1
|
Guo Y, Hormel TT, Gao M, You Q, Wang J, Flaxel CJ, Bailey ST, Hwang TS, Jia Y. Multi-Plexus Nonperfusion Area Segmentation in Widefield OCT Angiography Using a Deep Convolutional Neural Network. Transl Vis Sci Technol 2024; 13:15. [PMID: 39023443 PMCID: PMC11262538 DOI: 10.1167/tvst.13.7.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024] Open
Abstract
Purpose To train and validate a convolutional neural network to segment nonperfusion areas (NPAs) in multiple retinal vascular plexuses on widefield optical coherence tomography angiography (OCTA). Methods This cross-sectional study included 202 participants with a full range of diabetic retinopathy (DR) severities (diabetes mellitus without retinopathy, mild to moderate non-proliferative DR, severe non-proliferative DR, and proliferative DR) and 39 healthy participants. Consecutive 6 × 6-mm OCTA scans at the central macula, optic disc, and temporal region in one eye from 202 participants in a clinical DR study were acquired with a 70-kHz OCT commercial system (RTVue-XR). Widefield OCTA en face images were generated by montaging the scans from these three regions. A projection-resolved OCTA algorithm was applied to remove projection artifacts at the voxel scale. A deep convolutional neural network with a parallel U-Net module was designed to detect NPAs and distinguish signal reduction artifacts from flow deficits in the superficial vascular complex (SVC), intermediate capillary plexus (ICP), and deep capillary plexus (DCP). Expert graders manually labeled NPAs and signal reduction artifacts for the ground truth. Sixfold cross-validation was used to evaluate the proposed algorithm on the entire dataset. Results The proposed algorithm showed high agreement with the manually delineated ground truth for NPA detection in three retinal vascular plexuses on widefield OCTA (mean ± SD F-score: SVC, 0.84 ± 0.05; ICP, 0.87 ± 0.04; DCP, 0.83 ± 0.07). The extrafoveal avascular area in the DCP showed the best sensitivity for differentiating eyes with diabetes but no retinopathy (77%) from healthy controls and for differentiating DR by severity: DR versus no DR, 77%; referable DR (rDR) versus non-referable DR (nrDR), 79%; vision-threatening DR (vtDR) versus non-vision-threatening DR (nvtDR), 60%. The DCP also showed the best area under the receiver operating characteristic curve for distinguishing diabetes from healthy controls (96%), DR versus no DR (95%), and rDR versus nrDR (96%). The three-plexus-combined OCTA achieved the best result in differentiating vtDR and nvtDR (81.0%). Conclusions A deep learning network can accurately segment NPAs in individual retinal vascular plexuses and improve DR diagnostic accuracy. Translational Relevance Using a deep learning method to segment nonperfusion areas in widefield OCTA can potentially improve the diagnostic accuracy of diabetic retinopathy by OCT/OCTA systems.
Collapse
Affiliation(s)
- Yukun Guo
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Tristan T. Hormel
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Min Gao
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Qisheng You
- Kresge Eye Institute, Wayne State University, Detroit, MI, USA
| | - Jie Wang
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | | | - Steven T. Bailey
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Thomas S. Hwang
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Yali Jia
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
2
|
Hormel TT, Liang GB, Wei X, Guo Y, Gao M, Wang J, Huang D, Bailey ST, Hwang TS, Jia Y. Visualizing features with wide-field volumetric OCT angiography. OPTICS EXPRESS 2024; 32:10329-10347. [PMID: 38571248 PMCID: PMC11018334 DOI: 10.1364/oe.510640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/16/2024] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
Optical coherence tomography (OCT) and its extension OCT angiography (OCTA) have become essential clinical imaging modalities due to their ability to provide depth-resolved angiographic and tissue structural information non-invasively and at high resolution. Within a field of view, the anatomic detail available is sufficient to identify several structural and vascular pathologies that are clinically relevant for multiple prevalent blinding diseases, including age-related macular degeneration (AMD), diabetic retinopathy (DR), and vein occlusions. The main limitation in contemporary OCT devices is that this field of view is limited due to a fundamental trade-off between system resolution/sensitivity, sampling density, and imaging window dimensions. Here, we describe a swept-source OCT device that can capture up to a 12 × 23-mm field of view in a single shot and show that it can identify conventional pathologic features such as non-perfusion areas outside of conventional fields of view. We also show that our approach maintains sensitivity sufficient to visualize novel features, including choriocapillaris morphology beneath the macula and macrophage-like cells at the inner limiting membrane, both of which may have implications for disease.
