Journal Articles
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Item A Review on Carotid Ultrasound Atherosclerotic Tissue Characterization and Stroke Risk Stratification in Machine Learning Framework(Current Medicine Group LLC 1 info@phl.cursci.com, 2015) Sharma, A.M.; Gupta, A.; Kumar, P.K.; Rajan, J.; Saba, L.; Nobutaka, I.; Laird, J.R.; Nicolades, A.; Suri, J.S.Cardiovascular diseases (including stroke and heart attack) are identified as the leading cause of death in today’s world. However, very little is understood about the arterial mechanics of plaque buildup, arterial fibrous cap rupture, and the role of abnormalities of the vasa vasorum. Recently, ultrasonic echogenicity characteristics and morphological characterization of carotid plaque types have been shown to have clinical utility in classification of stroke risks. Furthermore, this characterization supports aggressive and intensive medical therapy as well as procedures, including endarterectomy and stenting. This is the first state-of-the-art review to provide a comprehensive understanding of the field of ultrasonic vascular morphology tissue characterization. This paper presents fundamental and advanced ultrasonic tissue characterization and feature extraction methods for analyzing plaque. Additionally, the paper shows how the risk stratification is achieved using machine learning paradigms. More advanced methods need to be developed which can segment the carotid artery walls into multiple regions such as the bulb region and areas both proximal and distal to the bulb. Furthermore, multimodality imaging is needed for validation of such advanced methods for stroke and cardiovascular risk stratification. © 2015, Springer Science+Business Media New York.Item A Review of Automatic Methods Based on Image Processing Techniques for Tuberculosis Detection from Microscopic Sputum Smear Images(Springer New York LLC barbara.b.bertram@gsk.com, 2016) Panicker, R.O.; Soman, B.; Saini, G.; Rajan, J.Tuberculosis (TB) is an infectious disease caused by the bacteria Mycobacterium tuberculosis. It primarily affects the lungs, but it can also affect other parts of the body. TB remains one of the leading causes of death in developing countries, and its recent resurgences in both developed and developing countries warrant global attention. The number of deaths due to TB is very high (as per the WHO report, 1.5 million died in 2013), although most are preventable if diagnosed early and treated. There are many tools for TB detection, but the most widely used one is sputum smear microscopy. It is done manually and is often time consuming; a laboratory technician is expected to spend at least 15 min per slide, limiting the number of slides that can be screened. Many countries, including India, have a dearth of properly trained technicians, and they often fail to detect TB cases due to the stress of a heavy workload. Automatic methods are generally considered as a solution to this problem. Attempts have been made to develop automatic approaches to identify TB bacteria from microscopic sputum smear images. In this paper, we provide a review of automatic methods based on image processing techniques published between 1998 and 2014. The review shows that the accuracy of algorithms for the automatic detection of TB increased significantly over the years and gladly acknowledges that commercial products based on published works also started appearing in the market. This review could be useful to researchers and practitioners working in the field of TB automation, providing a comprehensive and accessible overview of methods of this field of research. © 2015, Springer Science+Business Media New York.Item State-of-the-art review on automated lumen and adventitial border delineation and its measurements in carotid ultrasound(Elsevier Ireland Ltd, 2018) Kumar, P.K.; Araki, T.; Rajan, J.; Laird, J.R.; Nicolaïdes, A.; Suri, J.S.Background and objective: Accurate, reliable, efficient, and precise measurements of the lumen geometry of the common carotid artery (CCA) are important for (a) managing the progression/regression of atherosclerotic build-up and (b) the risk of stroke. The image-based degree of stenosis in the carotid artery and the plaque burden can be predicted using the automated carotid lumen diameter (LD)/inter-adventitial diameter (IAD) measurements from B-mode ultrasound images. The objective of this review is to present the state-of-the-art methods and systems for the measurement of LD/IAD in CCA based on automated or semi-automated strategies. Further, the performance of these systems is compared based on various metrics for its measurements. Methods: The automated algorithms proposed for the segmentation of carotid lumen are broadly classified into two different categories as: region-based and boundary-based. These techniques are discussed in detail specifying their pros and cons. Further, we discuss the challenges encountered in the segmentation process along with its quantitative assessment. Lastly, we present stenosis quantification and risk stratification strategies. Results: Even though, we have found more boundary-based approaches compared to region-based approaches in the literature, however, the region-based strategy yield more satisfactory performance. Novel risk stratification strategies are presented. On a patient database containing 203 patients, 9 patients are identified as high risk patients, whereas 27 patients are identified as medium risk patients. Conclusions: We have presented different techniques for the lumen segmentation of the