Liver CT enhancement using Fractional Differentiation and Integration

In this paper, a digital image filter is proposed to enhance the Liver CT image for improving the classification of tumors area in an infected Liver. The enhancement process is based on improving the main features within the image by utilizing the Fractional Differential and Integral in the wavelet sub-bands of an image. After enhancement, different features were extracted such as GLCM, GRLM, and LBP, among others. Then, the areas/cells are classified into tumor or non-tumor, using different models of classifiers to compare our proposed model with the original image and various established filters. Each image is divided into 15x15 non-overlapping blocks, to extract the desired features. The SVM, Random Forest, J48 and Simple Cart were trained on a supplied dataset, different from the test dataset. Finally, the block cells are identified whether they are classified as tumor or not. Our approach is validated on a group of patients’ CT liver tumor datasets. The experiment results demonstrated the efficiency of enhancement in the proposed technique

Automatic Esophageal Abnormality Detection and Classification

Esophageal cancer is counted as one of the deadliest cancers worldwide ranking the sixth among all types of cancers. Early esophageal cancer typically causes no symp- toms and mainly arises from overlooked/untreated premalignant abnormalities in the esophagus tube. Endoscopy is the main tool used for the detection of abnormalities, and the cell deformation stage is confirmed by taking biopsy samples. The process of detection and classification is considered challenging for several reasons such as; different types of abnormalities (including early cancer stages) can be located ran- domly throughout the esophagus tube, abnormal regions can have various sizes and appearances which makes it difficult to capture, and failure in discriminating between the columnar mucosa from the metaplastic epithelium. Although many studies have been conducted, it remains a challenging task and improving the accuracy of auto- matically classifying and detecting different esophageal abnormalities is an ongoing field. This thesis aims to develop novel automated methods for the detection and classification of the abnormal esophageal regions (precancerous and cancerous) from endoscopic images and videos. In this thesis, firstly, the abnormality stage of the esophageal cell deformation is clas- sified from confocal laser endomicroscopy (CLE) images. The CLE is an endoscopic tool that provides a digital pathology view of the esophagus cells. The classifica- tion is achieved by enhancing the internal features of the CLE image, using a novel enhancement filter that utilizes fractional integration and differentiation. Different imaging features including, Multi-Scale pyramid rotation LBP (MP-RLBP), gray level co-occurrence matrices (GLCM), fractal analysis, fuzzy LBP and maximally stable extremal regions (MSER), are calculated from the enhanced image to assure a robust classification result. The support vector machine (SVM) and random forest (RF) classifiers are employed to classify each image into its pathology stage. Secondly, we propose an automatic detection method to locate abnormality regions from high definition white light (HD-WLE) endoscopic images. We first investigate the performance of different deep learning detection methods on our dataset. Then we propose an approach that combines hand-designed Gabor features with extracted convolutional neural network features that are used by the Faster R-CNN to detect abnormal regions. Moreover, to further improve the detection performance, we pro- pose a novel two-input network named GFD-Faster RCNN. The proposed method generates a Gabor fractal image from the original endoscopic image using Gabor filters. Then features are learned separately from the endoscopic image and the gen- erated Gabor fractal image using the densely connected convolutional network to detect abnormal esophageal regions. Thirdly, we present a novel model to detect the abnormal regions from endoscopic videos. We design a 3D Sequential DenseConvLstm network to extract spatiotem- poral features from the input videos that are utilized by a region proposal network and ROI pooling layer to detect abnormality regions in each frame throughout the video. Additionally, we suggest an FS-CRF post-processing method that incorpor- ates the Conditional Random Field (CRF) on a frame-based level to recover missed abnormal regions in neighborhood frames within the same clip. The methods are evaluated on four datasets: (1) CLE dataset used for the classific- ation model, (2) Publicly available dataset named Kvasir, (3) MICCAI’15 Endovis challenge dataset, Both datasets (2) and (3) are used for the evaluation of detection model from endoscopic images. Finally, (4) Gastrointestinal Atlas dataset used for the evaluation of the video detection model. The experimental results demonstrate promising results of the different models and have outperformed the state-of-the-art methods

