Automatic vertebrae localization from CT scans using volumetric descriptors

The localization and identification of vertebrae in spinal CT images plays an important role in many clinical applications, such as spinal disease diagnosis, surgery planning, and post-surgery assessment. However, automatic vertebrae localization presents numerous challenges due to partial visibility, appearance similarity of different vertebrae, varying data quality, and the presence of pathologies. Most existing methods require prior information on which vertebrae are present in a scan, and perform poorly on pathological cases, making them of little practical value. In this paper we describe three novel types of local information descriptors which are used to build more complex contextual features, and train a random forest classifier. The three features are progressively more complex, systematically addressing a greater number of limitations of the current state of the art.Postprin

Robust semi-automated path extraction for visualising stenosis of the coronary arteries

Computed tomography angiography (CTA) is useful for diagnosing and planning treatment of heart disease. However, contrast agent in surrounding structures (such as the aorta and left ventricle) makes 3-D visualisation of the coronary arteries difficult. This paper presents a composite method employing segmentation and volume rendering to overcome this issue. A key contribution is a novel Fast Marching minimal path cost function for vessel centreline extraction. The resultant centreline is used to compute a measure of vessel lumen, which indicates the degree of stenosis (narrowing of a vessel). Two volume visualisation techniques are presented which utilise the segmented arteries and lumen measure. The system is evaluated and demonstrated using synthetic and clinically obtained datasets

Matching Local Invariant Features: How Can Contextual Information Help?

International audienceLocal invariant features are a powerful tool for finding correspondences between images since they are robust to cluttered background, occlusion and viewpoint changes. However, they suffer the lack of global information and fail to resolve ambiguities that can occur when an image has multiple similar regions. Considering some global information will clearly help to achieve better performances. The question is which information to use and how to use it. While previous approaches use context for description, this paper shows that better results are obtained if contextual information is included in the matching process. We compare two different methods which use context for matching and experiments show that a relaxation based approach gives better results

Semantic Segmentation of Pathological Lung Tissue with Dilated Fully Convolutional Networks

Early and accurate diagnosis of interstitial lung diseases (ILDs) is crucial for making treatment decisions, but can be challenging even for experienced radiologists. The diagnostic procedure is based on the detection and recognition of the different ILD pathologies in thoracic CT scans, yet their manifestation often appears similar. In this study, we propose the use of a deep purely convolutional neural network for the semantic segmentation of ILD patterns, as the basic component of a computer aided diagnosis (CAD) system for ILDs. The proposed CNN, which consists of convolutional layers with dilated filters, takes as input a lung CT image of arbitrary size and outputs the corresponding label map. We trained and tested the network on a dataset of 172 sparsely annotated CT scans, within a cross-validation scheme. The training was performed in an end-to-end and semi-supervised fashion, utilizing both labeled and non-labeled image regions. The experimental results show significant performance improvement with respect to the state of the art

Matching Local Invariant Features with Contextual Information : an Experimental Evaluation

The main advantage of using local invariant features is their local character which yields robustness to occlusion and varying background. Therefore, local features have proved to be a powerful tool for finding correspondences between images, and have been employed in many applications. However, the local character limits the descriptive capability of features descriptors, and local features fail to resolve ambiguities that can occur when an image shows multiple similar regions. Considering some global information will clearly help to achieve better performances. The question is which information to use and how to use it. Context can be used to enrich the description of the features, or used in the matching step to filter out mismatches. In this paper, we compare different recent methods which use context for matching and show that better results are obtained if contextual information is used during the matching process. We evaluate the methods in two applications: wide baseline matching and object recognition, and it appears that a relaxation based approach gives the best results

Generating semantically enriched diagnostics for radiological images using machine learning

Development of Computer Aided Diagnostic (CAD) tools to aid radiologists in pathology detection and decision making relies considerably on manually annotated images. With the advancement of deep learning techniques for CAD development, these expert annotations no longer need to be hand-crafted, however, deep learning algorithms require large amounts of data in order to generalise well. One way in which to access large volumes of expert-annotated data is through radiological exams consisting of images and reports. Using past radiological exams obtained from hospital archiving systems has many advantages: they are expert annotations available in large quantities, covering a population-representative variety of pathologies, and they provide additional context to pathology diagnoses, such as anatomical location and severity. Learning to auto-generate such reports from images presents many challenges such as the difficulty in representing and generating long, unstructured textual information, accounting for spelling errors and repetition or redundancy, and the inconsistency across different annotators. In this thesis, the problem of learning to automate disease detection from radiological exams is approached from three directions. Firstly, a report generation model is developed such that it is conditioned on radiological image features. Secondly, a number of approaches are explored aimed at extracting diagnostic information from free-text reports. Finally, an alternative approach to image latent space learning from current state-of-the-art is developed that can be applied to accelerated image acquisition.Open Acces

Autoencoder-based Image Recommendation for Lung Cancer Characterization

Neste projeto, temos como objetivo desenvolver um sistema de IA que recomende um conjunto de casos relativos (passados) para orientar a tomada de decisão do médico. Objetivo: A ambição é desenvolver um modelo de aprendizado baseado em IA para caracterização de câncer de pulmão, a fim de auxiliar na rotina clínica. Considerando a complexidade dos fenômenos biológicos que ocorrem durante o desenvolvimento do câncer, as relações entre eles e as manifestações visuais capturadas pela tomografia computadorizada (CT) têm sido exploradas nos últimos anos. No entanto, devido à falta de robustez dos métodos atuais de aprendizado profundo, essas correlações são frequentemente consideradas espúrias e se perdem quando confrontadas com dados coletados a partir de distribuições alteradas: diferentes instituições, características demográficas ou até mesmo estágios de desenvolvimento do câncer.In this project, we aim to develop an AI system that recommends a set of relative (past) cases to guide the decision-making of the clinician. Objective: The ambition is to develop an AI-based learning model for lung cancer characterization in order to assist in clinical routine. Considering the complexity of the biological phenomenat hat occur during cancer development, relationships between these and visual manifestations captured by CT have been explored in recent years; however, given the lack of robustness of current deep learning methods, these correlations are often found spurious and get lost when facing data collected from shifted distributions: different institutions, demographics or even stages of cancer development