Computer-aided detection of interstitial lung diseases: A texture approach

We have developed the flexible scheme for computer-aided detection (CAD) of interstitial lung diseases on chest radiographs. These schemes enable us to perform diagnostics in the broad circumstances of pneumonia and other interstitial lung diseases. It is applied in the case of children pneumonia when conditions are difficult to standardize. In the adults' case the schemes of CAD are more adaptive, as there are more characteristic interstitial lung tissue's changes to all kinds of pathological conditions. Even in the norm of drawing there are more visible and more highlighted features, leading to better results. The CAD scheme works as follows. For the first of all, we are using adopted algorithms of active contours to select the area of lungs, and then to divide this area into subareas - regions of interest (40 different ROI). Then ROIs were subjected to the 2-dimensional Daubechies wavelet transform, and only main transformation was used. For every transformation 12 texture measures were calculated. Principal component analysis (PCA) was used to extract 2 main components for each ROI, and these components were compared to predictive component region

Computer-aided diagnosis in chest radiography

Chest radiographs account for more than half of all radiological examinations; the chest is the mirror of health and disease. This thesis is about techniques for computer analysis of chest radiographs. It describes methods for texture analysis and segmenting the lung fields and rib cage in a chest film. It includes a description of an automatic system for detecting regions with abnormal texture, that is applied to a database of images from a tuberculosis screening program

Role of imaging in progressive-fibrosing interstitial lung diseases

Imaging techniques are an essential component of the diagnostic process for interstitial lung diseases (ILDs). Chest radiography is frequently the initial indicator of an ILD, and comparison of radiographs taken at different time points can show the rate of disease progression. However, radiography provides only limited specificity and sensitivity and is primarily used to rule out other diseases, such as left heart failure. High-resolution computed tomography (HRCT) is a more sensitive method and is considered central in the diagnosis of ILDs. Abnormalities observed on HRCT can help identify specific ILDs. HRCT also can be used to evaluate the patient's prognosis, while disease progression can be assessed through serial imaging. Other imaging techniques such as positron emission tomography-computed tomography and magnetic resonance imaging have been investigated, but they are not commonly used to assess patients with ILDs. Disease severity may potentially be estimated using quantitative methods, as well as visual analysis of images. For example, comprehensive assessment of disease staging and progression in patients with ILDs requires visual analysis of pulmonary features that can be performed in parallel with quantitative analysis of the extent of fibrosis. New approaches to image analysis, including the application of machine learning, are being developed

Analyse automatique de radiographies pulmonaires pour le diagnostic précoce du syndrome de détresse respiratoire aiguë