Robust Fuzzy Observer-based Fault Detection for Nonlinear Systems

With the increasing demand for higher performance, safety and reliability of dynamic systems, fault diagnosis has received more and more attention. The observer-based strategy is one of the active research fields, which is widely used to construct model-based fault detection systems for technical processes which can be well modelled as linear time invariant systems. Fault diagnosis for nonlinear system is an active area of research. Observer-based fault detection includes two stages, residual generation and residual evaluation. The residual generation problems and residual evaluation problems for systems with only deterministic disturbances or stochastic disturbances have been widely separately studied. Recently some efforts have been made in the integrated design of fault detection systems for systems with deterministic disturbances and stochastic disturbances. Recently, successful results of applying Takagi-Sugeno (TS) fuzzy model-based technique to solve fault detection and isolation problems met in the nonlinear system have been achieved. With TS model, a nonlinear dynamic system can be linearised around a number of operating points. Each linear model represents the local system behaviour around the operating point. The global system behaviour is described by a fuzzy IF-THEN rules which represent local linear input/output relations of the nonlinear system. Applying the Takagi-Sugeno fuzzy model based technique to solve fault detection and isolation problems in the nonlinear systems is active area of research. The main contribution of this thesis is the design of robust fault detection systems based on Takagi-Sugeno fuzzy filters. There are a number of schemes to achieve robustness problem in fault detection. One of them is to introduce a performance index. It is function of unknown input signal and fault signal. For continuous time system, first, robust fault detection system will be designed for nonlinear system with only deterministic disturbance as unknown inputs. Second, robust fault detection system will be designed for nonlinear system with deterministic disturbance as unknown inputs and parameter uncertainties. Finally, robust fault detection system will be designed for nonlinear system with deterministic disturbance as unknown inputs and stated delay. Sufficient conditions for solving robustness problem are given in terms of Linear Matrix Inequalities (LMIs). For discrete time system, kalman filter design for nonlinear system is diffcult. In this thesis new fault detection approach will be presented for nonlinear system with only stochastic disturbance. Fault Detection (FD) system for each local subsystem is design by solving the corresponding Discrete-time Algebraic Riccati Equation (DARE). Optimisation algorithm based on minimizing the residual covariance matrix is used to obtain a robust FD system optimised for global system behaviour. The optimisation algorithm is established in terms of LMIs. The different robust fault diagnosis system are developed to detect sensor faults of vehicle lateral dynamic control systems

Automatic grade classification of Barretts Esophagus through feature enhancement

Barretts Esophagus (BE) is a precancerous condition that affects the esophagus tube and has the risk of develop- ing esophageal adenocarcinoma. BE is the process of developing metaplastic intestinal epithelium and replacing the normal cells in the esophageal area. The detection of BE is considered difficult due to its appearance and properties. The diagnosis is usually done through both endoscopy and biopsy. Recently, Computer Aided Diag- nosis systems have been developed to support physicians opinion when facing difficulty in detection/classification in different types of diseases. In this paper, an automatic classification of Barretts Esophagus condition is intro- duced. The presented method enhances the internal features of a Confocal Laser Endomicroscopy (CLE) image by utilizing a proposed enhancement filter. This filter depends on fractional differentiation and integration that improve the features in the discrete wavelet transform of an image. Later on, various features are extracted from each enhanced image on different levels for the multi-classification process. Our approach is validated on a dataset that consists of a group of 32 patients with 262 images with different histology grades. The experimental results demonstrated the efficiency of the proposed technique. Our method helps clinicians for more accurate classification. This potentially helps to reduce the need for biopsies needed for diagnosis, facilitate the regular monitoring of treatment/development of the patients case and can help train doctors with the new endoscopy technology. The accurate automatic classification is particularly important for the Intestinal Metaplasia (IM) type, which could turn into deadly cancerous. Hence, this work contributes to automatic classification that facilitates early intervention/treatment and decreasing biopsy samples needed