Collapse
Affiliation(s)
- Tristan T. Hormel
- Casey Eye Institutue, Oregon Health and Science University, Portland, OR 97239, USA
| | - Guangru B. Liang
- Casey Eye Institutue, Oregon Health and Science University, Portland, OR 97239, USA
| | - Xiang Wei
- Casey Eye Institutue, Oregon Health and Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA
| | - Yukun Guo
- Casey Eye Institutue, Oregon Health and Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA
| | - Min Gao
- Casey Eye Institutue, Oregon Health and Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA
| | - Jie Wang
- Casey Eye Institutue, Oregon Health and Science University, Portland, OR 97239, USA
| | - David Huang
- Casey Eye Institutue, Oregon Health and Science University, Portland, OR 97239, USA
| | - Steven T. Bailey
- Casey Eye Institutue, Oregon Health and Science University, Portland, OR 97239, USA
| | - Thomas S. Hwang
- Casey Eye Institutue, Oregon Health and Science University, Portland, OR 97239, USA
| | - Yali Jia
- Casey Eye Institutue, Oregon Health and Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, USA
| |
Collapse
|
3
|
Qian B, Chen H, Wang X, Guan Z, Li T, Jin Y, Wu Y, Wen Y, Che H, Kwon G, Kim J, Choi S, Shin S, Krause F, Unterdechler M, Hou J, Feng R, Li Y, El Habib Daho M, Yang D, Wu Q, Zhang P, Yang X, Cai Y, Tan GSW, Cheung CY, Jia W, Li H, Tham YC, Wong TY, Sheng B. DRAC 2022: A public benchmark for diabetic retinopathy analysis on ultra-wide optical coherence tomography angiography images. PATTERNS (NEW YORK, N.Y.) 2024; 5:100929. [PMID: 38487802 PMCID: PMC10935505 DOI: 10.1016/j.patter.2024.100929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/09/2023] [Accepted: 01/15/2024] [Indexed: 03/17/2024]
Abstract
We described a challenge named "DRAC - Diabetic Retinopathy Analysis Challenge" in conjunction with the 25th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022). Within this challenge, we provided the DRAC datset, an ultra-wide optical coherence tomography angiography (UW-OCTA) dataset (1,103 images), addressing three primary clinical tasks: diabetic retinopathy (DR) lesion segmentation, image quality assessment, and DR grading. The scientific community responded positively to the challenge, with 11, 12, and 13 teams submitting different solutions for these three tasks, respectively. This paper presents a concise summary and analysis of the top-performing solutions and results across all challenge tasks. These solutions could provide practical guidance for developing accurate classification and segmentation models for image quality assessment and DR diagnosis using UW-OCTA images, potentially improving the diagnostic capabilities of healthcare professionals. The dataset has been released to support the development of computer-aided diagnostic systems for DR evaluation.
Collapse
Affiliation(s)
- Bo Qian
- Shanghai Belt and Road International Joint Laboratory for Intelligent Prevention and Treatment of Metabolic Disorders, Department of Computer Science and Engineering, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Department of Endocrinology and Metabolism, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai 200240, China
- MOE Key Laboratory of AI, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Chen
- Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | - Xiangning Wang
- Shanghai Belt and Road International Joint Laboratory for Intelligent Prevention and Treatment of Metabolic Disorders, Department of Computer Science and Engineering, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Department of Endocrinology and Metabolism, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai 200240, China
- Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Zhouyu Guan
- Shanghai Belt and Road International Joint Laboratory for Intelligent Prevention and Treatment of Metabolic Disorders, Department of Computer Science and Engineering, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Department of Endocrinology and Metabolism, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai 200240, China
| | - Tingyao Li
- Shanghai Belt and Road International Joint Laboratory for Intelligent Prevention and Treatment of Metabolic Disorders, Department of Computer Science and Engineering, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Department of Endocrinology and Metabolism, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai 200240, China
- MOE Key Laboratory of AI, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yixiao Jin
- Tsinghua Medicine, Tsinghua University, Beijing 100084, China
| | - Yilan Wu
- Tsinghua Medicine, Tsinghua University, Beijing 100084, China
| | - Yang Wen
- School of Electronic and Information Engineering, Shenzhen University, Shenzhen 518060, China
| | - Haoxuan Che
- Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Hong Kong 999077, China
| | | | | | - Sungjin Choi
- AI/DX Convergence Business Group, KT, Seongnam 13606, Korea
| | - Seoyoung Shin
- AI/DX Convergence Business Group, KT, Seongnam 13606, Korea
| | - Felix Krause
- Johannes Kepler University Linz, Linz 4040, Austria
| | | | - Junlin Hou
- School of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, China
| | - Rui Feng
- School of Computer Science, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University, Shanghai 200433, China
- Academy for Engineering and Technology, Fudan University, Shanghai 200433, China
| | - Yihao Li
- LaTIM UMR 1101, INSERM, 29609 Brest, France
- University of Western Brittany, 29238 Brest, France
| | - Mostafa El Habib Daho
- LaTIM UMR 1101, INSERM, 29609 Brest, France
- University of Western Brittany, 29238 Brest, France
| | - Dawei Yang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Qiang Wu
- Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Ping Zhang
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaokang Yang
- MOE Key Laboratory of AI, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yiyu Cai
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Gavin Siew Wei Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
| | - Carol Y. Cheung
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Weiping Jia
- Shanghai Belt and Road International Joint Laboratory for Intelligent Prevention and Treatment of Metabolic Disorders, Department of Computer Science and Engineering, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Department of Endocrinology and Metabolism, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai 200240, China
| | - Huating Li
- Shanghai Belt and Road International Joint Laboratory for Intelligent Prevention and Treatment of Metabolic Disorders, Department of Computer Science and Engineering, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Department of Endocrinology and Metabolism, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai 200240, China
| | - Yih Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
- Centre for Innovation and Precision Eye Health; and Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Tien Yin Wong
- Tsinghua Medicine, Tsinghua University, Beijing 100084, China
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore 168751, Singapore
- School of Clinical Medicine, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Bin Sheng
- Shanghai Belt and Road International Joint Laboratory for Intelligent Prevention and Treatment of Metabolic Disorders, Department of Computer Science and Engineering, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Department of Endocrinology and Metabolism, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Diabetes Institute, Shanghai Clinical Center for Diabetes, Shanghai 200240, China
- MOE Key Laboratory of AI, School of Electronic, Information, and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
4
|
Hormel TT, Jia Y. OCT angiography and its retinal biomarkers [Invited]. BIOMEDICAL OPTICS EXPRESS 2023; 14:4542-4566. [PMID: 37791289 PMCID: PMC10545210 DOI: 10.1364/boe.495627] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 10/05/2023]
Abstract
Optical coherence tomography angiography (OCTA) is a high-resolution, depth-resolved imaging modality with important applications in ophthalmic practice. An extension of structural OCT, OCTA enables non-invasive, high-contrast imaging of retinal and choroidal vasculature that are amenable to quantification. As such, OCTA offers the capability to identify and characterize biomarkers important for clinical practice and therapeutic research. Here, we review new methods for analyzing biomarkers and discuss new insights provided by OCTA.
