165 research outputs found

    Deep Learning based HEp-2 Image Classification: A Comprehensive Review

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    Classification of HEp-2 cell patterns plays a significant role in the indirect immunofluorescence test for identifying autoimmune diseases in the human body. Many automatic HEp-2 cell classification methods have been proposed in recent years, amongst which deep learning based methods have shown impressive performance. This paper provides a comprehensive review of the existing deep learning based HEp-2 cell image classification methods. These methods perform HEp-2 image classification at two levels, namely, cell-level and specimen-level. Both levels are covered in this review. At each level, the methods are organized with a deep network usage based taxonomy. The core idea, notable achievements, and key strengths and weaknesses of each method are critically analyzed. Furthermore, a concise review of the existing HEp-2 datasets that are commonly used in the literature is given. The paper ends with a discussion on novel opportunities and future research directions in this field. It is hoped that this paper would provide readers with a thorough reference of this novel, challenging, and thriving field.Comment: Published in Medical Image Analysi

    Interpretation of immunofluorescence slides by deep learning techniques: anti-nuclear antibodies case study

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    Nowadays, diseases are increasing in numbers and severity by the hour. Immunity diseases, affecting 8\% of the world population in 2017 according to the World Health Organization (WHO), is a field in medicine worth attention due to the high rate of disease occurrence classified under this category. This work presents an up-to-date review of state-of-the-art immune diseases healthcare solutions. We focus on tackling the issue with modern solutions such as Deep Learning to detect anomalies in the early stages hence providing health practitioners with efficient tools. We rely on advanced deep learning techniques such as Convolutional Neural Networks (CNN) to fulfill our objective of providing an efficient tool while providing a proficient analysis of this solution. The proposed solution was tested and evaluated by the immunology department in the Principal Military Hospital of Instruction of Tunis, which considered it a very helpful tool

    Local and deep texture features for classification of natural and biomedical images

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    Developing efficient feature descriptors is very important in many computer vision applications including biomedical image analysis. In the past two decades and before the popularity of deep learning approaches in image classification, texture features proved to be very effective to capture the gradient variation in the image. Following the success of the Local Binary Pattern (LBP) descriptor, many variations of this descriptor were introduced to further improve the ability of obtaining good classification results. However, the problem of image classification gets more complicated when the number of images increases as well as the number of classes. In this case, more robust approaches must be used to address this problem. In this thesis, we address the problem of analyzing biomedical images by using a combination of local and deep features. First, we propose a novel descriptor that is based on the motif Peano scan concept called Joint Motif Labels (JML). After that, we combine the features extracted from the JML descriptor with two other descriptors called Rotation Invariant Co-occurrence among Local Binary Patterns (RIC-LBP) and Joint Adaptive Medina Binary Patterns (JAMBP). In addition, we construct another descriptor called Motif Patterns encoded by RIC-LBP and use it in our classification framework. We enrich the performance of our framework by combining these local descriptors with features extracted from a pre-trained deep network called VGG-19. Hence, the 4096 features of the Fully Connected 'fc7' layer are extracted and combined with the proposed local descriptors. Finally, we show that Random Forests (RF) classifier can be used to obtain superior performance in the field of biomedical image analysis. Testing was performed on two standard biomedical datasets and another three standard texture datasets. Results show that our framework can beat state-of-the-art accuracy on the biomedical image analysis and the combination of local features produce promising results on the standard texture datasets.Includes bibliographical reference

    Deep CNN for IIF Images Classification in Autoimmune Diagnostics

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    The diagnosis and monitoring of autoimmune diseases are very important problem in medicine. The most used test for this purpose is the antinuclear antibody (ANA) test. An indirect immunofluorescence (IIF) test performed by Human Epithelial type 2 (HEp-2) cells as substrate antigen is the most common methods to determine ANA. In this paper we present an automatic HEp-2 specimen system based on a convolutional neural network method able to classify IIF images. The system consists of a module for features extraction based on a pre-trained AlexNet network and a classification phase for the cell-pattern association using six support vector machines and a k-nearest neighbors classifier. The classification at the image-level was obtained by analyzing the pattern prevalence at cell-level. The layers of the pre-trained network and various system parameters were evaluated in order to optimize the process. This system has been developed and tested on the HEp-2 images indirect immunofluorescence images analysis (I3A) public database. To test the generalisation performance of the method, the leave-one-specimen-out procedure was used in this work. The performance analysis showed an accuracy of 96.4% and a mean class accuracy equal to 93.8%. The results have been evaluated comparing them with some of the most representative works using the same database

    Deep Active Learning for Automatic Mitotic Cell Detection on HEp-2 Specimen Medical Images

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    Identifying Human Epithelial Type 2 (HEp-2) mitotic cells is a crucial procedure in anti-nuclear antibodies (ANAs) testing, which is the standard protocol for detecting connective tissue diseases (CTD). Due to the low throughput and labor-subjectivity of the ANAs' manual screening test, there is a need to develop a reliable HEp-2 computer-aided diagnosis (CAD) system. The automatic detection of mitotic cells from the microscopic HEp-2 specimen images is an essential step to support the diagnosis process and enhance the throughput of this test. This work proposes a deep active learning (DAL) approach to overcoming the cell labeling challenge. Moreover, deep learning detectors are tailored to automatically identify the mitotic cells directly in the entire microscopic HEp-2 specimen images, avoiding the segmentation step. The proposed framework is validated using the I3A Task-2 dataset over 5-fold cross-validation trials. Using the YOLO predictor, promising mitotic cell prediction results are achieved with an average of 90.011% recall, 88.307% precision, and 81.531% mAP. Whereas, average scores of 86.986% recall, 85.282% precision, and 78.506% mAP are obtained using the Faster R-CNN predictor. Employing the DAL method over four labeling rounds effectively enhances the accuracy of the data annotation, and hence, improves the prediction performance. The proposed framework could be practically applicable to support medical personnel in making rapid and accurate decisions about the mitotic cells' existence
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