An automated pattern recognition system for classifying indirect immunofluorescence images for HEp-2 cells and specimens

AbstractImmunofluorescence antinuclear antibody tests are important for diagnosis and management of autoimmune conditions; a key step that would benefit from reliable automation is the recognition of subcellular patterns suggestive of different diseases. We present a system to recognize such patterns, at cellular and specimen levels, in images of HEp-2 cells. Ensembles of SVMs were trained to classify cells into six classes based on sparse encoding of texture features with cell pyramids, capturing spatial, multi-scale structure. A similar approach was used to classify specimens into seven classes. Software implementations were submitted to an international contest hosted by ICPR 2014 (Performance Evaluation of Indirect Immunofluorescence Image Analysis Systems). Mean class accuracies obtained on heldout test data sets were 87.1% and 88.5% for cell and specimen classification respectively. These were the highest achieved in the competition, suggesting that our methods are state-of-the-art. We provide detailed descriptions and extensive experiments with various features and encoding methods

Automatic Classification of Human Epithelial Type 2 Cell Indirect Immunofluorescence Images using Cell Pyramid Matching

This paper describes a novel system for automatic classification of images obtained from Anti-Nuclear Antibody (ANA) pathology tests on Human Epithelial type 2 (HEp-2) cells using the Indirect Immunofluorescence (IIF) protocol. The IIF protocol on HEp-2 cells has been the hallmark method to identify the presence of ANAs, due to its high sensitivity and the large range of antigens that can be detected. However, it suffers from numerous shortcomings, such as being subjective as well as time and labour intensive. Computer Aided Diagnostic (CAD) systems have been developed to address these problems, which automatically classify a HEp-2 cell image into one of its known patterns (eg. speckled, homogeneous). Most of the existing CAD systems use handpicked features to represent a HEp-2 cell image, which may only work in limited scenarios. We propose a novel automatic cell image classification method termed Cell Pyramid Matching (CPM), which is comprised of regional histograms of visual words coupled with the Multiple Kernel Learning framework. We present a study of several variations of generating histograms and show the efficacy of the system on two publicly available datasets: the ICPR HEp-2 cell classification contest dataset and the SNPHEp-2 dataset.Comment: arXiv admin note: substantial text overlap with arXiv:1304.126

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

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 Learning based HEp-2 Image Classification: A Comprehensive Review

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

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

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