Faculty Publications
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Item Accurate lumen diameter measurement in curved vessels in carotid ultrasound: an iterative scale-space and spatial transformation approach(Springer Verlag service@springer.de, 2017) Krishna Kumar, P.; Araki, T.; Rajan, J.; Saba, L.; Lavra, F.; Ikeda, N.; Sharma, A.M.; Shafique, S.; Nicolaïdes, A.; Laird, J.R.; Gupta, A.; Suri, J.S.Monitoring of cerebrovascular diseases via carotid ultrasound has started to become a routine. The measurement of image-based lumen diameter (LD) or inter-adventitial diameter (IAD) is a promising approach for quantification of the degree of stenosis. The manual measurements of LD/IAD are not reliable, subjective and slow. The curvature associated with the vessels along with non-uniformity in the plaque growth poses further challenges. This study uses a novel and generalized approach for automated LD and IAD measurement based on a combination of spatial transformation and scale-space. In this iterative procedure, the scale-space is first used to get the lumen axis which is then used with spatial image transformation paradigm to get a transformed image. The scale-space is then reapplied to retrieve the lumen region and boundary in the transformed framework. Then, inverse transformation is applied to display the results in original image framework. Two hundred and two patients’ left and right common carotid artery (404 carotid images) B-mode ultrasound images were retrospectively analyzed. The validation of our algorithm has done against the two manual expert tracings. The coefficient of correlation between the two manual tracings for LD was 0.98 (p < 0.0001) and 0.99 (p < 0.0001), respectively. The precision of merit between the manual expert tracings and the automated system was 97.7 and 98.7%, respectively. The experimental analysis demonstrated superior performance of the proposed method over conventional approaches. Several statistical tests demonstrated the stability and reliability of the automated system. © 2016, International Federation for Medical and Biological Engineering.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 Automated Molecular Subtyping of Breast Carcinoma Using Deep Learning Techniques(Institute of Electrical and Electronics Engineers Inc., 2023) Niyas, S.; Bygari, R.; Naik, R.; Viswanath, B.; Ugwekar, D.; Mathew, T.; Kavya, J.; Kini, J.R.; Rajan, J.Objective: Molecular subtyping is an important procedure for prognosis and targeted therapy of breast carcinoma, the most common type of malignancy affecting women. Immunohistochemistry (IHC) analysis is the widely accepted method for molecular subtyping. It involves the assessment of the four molecular biomarkers namely estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and antigen Ki67 using appropriate antibody reagents. Conventionally, these biomarkers are assessed manually by a pathologist, who finally combines individual results to identify the molecular subtype. Molecular subtyping necessitates the status of all the four biomarkers together, and to the best of our knowledge, no such automated method exists. This paper proposes a novel deep learning framework for automatic molecular subtyping of breast cancer from IHC images. Methods and procedures: A modified LadderNet architecture is proposed to segment the immunopositive elements from ER, PR, HER2, and Ki67 biomarker slides. This architecture uses long skip connections to pass encoder feature space from different semantic levels to the decoder layers, allowing concurrent learning with multi-scale features. The entire architecture is an ensemble of multiple fully convolutional neural networks, and learning pathways are chosen adaptively based on input data. The segmentation stage is followed by a post-processing stage to quantify the extent of immunopositive elements to predict the final status for each biomarker. Results: The performance of segmentation models for each IHC biomarker is evaluated qualitatively and quantitatively. Furthermore, the biomarker prediction results are also evaluated. The results obtained by our method are highly in concordance with manual assessment by pathologists. Clinical impact: Accurate automated molecular subtyping can speed up this pathology procedure, reduce pathologists' workload and associated costs, and facilitate targeted treatment to obtain better outcomes. © 2013 IEEE.Item A deep learning based classifier framework for automated nuclear atypia scoring of breast carcinoma(Elsevier Ltd, 2023) Mathew, T.; Johnpaul, C.I.; Ajith, B.; Kini, J.R.; Rajan, J.Nuclear atypia scoring is an essential procedure in the grading of breast carcinoma. Manual procedure of nuclear atypia scoring is error-prone, and marked by pathologists’ disagreement and low reproducibility. Automated methods are actively attempted by researchers to solve the problems of manual scoring. In this work, we propose a novel deep learning-based framework for automated nuclear atypia scoring of breast cancer from histopathology slide images. The framework consists of three major phases namely preprocessing, deep learning, and postprocessing. The original three-class problem of atypia scoring at slide level is not suitable for direct application of deep learning algorithms. This is due to the large dimensions and structural complexity of slide images, compounded by the small sample size of the available dataset. Redesign of this problem into a six-class nuclei classification problem through a set of preprocessing steps to facilitate effective use of deep learning algorithms, and the flexibility of the proposed three-phase framework to use different algorithms in each phase are the novel aspects of the proposed work. We used the publicly available slide image dataset MITOS-ATYPIA that contains 600 slide images of high spatial dimension for the experiments. A five-fold cross validation with the train-test sample ratio 80:20 in each fold is used for the performance evaluation. The performance of the method based on this framework exceeds the state-of-the-art with the results 0.8766, 0.8760, and 0.8745 for the metrics precision, recall, and F1 score respectively. © 2023 Elsevier LtdItem Multilevel Multimodal Framework for Automatic Collateral Scoring in Brain Stroke(Institute of Electrical and Electronics Engineers Inc., 2024) Raj, R.; Dayananda, D.; Gupta, A.; Mathew, J.; Kannath, S.K.; Prakash, A.; Rajan, J.In patients with ischemic brain stroke, collateral circulation plays a crucial role in selecting patients suitable for endovascular therapy. The presence of well-developed collaterals improves the patient's chances of recovery. In clinical practice, the presence of collaterals is diagnosed on a Computed Tomography Angiography scan. The radiologist grades it on the basis of subjective visual assessment, which is prone to interobserver and intraobserver variability. Computer-based methods of collateral assessment face the challenge of non-uniform scan volume, leading to manual selection of slices, meaning that the most imperative slices have to be manually selected by the radiologist. This paper proposes a multilevel multimodal hierarchical framework for automated collateral scoring. Specifically, we propose deploying a Convolutional Neural Network for image selection based on the visibility of collaterals and a multimodal model for comparing the occluded and contralateral sides of the brain for collateral scoring. We also generate a patient-level prediction by integrating automated machine learning in the proposed framework. While the proposed multimodal predictor contributes to Artificial Intelligence, the proposed end-to-end framework is an application in engineering. The proposed framework has been trained and tested on 116 patients, with five-fold cross-validation, achieving an accuracy of 91.17% for multi-class collateral scores and 94.118% for binary class collateral scores. The proposed multimodal predictor achieved a weighted F1 score of 0.86 and 0.95 on multi-class and binary-class collateral scores, respectively. The proposed framework is fast, efficient, and scalable for real-world deployments. Automated evaluation of collaterals with attention maps for explainability would complement radiologists' efforts. Code for the proposed framework is available at: https://github.com/rishiraj-cs/collaterals_ML_MM. © 2013 IEEE.