RÉSUMÉ Le Syndrome de Détresse Respiratoire Aiguë (SDRA) est une maladie pulmonaire qui représente la forme la plus grave de l’insuffisance respiratoire aiguë. Elle consiste en une atteinte inflammatoire aiguë des poumons et se manifeste au niveau de la radiographie pulmonaire sous forme d’opacités bilatérales. Le diagnostic de cette maladie est effectué à partir de données sur l’hypoxémie et de l’analyse de la radiographie pulmonaire. L’interprétation de la radiographie pulmonaire par des experts souffre d’une variabilité inter-observateurs élevée, ce qui peut entraîner un diagnostic tardif. Cela est problématique, car un diagnostic retardé d’un patient atteint du SDRA rend son traitement moins efficace et peut, par conséquent, grever son pronostic. D’où l’intérêt de développer un système d’aide à la décision clinique (SADC) pour aider le médecin à établir un diagnostic précoce de la maladie. Les SADC pour le diagnostic automatique de maladies à partir des radiographies sont devenus des outils très importants. Ils consistent à analyser automatiquement les radiographies pour identifier les anomalies et procurer un deuxième avis diagnostic aux médecins. Même si plusieurs SADC ont été déjà développés, il n’existe aucun SADC pour le diagnostic du SDRA. La difficulté principale est due à la superposition de structures osseuses telle que la cage thoracique, dont la propriété de radio-opacité rend leur apparence très similaire à celle des opacités diffuses liées au SDRA dans la radiographie pulmonaire. Une segmentation préalable des côtes entières est requise dans le but de les exclure de l’analyse et de focaliser sur l’étude des opacités diffuses due au SDRA. Pour pouvoir valider un SADC pour le diagnostic du SDRA, la création d’une base de radiographies pulmonaires diagnostiquées avec précision est aussi indispensable. La première partie de cette thèse propose un SADC original pour le diagnostic du SDRA à partir de radiographies pulmonaires. Comme il n’existe actuellement aucun système dédié pour cette pathologie, il a fallu le construire de novo. Le SADC développé consiste à analyser une radiographie du thorax après soustraction des côtes entières (postérieures et antérieures) pour pouvoir extraire des régions d’intérêt (ROI) intercostales qui se composent de tissus pulmonaires et analyser uniquement ces régions. Des caractéristiques statistiques et spectrales sont extraites pour chaque ROI. Ensuite, une méthode de transformation des caractéristiques est appliquée en utilisant l’analyse discriminante linéaire (Linear Discriminant Analysis). Les ROI sont ensuite classifiées comme normales ou anormales en utilisant un classifieur SVM. Finalement, le pourcentage des ROI anormales est calculé pour chaque cadran (chaque poumon est divisé en deux parties appelées cadrans). Si ce pourcentage est supérieur à 34%, le cadran donné est alors considéré comme touché. Et si au moins un cadran du poumon gauche et un cadran du poumon droit sont touchés, alors la radiographie pulmonaire est considérée comme un cas de SDRA. Le SADC proposé a été évalué en utilisant une base de radiographies pulmonaires diagnostiquées avec consensus entre plusieurs experts et des mesures de performance telles que la sensibilité et la spécificité ont été calculées. Le système automatisé développé pour le diagnostic du SDRA a permis d’obtenir une bonne sensibilité et une bonne spécificité (sensibilité = 90.6% et spécificité = 86.5%). La deuxième partie de cette thèse présente une étude sur la variabilité inter-observateurs pour le diagnostic du SDRA à partir de radiographies pulmonaires en utilisant notre système, soit individuellement, soit comme deuxième avis. Cette étude a été réalisée en calculant le coefficient Kappa, d’abord entre les experts, ensuite en utilisant le système d’analyse développé. Notre système d’analyse automatique a permis d’améliorer le coefficient Kappa et d’obtenir une bonne concordance de diagnostic en l’utilisant individuellement (Kappa = 0.77) ainsi qu’une meilleure concordance ou une concordance presque parfaite de diagnostic en l’utilisant comme deuxième avis (Kappa = 0.79-0.86). La troisième partie de cette thèse est consacrée à une analyse des besoins pour un SADC déployable en clinique. Dans cette étude, nous avons remarqué que peu de SADC pour l’interprétation de radiographies pulmonaires ont été commercialisés. Aussi, nous avons montré que plusieurs facteurs doivent être considérés pour développer un SADC en soins intensifs. Ces facteurs incluent : la segmentation interactive pour l’extraction des régions d’intérêt (ROI) afin d’améliorer la performance; le choix des caractéristiques devrait être basé sur les différents aspects qui caractérisent l’apparence de la pathologie sur les radiographies pulmonaires et devraient être combinées pour atteindre une meilleure performance; et la construction de la base de données pour la validation du système joue un rôle très important dans la performance de tout SADC. Ce dernier facteur implique que la base des radiographies pulmonaires doit être construite avec précaution en considérant les facteurs suivants: le nombre de radiographies normales et anormales à utiliser ainsi que la représentativité de la diversité des anomalies; la méthodologie à utiliser pour élaborer l’interprétation des radiographies pulmonaires; et la qualité des images à utiliser. Finalement, la création de bases de radiographies pulmonaires publiques permettrait de comparer différents SADC et de choisir celui ayant la meilleure performance, et par conséquent celui qui doit être testé en premier en clinique. En conclusion, ce projet propose un SADC pour le diagnostic précoce du SDRA à partir de radiographies pulmonaires. Son évaluation a permis de confirmer qu’il peut être utilisé par les médecins pour fournir un deuxième avis afin d’élaborer un diagnostic plus précis. En perspective, pour utiliser notre système tout au long du traitement d’un patient atteint du SDRA, une fusion multimodale d’images (RX/ CT/ TIE) permettrait de visualiser à la fois l’information fonctionnelle et l’information morphologique, ainsi que de connaître l’état actuel du patient. Ceci donnerait lieu à un suivi clinique plus efficace au chevet du patient, entre autres en choisissant les paramètres optimaux pour la ventilation mécanique.----------ABSTRACT Acute Respiratory Distress Syndrome (ARDS) is a lung disease which represents the most severe form of acute respiratory failure. It consists of an acute inflammation of the lungs and manifests as bilateral opacities in chest radiographs. The diagnosis of this disease is done using the chest X-ray and hypoxemia criteria. However, interpretation of chest X-ray by medical experts suffers from high inter-observer variability, which can lead to a delayed diagnosis. This is problematic because any delay in diagnosing ARDS makes its treatment less effective and may, therefore, burden the patient’s prognosis. Hence, there is a clear clinical motivation to develop a computer-aided diagnosis (CAD) system to help the doctor establish an early chest X-ray diagnosis of the disease. CAD systems using X-rays for automatic diagnosis of diseases have become very important tools. They consist in automatically analyzing radiographs to identify abnormalities and providing a second diagnostic opinion to physicians. Even though several CAD systems have already been developed, there is currently no such system for the diagnosis of ARDS. The main difficulty is due to the superposition of bone structures such as the rib cage, whose radiopacity makes their appearance very similar to that of diffuse opacities associated with ARDS in chest radiographs. A preliminary segmentation of the whole ribs is thereby required in order to exclude them from the analysis and to focus on studying only the diffuse opacities linked with ARDS. To validate a CAD system for diagnosing ARDS, the creation of a database of chest X-rays diagnosed accurately is also essential. The first part of this thesis proposes a novel CAD system for the diagnosis of ARDS from chest radiographs. As there is currently no dedicated system for this disease, it was necessary to build it de novo. The CAD system we developed consists in analyzing a chest radiograph by first subtracting the whole ribs (anterior and posterior) from the image, and subsequently extracting intercostal patches and analyzing these regions of interest only, which are made up of lung tissues. Statistical and spectral features are extracted from each patch. A feature transformation method is then applied using Linear Discriminant Analysis (LDA). The patches are then classified as either normal or abnormal using an SVM classifier. Finally, the rate of abnormal patches is calculated for each quadrant (each lung is divided into two parts called quadrants). If this rate is greater than 34%, the given quadrant is then considered as affected. And if at least one quadrant of the left lung and one of the right lung are affected, then the chest radiograph is considered as an ARDS case. The proposed CAD system was evaluated using a database of chest radiographs diagnosed with consensus among several experts, and performance measurements such as sensitivity and specificity were calculated. The automated system developed for diagnosing ARDS achieved a sensitivity and specificity that are both good (sensitivity = 90.6% and specificity = 86.5%). The second part of this thesis presents a study of the inter-observer variability for the diagnosis of ARDS from chest radiographs using our system either by itself or as providing a second opinion. This study was carried out by calculating the Kappa coefficient, first between the medical experts, then by using the proposed CAD system. Our automatic analysis system improved the Kappa coefficient and showed a good diagnostic agreement when used individually (Kappa = 0.77) and a better diagnostic agreement or an almost perfect agreement diagnosis using it to give a second opinion (kappa = 0.79-0.86). The third part of this thesis is devoted to a requirements analysis for a CAD system to be used in the clinical setting. In this study, we noticed that only a few CAD systems for chest X-ray interpretation are commercially available. Thus, we showed that several factors must be considered when developing a CAD system for use in intensive care. These factors include: interactive segmentation for extracting regions of interest (ROI) to improve performance; the choice of features should be based on the different aspects that characterize the appearance of the pathology in chest X-rays and should be combined to achieve better performance; and the construction of a validation database, which plays a very important role in the performance of any CAD system. The latter implies that the database must be carefully constructed by considering the following factors: the number of normal and abnormal chest X-rays to be used and the representativeness of the diversity of abnormalities, the methodology used to interpret the chest X-rays, and the quality of the images to use. Finally, the creation of public databases of pulmonary radiographs would make it easier to compare different CAD systems and to choose the one that performs best and therefore the one to be tested first in the clinical setting. In conclusion, this project proposes a CAD system for the early diagnosis of ARDS from chest X-rays. Its evaluation allowed us to confirm that it can be used by doctors to provide a second opinion with the aim of elaborating a more accurate diagnosis. In future work, to utilize our system throughout the treatment of an ARDS patient, a multimodal image fusion approach (RX / CT / EIT) would allow the visualization of both functional and morphological information, as well as knowing the patient's current condition. This would give rise to more efficient monitoring at the patient’s bedside, in particular by choosing the optimal settings for mechanical ventilation