common carotid artery from B-mode ultrasound images and measurement of lumen diameter and inter-adventitial diameter. We believe that the issue regarding boundary-based techniques can be compensated by taking regional statistics embedded with boundary-based information. © 2018 Elsevier B.V.Item Computational methods for automated mitosis detection in histopathology images: A review(Elsevier Sp. z o.o., 2021) Mathew, T.; Kini, J.R.; Rajan, J.Mitosis detection is an important step in pathology procedures in the context of cancer diagnosis and prognosis. Prevalent process for this task is by manually observing Hematoxylin and Eosin (H & E) stained histopathology sections on glass slides through a microscope by trained pathologists. This conventional approach is tedious, error-prone, and has shown high inter-observer variability. With the advancement of computational technologies, automating mitosis detection by the use of image processing algorithms has attracted significant research interest. In the past decade, several methods appeared in the literature, addressing this problem and they have shown encouraging incremental progress towards a clinically usable solution. Mitosis count is an important parameter in grading of breast cancer and glioma, unlike other cancer types. Driven by the availability of multiple public datasets and open contests, most of the methods in literature address mitosis detection in breast cancer images. This paper is a comprehensive review of the methods published in the area of automated mitotic cell detection in H & E stained histopathology images of breast cancer in the last 10 years. We also discuss the current trends and future prospects of this clinically relevant task, augmenting humanity's fight against cancer. © 2020 Nalecz Institute of Biocybernetics and Biomedical Engineering of the Polish Academy of SciencesItem Machine learning techniques for periodontitis and dental caries detection: A narrative review(Elsevier Ireland Ltd, 2023) Radha, R.C.; Raghavendra, B.S.; Subhash, B.V.; Rajan, J.; Narasimhadhan, A.V.Objectives: In recent years, periodontitis, and dental caries have become common in humans and need to be diagnosed in the early stage to prevent severe complications and tooth loss. These dental issues are diagnosed by visual inspection, measuring pocket probing depth, and radiographs findings from experienced dentists. Though a glut of machine learning (ML) algorithms has been proposed for the automated detection of periodontitis, and dental caries, determining which ML techniques are suitable for clinical practice remains under debate. This review aims to identify the research challenges by analyzing the limitations of current methods and how to address these to obtain robust systems suitable for clinical use or point-of-care testing. Methods: An extensive search of the literature published from 2015 to 2022 written in English, related to the subject of study was sought by searching the electronic databases: PubMed, Institute of Electrical and Electronics Engineers (IEEE) Xplore, and ScienceDirect. Results: The initial electronic search yielded 1743 titles, and 55 studies were eventually included based on the selection criteria adopted in this review. Studies selected were on ML applications for the automatic detection of periodontitis and dental caries and related dental issues: Apical lessons, Periodontal bone loss, and Vertical root fracture. Conclusion: While most of the ML-based studies use radiograph images for the detection of periodontitis and dental caries, few pieces of the literature revealed that good diagnostic accuracy could be achieved by training the ML model even with mobile photos representing the images of dental issues. Nowadays smartphones are used in every sector for different applications. Training the ML model with as many images of dental issues captured by the smartphone can achieve good accuracy, reduce the cost of clinical diagnosis, and provide user interaction. © 2023 Elsevier B.V.Item A new non-local maximum likelihood estimation method for Rician noise reduction in magnetic resonance images using the Kolmogorov-Smirnov test(Elsevier, 2014) Rajan, J.; den Dekker, A.J.; Sijbers, J.Denoising algorithms play an important role in the enhancement of magnetic resonance (MR) images. Effective denoising is vital for proper analysis and accurate quantitative measurements from MR images. Maximum Likelihood (ML) estimation methods were proved to be very effective in denoising MR images. Among the ML based methods, the recently proposed non-local maximum likelihood (NLML) approach gained much attention. In the NLML method, the samples for the ML estimation of the true underlying intensity are selected in a non-local way based on the intensity similarity of the pixel neighborhoods. This similarity is generally measured using the Euclidean distance. A drawback of this approach is the usage of a fixed sample size for the ML estimation resulting in over- or under-smoothing. In this work, we propose an NLML estimation method for denoising MR images in which the samples are selected in an adaptive and statistically supported way using the Kolmogorov-Smirnov (KS) similarity test. The method has been tested both on simulated and real data, showing its effectiveness. © 2013 Elsevier B.V.Item Nonlocal linear minimum mean square error methods for denoising MRI(Elsevier Ltd, 2015) Sudeep, P.V.; Ponnusamy, P.; Kesavadas, C.; Rajan, J.The presence of noise results in quality deterioration of magnetic resonance (MR) images and thus limits the visual