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

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

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

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

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

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

Trends in Computer-Aided Diagnosis Using Deep 2 Learning Techniques: A Review of Recent Studies on 3 Algorithm Development 4

With recent focus on deep neural network architectures for development of algorithms for computer-aided diagnosis (CAD), we provide a review of studies within the last 3 years (2015-2017) reported in selected top journals and conferences. 29 studies that met our inclusion criteria were reviewed to identify trends in this field and to inform future development. Studies have focused mostly on cancer-related diseases within internal medicine while diseases within gender-/age-focused fields like gynaecology/pediatrics have not received much focus. All reviewed studies employed image datasets, mostly sourced from publicly available databases (55.2%) and few based on data from human subjects (31%) and non-medical datasets (13.8%), while CNN architecture was employed in most (70%) of the studies. Confirmation of the effect of data manipulation on quality of output and adoption of multi-class rather than binary classification also require more focus. Future studies should leverage collaborations with medical experts to aid future with actual clinical testing with reporting based on some generally applicable index to enable comparison. Our next steps on plans for CAD development for osteoarthritis (OA), with plans to consider multi-class classification and comparison across deep learning approaches and unsupervised architectures were also highlighted

Studying the Applicability of Generative Adversarial Networks on HEp-2 Cell Image Augmentation

The Anti-Nuclear Antibodies (ANAs) testing is the primary serological diagnosis screening test for autoimmune diseases. ANAs testing is conducted mainly by the Indirect Immunofluorescence (IIF) on Human Epithelial cell-substrate (HEp-2) protocol. However, due to its high variability, human-subjectivity, and low throughput, there is an insistent need to develop an efficient Computer-Aided Diagnosis system (CADs) to automate this protocol. Many recently proposed Convolutional Neural Networks (CNNs) demonstrated promising results in HEp-2 cell image classification, which is the main task of the HE-p2 IIF protocol. However, the lack of large labeled datasets is still the main challenge in this field. This work provides a detailed study of the applicability of using generative adversarial networks (GANs) algorithms as an augmentation method. Different types of GANs were employed to synthesize HEp-2 cell images to address the data scarcity problem. For systematic comparison, empirical quantitative metrics were implemented to evaluate different GAN models' performance of learning the real data representations. The results of this work showed that though the high visual similarity with the real images, GANs' capacity to generate diverse data is still limited. This deficiency in the generated data diversity is found to be of a crucial impact when used as a standalone method for augmentation. However, combining limited-size GANs-generated data with classic augmentation improves the classification accuracy across different variants of CNNs. Our results demonstrated a competitive performance for the overall classification accuracy and the mean class accuracy of the HEp-2 cell image classification task