Imaging Lung Disease in Systemic Sclerosis

Interstitial lung disease and pulmonary hypertension (PH) are the most common cardiopulmonary findings in patients with systemic sclerosis (SSc). About two thirds of patients suffering from SSc develop scleroderma interstitial lung disease. PH is present in about 20% of SSc patients and is typically associated with severe lung disease, although it may be an isolated manifestation of SSc. High-resolution CT scanning is a key method for evaluating chest involvement. There are four roles of imaging in scleroderma interstitial lung disease: 1) detection of lung involvement, 2) identification of patients likely to respond to treatment, 3) assessment of treatment efficacy, and 4) exclusion of other significant diseases to include PH and cardiac and esophageal abnormalities

Texture Analysis and Machine Learning to Predict Pulmonary Ventilation from Thoracic Computed Tomography

Chronic obstructive pulmonary disease (COPD) leads to persistent airflow limitation, causing a large burden to patients and the health care system. Thoracic CT provides an opportunity to observe the structural pathophysiology of COPD, whereas hyperpolarized gas MRI provides images of the consequential ventilation heterogeneity. However, hyperpolarized gas MRI is currently limited to research centres, due to the high cost of gas and polarization equipment. Therefore, I developed a pipeline using texture analysis and machine learning methods to create predicted ventilation maps based on non-contrast enhanced, single-volume thoracic CT. In a COPD cohort, predicted ventilation maps were qualitatively and quantitatively related to ground-truth MRI ventilation, and both maps were related to important patient lung function and quality-of-life measures. This study is the first to demonstrate the feasibility of predicting hyperpolarized MRI-based ventilation from single-volume, breath-hold thoracic CT, which has potential to translate pulmonary ventilation information to widely available thoracic CT imaging