Learning spatiotemporal features for esophageal abnormality detection from endoscopic videos

Esophageal cancer is categorized as a type of disease with a high mortality rate. Early detection of esophageal abnormalities (i.e. precancerous and early can- cerous) can improve the survival rate of the patients. Re- cent deep learning-based methods for selected types of esophageal abnormality detection from endoscopic images have been proposed. However, no methods have been introduced in the literature to cover the detection from endoscopic videos, detection from challenging frames and detection of more than one esophageal abnormality type. In this paper, we present an efficient method to automat- ically detect different types of esophageal abnormalities from endoscopic videos. We propose a novel 3D Sequen- tial DenseConvLstm network that extracts spatiotemporal features from the input video. Our network incorporates 3D Convolutional Neural Network (3DCNN) and Convolu- tional Lstm (ConvLstm) to efficiently learn short and long term spatiotemporal features. The generated feature map is utilized by a region proposal network and ROI pooling layer to produce a bounding box that detects abnormal- ity regions in each frame throughout the video. Finally, we investigate a post-processing method named Frame Search Conditional Random Field (FS-CRF) that improves the overall performance of the model by recovering the missing regions in neighborhood frames within the same clip. We extensively validate our model on an endoscopic video dataset that includes a variety of esophageal ab- normalities. Our model achieved high performance using different evaluation metrics showing 93.7% recall, 92.7% precision, and 93.2% F-measure. Moreover, as no results have been reported in the literature for the esophageal abnormality detection from endoscopic videos, to validate the robustness of our model, we have tested the model on a publicly available colonoscopy video dataset, achieving the polyp detection performance in a recall of 81.18%, precision of 96.45% and F-measure 88.16%, compared to the state-of-the-art results of 78.84% recall, 90.51% preci- sion and 84.27% F-measure using the same dataset. This demonstrates that the proposed method can be adapted to different gastrointestinal endoscopic video applications with a promising performance

Liver tumor detection by classification through FD enhancement of CT image

In this paper, an approach for the liver tumor detection in computed tomography (CT) images is represented. The detection process is based on classifying the features of target liver cell to either tumor or non-tumor. Fractional differential (FD) is applied for enhancement of Liver CT images, with the aim of enhancing texture and edge features. Later on, a fusion method is applied to merge between the various enhanced images and produce a variety of feature improvement, which will increase the accuracy of classification. Each image is divided into NxN non-overlapping blocks, to extract the desired features. Support vector machines (SVM) classifier is trained later on a supplied dataset different from the tested one. Finally, the block cells are identified whether they are classified as tumor or not. Our approach is validated on a group of patients’ CT liver tumor datasets. The experiment results demonstrated the efficiency of detection in the proposed technique

Esophageal Abnormality Detection Using DenseNet Based Faster R-CNN With Gabor Features

Early detection of esophageal abnormalities can help in preventing the progression of the disease into later stages. During esophagus examination, abnormalities are often overlooked due to the irregular shape, variable size, and the complex surrounding area which requires a significant effort and experience. In this paper, a novel deep learning model which is based on faster region-based convolutional neural network (Faster R-CNN) is presented to automatically detect abnormalities in the esophagus from endoscopic images. The proposed detection system is based on a combination of Gabor handcrafted features with the CNN features. The densely connected convolutional networks (DenseNets) architecture is embraced to extract the CNN features providing a strengthened feature propagation between the layers and alleviate the vanishing gradient problem. To address the challenges of detecting abnormal complex regions, we propose fusing extracted Gabor features with the CNN features through concatenation to enhance texture details in the detection stage. Our newly designed architecture is validated on two datasets (Kvasir and MICCAI 2015). Regarding the Kvasir, the results show an outstanding performance with a recall of 90.2% and a precision of 92.1% with a mean of average precision (mAP) of 75.9%. While for the MICCAI 2015 dataset, the model is able to surpass the state-of-the-art performance with 95% recall and 91% precision with mAP value of 84%. The experimental results demonstrate that the system is able to detect abnormalities in endoscopic images with good performance without any human intervention

