Faculty Publications
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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.Item A benchmark study of automated intra-retinal cyst segmentation algorithms using optical coherence tomography B-scans(Elsevier Ireland Ltd, 2018) Girish, G.N.; Anima, V.A.; Kothari, A.R.; Sudeep, P.V.; Roychowdhury, S.; Rajan, J.(Background and objectives) Retinal cysts are formed by accumulation of fluid in the retina caused by leakages from inflammation or vitreous fractures. Analysis of the retinal cystic spaces holds significance in detection and treatment of several ocular diseases like age-related macular degeneration, diabetic macular edema etc. Thus, segmentation of intra-retinal cysts and quantification of cystic spaces are vital for retinal pathology and severity detection. In the recent years, automated segmentation of intra-retinal cysts using optical coherence tomography B-scans has gained significant importance in the field of retinal image analysis. The objective of this paper is to compare different intra-retinal cyst segmentation algorithms for comparative analysis and benchmarking purposes. (Methods) In this work, we employ a modular approach for standardizing the different segmentation algorithms. Further, we analyze the variations in automated cyst segmentation performances and method scalability across image acquisition systems by using the publicly available cyst segmentation challenge dataset (OPTIMA cyst segmentation challenge). (Results) Several key automated methods are comparatively analyzed using quantitative and qualitative experiments. Our analysis demonstrates the significance of variations in signal-to-noise ratio (SNR), retinal layer morphology and post-processing steps on the automated cyst segmentation processes. (Conclusion) This benchmarking study provides insights towards the scalability of automated processes across vendor-specific imaging modalities to provide guidance for retinal pathology diagnostics and treatment processes. © 2017 Elsevier B.V.Item Segmentation of intra-retinal cysts from optical coherence tomography images using a fully convolutional neural network model(Institute of Electrical and Electronics Engineers Inc., 2019) Girish, G.N.; Thakur, B.; Chowdhury, S.R.; Kothari, A.R.; Rajan, J.Optical coherence tomography (OCT) is an imaging modality that is used extensively for ophthalmic diagnosis, near-histological visualization, and quantification of retinal abnormalities such as cysts, exudates, retinal layer disorganization, etc. Intra-retinal cysts (IRCs) occur in several macular disorders such as, diabetic macular edema, retinal vascular disorders, age-related macular degeneration, and inflammatory disorders. Automated segmentation of IRCs poses challenges owing to variations in the acquisition system scan intensities, speckle noise, and imaging artifacts. Several segmentation methods have been proposed in the literature for IRC segmentation on vendor-specific OCT images that lack generalizability across imaging systems. In this paper, we propose a fully convolutional network (FCN) model for vendor-independent IRC segmentation. The proposed method counteracts image noise variabilities and trains FCN models on OCT sub-images from the OPTIMA cyst segmentation challenge dataset (with four different vendor-specific images, namely, Cirrus, Nidek, Spectralis, and Topcon). Further, optimal data augmentation and model hyperparametrization are shown to prevent over-fitting for IRC area segmentation. The proposed method is evaluated on the test dataset with a recall/precision rate of 0.66/0.79 across imaging vendors. The Dice correlation coefficient of the proposed method outperforms that of the published algorithms in the OPTIMA cyst segmentation challenge with a Dice rate of 0.71 across the vendors. © 2013 IEEE.Item Stack generalized deep ensemble learning for retinal layer segmentation in Optical Coherence Tomography images(Elsevier Sp. z o.o., 2020) Anoop, B.N.; Pavan, R.; Girish, G.N.; Kothari, A.R.; Rajan, J.Segmentation of retinal layers is a vital and important step in computerized processing and the study of retinal Optical Coherence Tomography (OCT) images. However, automatic segmentation of retinal layers is challenging due to the presence of noise, widely varying reflectivity of image components, variations in morphology and alignment of layers in the presence of retinal diseases. In this paper, we propose a Fully Convolutional Network (FCN) termed as DelNet based on a deep ensemble learning approach to selectively segment retinal layers from OCT scans. The proposed model is tested on a publicly available DUKE DME dataset. Comparative analysis with other state-of-the-art methods on a benchmark dataset shows that the performance of DelNet is superior to other methods. © 2020 Nalecz Institute of Biocybernetics and Biomedical Engineering of the Polish Academy of SciencesItem A cascaded convolutional neural network architecture for despeckling OCT images(Elsevier Ltd, 2021) Anoop, B.N.; Kalmady, K.S.; Udathu, A.; Siddharth, V.; Girish, G.N.; Kothari, A.R.; Rajan, J.Optical Coherence Tomography (OCT) is an imaging technique widely used for medical imaging. Noise in an OCT image generally degrades its quality, thereby obscuring clinical features and making the automated segmentation task suboptimal. Obtaining higher quality images requires sophisticated equipment and technology, available only in selected research settings, and is expensive to acquire. Developing effective denoising methods to improve the quality of the images acquired on systems currently in use has potential for vastly improving image quality and automated quantitative analysis. Noise characteristics in images acquired from machines of different makes and models may vary. Our experiments show that any single state-of-the-art method for noise reduction fails to perform equally well on images from various sources. Therefore, detailed analysis is required to determine the exact noise type in images acquired using different OCT machines. In this work we studied noise characteristics in the publicly available DUKE and OPTIMA datasets to build a more efficient model for noise reduction. These datasets have OCT images acquired using machines of different manufacturers. We further propose a patch-wise training methodology to build a system to effectively denoise OCT images. We have performed an extensive range of experiments to show that the proposed method performs superior to other state-of-the-art-methods. © 2021 Elsevier LtdItem Capsule Network–based architectures for the segmentation of sub-retinal serous fluid in optical coherence tomography images of central serous chorioretinopathy(Springer Science and Business Media Deutschland GmbH, 2021) Pawan, S.J.; Sankar, R.; Jain, A.; Jain, M.; Darshan, D.V.; Anoop, B.N.; Kothari, A.R.; Venkatesan, M.; Rajan, J.Central serous chorioretinopathy (CSCR) is a chorioretinal disorder of the eye characterized by serous detachment of the neurosensory retina at the posterior pole of the eye. CSCR results from the accumulation of subretinal fluid (SRF) due to idiopathic defects at the level of the retinal pigment epithelial (RPE) that allows serous fluid from the choriocapillaris to diffuse into the subretinal space between RPE and neurosensory retinal layers. This condition is presently investigated by clinicians using invasive angiography or non-invasive optical coherence tomography (OCT) imaging. OCT images provide a representation of the fluid underlying the retina, and in the absence of automated segmentation tools, currently only a qualitative assessment of the same is used to follow the progression of the disease. Automated segmentation of the SRF can prove to be extremely useful for the assessment of progression and for the timely management of CSCR. In this paper, we adopt an existing architecture called SegCaps, which is based on the recently introduced Capsule Networks concept, for the segmentation of SRF from CSCR OCT images. Furthermore, we propose an enhancement to SegCaps, which we have termed as DRIP-Caps, that utilizes the concepts of Dilation, Residual Connections, Inception Blocks, and Capsule Pooling to address the defined problem. The proposed model outperforms the benchmark UNet architecture while reducing the number of trainable parameters by 54.21%. Moreover, it reduces the computation complexity of SegCaps by reducing the number of trainable parameters by 37.85%, with competitive performance. The experiments demonstrate the generalizability of the proposed model, as evidenced by its remarkable performance even with a limited number of training samples. [Figure not available: see fulltext.]. © 2021, International Federation for Medical and Biological Engineering.