inspection and influence the quantitative measurements from the data. In this work, an efficient two stage linear minimum mean square error (LMMSE) method is proposed for the enhancement of magnitude MR images in which data in the presence of noise follows a Rician distribution. The conventional Rician LMMSE estimator determines a closed-form analytical solution to the aforementioned inverse problem. Even-though computationally efficient, this approach fails to take advantage of data redundancy in the 3D MR data and hence leads to a suboptimal filtering performance. Motivated by this observation, we put forward the concept of nonlocal implementation with LMMSE estimation method. To select appropriate samples for the nonlocal version of the LMMSE estimation, the similarity weights are computed using Euclidean distance between either the gray level values in the spatial domain or the coefficients in the transformed domain. Assuming that the signal dependent component of the noise is optimally suppressed by this filtering and the rest is a white and uncorrelated noise with the image, we adopt a second stage LMMSE filtering in the principal component analysis (PCA) domain to further enhance the image and the noise variance is adaptively adjusted. Experiments on both simulated and real data show that the proposed filters have excellent filtering performance over other state-of-the-art methods. © 2015 Elsevier Ltd. All rights reserved.Item Magnetic resonance image denoising using nonlocal maximum likelihood paradigm in DCT-framework(John Wiley and Sons Inc, 2015) Kumar, P.K.; Darshan, P.; Kumar, S.; Ravindra, R.; Rajan, J.; Saba, L.; Suri, J.S.The data acquired by magnetic resonance (MR) imaging system are inherently degraded by noise that has its origin in the thermal Brownian motion of electrons. Denoising can enhance the quality (by improving the SNR) of the acquired MR image, which is important for both visual analysis and other post processing operations. Recent works on maximum likelihood (ML) based denoising shows that ML methods are very effective in denoising MR images and has an edge over the other state-of-the-art methods for MRI denoising. Among the ML based approaches, the Nonlocal maximum likelihood (NLML) method is commonly used. In the conventional NLML method, the samples for the ML estimation of the unknown true pixel are chosen in a nonlocal fashion based on the intensity similarity of the pixel neighborhoods. Euclidean distance is generally used to measure this similarity. It has been recently shown that computing similarity measure is more robust in discrete cosine transform (DCT) subspace, compared with Euclidean image subspace. Motivated by this observation, we integrated DCT into NLML to produce an improved MRI filtration process. Other than improving the SNR, the time complexity of the conventional NLML can also be significantly reduced through the proposed approach. On synthetic MR brain image, an average improvement of 5% in PSNR and 86%reduction in execution time is achieved with a search window size of 91 × 91 after incorporating the improvements in the existing NLML method. On an experimental kiwi fruit image an improvement of 10% in PSNR is achieved. We did experiments on both simulated and real data sets to validate and to demonstrate the effectiveness of the proposed method. © 2015 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 25, 256-264, 2015 © 2015 Wiley Periodicals, Inc.Item Iterative bilateral filter for Rician noise reduction in MR images(Springer London, 2015) Riji, R.; Rajan, J.; Sijbers, J.; Nair, M.S.Noise removal from magnetic resonance images is important for further processing and visual analysis. Bilateral filter is known for its effectiveness in edge-preserved image denoising. In this paper, an iterative bilateral filter for filtering the Rician noise in the magnitude magnetic resonance images is proposed. The proposed iterative bilateral filter improves the denoising efficiency, preserves the fine structures and also reduces the bias due to Rician noise. The visual and diagnostic quality of the image is well preserved. The quantitative analysis based on the standard metrics like peak signal-to-noise ratio and mean structural similarity index matrix shows that the proposed method performs better than the other recently proposed denoising methods for MRI. © 2014, Springer-Verlag London.Item Enhancement and bias removal of optical coherence tomography images: An iterative approach with adaptive bilateral filtering(Elsevier Ltd, 2016) Sudeep, P.V.; Issac Niwas, S.; Ponnusamy, P.; Rajan, J.; Xiaojun, Y.; Wang, X.; Luo, Y.; Liu, L.Optical coherence tomography (OCT) has continually evolved and expanded as one of the most valuable routine tests in ophthalmology. However, noise (speckle) in the acquired images causes quality degradation of OCT images and makes it difficult to analyze the acquired images. In this paper, an iterative approach based on bilateral filtering is proposed for speckle reduction in multiframe OCT data. Gamma noise model is assumed for the observed OCT image. First, the adaptive version of the conventional bilateral filter is applied to enhance the multiframe OCT data and then the bias due to noise is reduced from each of the filtered frames. These unbiased filtered frames are then refined using an iterative approach. Finally, these refined frames are averaged to produce the denoised OCT image. Experimental results on phantom images and real OCT retinal images demonstrate the effectiveness of the proposed filter. © 2016 Elsevier Ltd.