In-vivo Barrett’s esophagus digital pathology stage classification through feature enhancement of confocal laser endomicroscopy

Barrett’s esophagus (BE) is a premalignant condition that has an increased risk to turn into esophageal adenocarcinoma. Classification and staging of the different changes (BE in particular) in the esophageal mucosa are challenging since they have a very similar appearance. Confocal laser endomicroscopy (CLE) is one of the newest endoscopy tools that is commonly used to identify the pathology type of the suspected area of the esophageal mucosa. However, it requires a well-trained physician to classify the image obtained from CLE. An automatic stage classification of esophageal mucosa is presented. The proposed model enhances the internal features of CLE images using an image filter that combines fractional integration with differentiation. Various features are then extracted on a multiscale level, to classify the mucosal tissue into one of its four types: normal squamous (NS), gastric metaplasia (GM), intestinal metaplasia (IM or BE), and neoplasia. These sets of features are used to train two conventional classifiers: support vector machine (SVM) and random forest. The proposed method was evaluated on a dataset of 96 patients with 557 images of different histopathology types. The SVM classifier achieved the best performance with 96.05% accuracy based on a leave-one-patient-out cross-validation. Additionally, the dataset was divided into 60% training and 40% testing; the model achieved an accuracy of 93.72% for the testing data using the SVM. The presented model showed superior performance when compared with four state-of-the-art methods. Accurate classification is essential for the intestinal metaplasia grade, which most likely develops into esophageal cancer. Not only does our method come to the aid of physicians for more accurate diagnosis by acting as a second opinion, but it also acts as a training method for junior physicians who need practice in using CLE. Consequently, this work contributes to an automatic classification that facilitates early intervention and decreases samples of required biopsy

Predicting Mid-term All-cause Mortality in Patients Undergoing Elective Endovascular Repair of a Descending Thoracic Aortic Aneurysm.

INTRODUCTION: All-cause mortality in patients after repair of aortic aneurysms of the descending thoracic aorta thoracic endovascular aortic repair (TEVAR) is relatively high at mid-term follow-up. The aim of this study was to derive and validate a system that could predict all-cause mortality after TEVAR to aid with patient selection. METHODS: The MOTHER database contained 625 patients that underwent elective surgery for descending thoracic aortic aneurysms. Univariate analysis identified preoperative factors associated with mid-term all-cause mortality, and a Cox proportional hazards model was developed. The model was internally validated using Kaplan-Meier comparison of observed vs predicted mortality. External validation was performed using a data set from the University of Florida College of Medicine. RESULTS: There were 625 patients that underwent TEVAR for descending thoracic aortic aneurysm in the MOTHER database and 231 in the University of Florida College of Medicine validation set. The mid-term mortality rate at 6 years of follow-up was 34.4% and 34%, respectively. The all-cause mortality risk score was calculated using 0.0398 × (age) + 0.516 × (renal insufficiency) + 0.46 × (previous cerebrovascular disease) + 0.352 × (prior tobacco use) + 0.376 × (number of devices >2) + 0.016 × (maximum aneurysm diameter). Using this score, low-, medium-, and high-risk groups were defined, with predicted survival at 5 years of 80%, 60%, and 40%. Patients at high risk of mid-term all-cause death were identified in the validation cohort using the prediction rule. CONCLUSIONS: Identifying patients with a limited life expectancy after TEVAR is possible using a preoperative risk-stratification system. This information can be used to inform decision making regarding when and whether to proceed with TEVAR