonance Imaging (MRI) and Computed Tomography (CT)). Experimental results are presented on diseased livers, which pose complex challenges because both the overall organ shape and the vessels can be severely deformed. A mean DICE score of 0.915 is obtained for the liver segmentation, and an average accuracy of 0.98 for the vascular network. Finally, we present an evaluation of our method for performing the Couinaud segmentation thanks to medical reports with promising results. CONCLUSIONS: We were able to automatically reconstruct 3-D volumes of the liver and its vessels on MRI and CT scans. Our goal is to develop an improved method to help radiologists with tumor localization.

A robust multi-variability model based liver segmentation algorithm for CT-scan and MRI modalities.

Developing methods to segment the liver in medical images, study and analyze it remains a significant challenge. The shape of the liver can vary considerably from one patient to another, and adjacent organs are visualized in medical images with similar intensities, making the boundaries of the liver ambiguous. Consequently, automatic or semi-automatic segmentation of liver is a difficult task. Moreover, scanning systems and magnetic resonance imaging have different settings and parameters. Thus the images obtained differ from one machine to another. In this article, we propose an automatic model-based segmentation that allows building a faithful 3-D representation of the liver, with a mean Dice value equal to 90.3% on CT and MRI datasets. We compare our algorithm with a semi-automatic method and with other approaches according to the state of the art. Our method works with different data sources, we use a large quantity of CT and MRI images from machines in various hospitals and multiple DICOM images available from public challenges. Finally, for evaluation of liver segmentation approaches in state of the art, robustness is not adequacy addressed with a precise definition. Another originality of this article is the introduction of a novel measure of robustness, which takes into account the liver variability at different scales.

Tree leaves extraction in natural images: comparative study of preprocessing tools and segmentation methods.

In this paper, we propose a comparative study of various segmentation methods applied to the extraction of tree leaves from natural images. This study follows the design of a mobile application, developed by Cerutti et al. (published in ReVeS Participation--Tree Species Classification Using Random Forests and Botanical Features. CLEF 2012), to highlight the impact of the choices made for segmentation aspects. All the tests are based on a database of 232 images of tree leaves depicted on natural background from smartphones acquisitions. We also propose to study the improvements, in terms of performance, using preprocessing tools, such as the interaction between the user and the application through an input stroke, as well as the use of color distance maps. The results presented in this paper shows that the method developed by Cerutti et al. (denoted Guided Active Contour), obtains the best score for almost all observation criteria. Finally, we detail our online benchmark composed of 14 unsupervised methods and 6 supervised ones.