180 research outputs found
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
A Survey on Deep Learning in Medical Image Analysis
Deep learning algorithms, in particular convolutional networks, have rapidly
become a methodology of choice for analyzing medical images. This paper reviews
the major deep learning concepts pertinent to medical image analysis and
summarizes over 300 contributions to the field, most of which appeared in the
last year. We survey the use of deep learning for image classification, object
detection, segmentation, registration, and other tasks and provide concise
overviews of studies per application area. Open challenges and directions for
future research are discussed.Comment: Revised survey includes expanded discussion section and reworked
introductory section on common deep architectures. Added missed papers from
before Feb 1st 201
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
MITOTIC HEp-2 CELL RECOGNITION USING LOCAL BINARY PATTERN (LBP) AND k-NEAREST NEIGHBOUR (k-NN) CLASSIFIER
Immune system produces autoantibody either randomly or as a result of an unknown material in the body itself. A failure of the body’s own defences against diseases has result to the auto immune diseases. Auto immune diseases will start attacking its own cell as they unable to differentiate between the foreign material and its own cell. An antinuclear antibody (ANA) is required as an indicator of the autoimmune process. IIF is the recommended technique for ANA detection in patient serum. IIF slides are observed by specialists reporting for the fluorescence intensity, staining pattern and looking for the mitotic cells. Indeed, the presence of the mitotic cells significantly important due to several key factors, first to guarantee the correctness of the slide preparation process and reported the staining pattern. Therefore the ability to detect mitotic cells is acquired to develop Computer-Aided Diagnosis (CAD) system in IIF to support the specialists form image acquisition up to image classification. This work aims to highlight the features of mitotic cells and to develop recognition algorithm for mitotic cell by incorporated Local Binary Pattern (LBP) and k-Nearest Neighbour to classified unlabelled image. A completed modelling of the LBP operator is proposed which is represented by its centre pixel and a local sign-magnitude transform (LDSMT). k-NN classifies unlabelled images based on the utmost majority samples in the feature space. This work involves five stages; image acquisition, pre-processing, feature extraction, distance measurement and classification
Maximum margin learning of t-SPNs for cell classification with filtered input
An algorithm based on a deep probabilistic architecture referred to as a
tree-structured sum-product network (t-SPN) is considered for cell
classification. The t-SPN is constructed such that the unnormalized probability
is represented as conditional probabilities of a subset of most similar cell
classes. The constructed t-SPN architecture is learned by maximizing the
margin, which is the difference in the conditional probability between the true
and the most competitive false label. To enhance the generalization ability of
the architecture, L2-regularization (REG) is considered along with the maximum
margin (MM) criterion in the learning process. To highlight cell features, this
paper investigates the effectiveness of two generic high-pass filters: ideal
high-pass filtering and the Laplacian of Gaussian (LOG) filtering. On both
HEp-2 and Feulgen benchmark datasets, the t-SPN architecture learned based on
the max-margin criterion with regularization produced the highest accuracy rate
compared to other state-of-the-art algorithms that include convolutional neural
network (CNN) based algorithms. The ideal high-pass filter was more effective
on the HEp-2 dataset, which is based on immunofluorescence staining, while the
LOG was more effective on the Feulgen dataset, which is based on Feulgen
staining
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
Multi-dimensional local binary pattern texture descriptors and their application for medical image analysis
Texture can be broadly stated as spatial variation of image intensities. Texture analysis and classification is a well researched area for its importance to many computer vision applications. Consequently, much research has focussed on deriving powerful and efficient texture descriptors. Local binary patterns (LBP) and its variants are simple yet powerful texture descriptors. LBP features describe the texture neighbourhood of a pixel using simple comparison operators, and are often calculated based on varying neighbourhood radii to provide multi-resolution texture descriptions.
A comprehensive evaluation of different LBP variants on a common benchmark dataset is missing in the literature. This thesis presents the performance for different LBP variants on texture classification and retrieval tasks. The results show that multi-scale local binary pattern variance (LBPV) gives the best performance over eight benchmarked datasets. Furthermore, improvements to the Dominant LBP (D-LBP) by ranking dominant patterns over complete training set and Compound LBP (CM-LBP) by considering 16 bits binary codes are suggested which are shown to outperform their original counterparts.
The main contribution of the thesis is the introduction of multi-dimensional LBP features, which preserve the relationships between different scales by building a multi-dimensional histogram. The results on benchmarked classification and retrieval datasets clearly show that the multi-dimensional LBP (MD-LBP) improves the results compared to conventional multi-scale LBP. The same principle is applied to LBPV (MD-LBPV), again leading to improved performance. The proposed variants result in relatively large feature lengths which is addressed using three different feature length reduction techniques. Principle component analysis (PCA) is shown to give the best performance when the feature length is reduced to match that of conventional multi-scale LBP.
The proposed multi-dimensional LBP variants are applied for medical image analysis application. The first application is nailfold capillary (NC) image classification. Performance of MD-LBPV on NC images is highest, whereas for second application, HEp-2 cell classification, performance of MD-LBP is highest. It is observed that the proposed texture descriptors gives improved texture classification accuracy
- …