Collapse
Affiliation(s)
- Tristan T. Hormel
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Yali Jia
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| |
Collapse
|
5
|
Deep Learning in Optical Coherence Tomography Angiography: Current Progress, Challenges, and Future Directions. Diagnostics (Basel) 2023; 13:diagnostics13020326. [PMID: 36673135 PMCID: PMC9857993 DOI: 10.3390/diagnostics13020326] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Optical coherence tomography angiography (OCT-A) provides depth-resolved visualization of the retinal microvasculature without intravenous dye injection. It facilitates investigations of various retinal vascular diseases and glaucoma by assessment of qualitative and quantitative microvascular changes in the different retinal layers and radial peripapillary layer non-invasively, individually, and efficiently. Deep learning (DL), a subset of artificial intelligence (AI) based on deep neural networks, has been applied in OCT-A image analysis in recent years and achieved good performance for different tasks, such as image quality control, segmentation, and classification. DL technologies have further facilitated the potential implementation of OCT-A in eye clinics in an automated and efficient manner and enhanced its clinical values for detecting and evaluating various vascular retinopathies. Nevertheless, the deployment of this combination in real-world clinics is still in the "proof-of-concept" stage due to several limitations, such as small training sample size, lack of standardized data preprocessing, insufficient testing in external datasets, and absence of standardized results interpretation. In this review, we introduce the existing applications of DL in OCT-A, summarize the potential challenges of the clinical deployment, and discuss future research directions.
Collapse
|
6
|
Ma D, Pasquale LR, Girard MJA, Leung CKS, Jia Y, Sarunic MV, Sappington RM, Chan KC. Reverse translation of artificial intelligence in glaucoma: Connecting basic science with clinical applications. FRONTIERS IN OPHTHALMOLOGY 2023; 2:1057896. [PMID: 36866233 PMCID: PMC9976697 DOI: 10.3389/fopht.2022.1057896] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/05/2022] [Indexed: 04/16/2023]
Abstract
Artificial intelligence (AI) has been approved for biomedical research in diverse areas from bedside clinical studies to benchtop basic scientific research. For ophthalmic research, in particular glaucoma, AI applications are rapidly growing for potential clinical translation given the vast data available and the introduction of federated learning. Conversely, AI for basic science remains limited despite its useful power in providing mechanistic insight. In this perspective, we discuss recent progress, opportunities, and challenges in the application of AI in glaucoma for scientific discoveries. Specifically, we focus on the research paradigm of reverse translation, in which clinical data are first used for patient-centered hypothesis generation followed by transitioning into basic science studies for hypothesis validation. We elaborate on several distinctive areas of research opportunities for reverse translation of AI in glaucoma including disease risk and progression prediction, pathology characterization, and sub-phenotype identification. We conclude with current challenges and future opportunities for AI research in basic science for glaucoma such as inter-species diversity, AI model generalizability and explainability, as well as AI applications using advanced ocular imaging and genomic data.
Collapse
Affiliation(s)
- Da Ma
- School of Medicine, Wake Forest University, Winston-Salem, NC, United States
- Atrium Health Wake Forest Baptist Medical Center, Winston-Salem, NC, United States
- School of Engineering Science, Simon Fraser University, Burnaby, BC, Canada
| | - Louis R. Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Michaël J. A. Girard
- Ophthalmic Engineering & Innovation Laboratory (OEIL), Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Institute for Molecular and Clinical Ophthalmology, Basel, Switzerland
| | | | - Yali Jia
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, United States
| | - Marinko V. Sarunic
- School of Engineering Science, Simon Fraser University, Burnaby, BC, Canada
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Rebecca M. Sappington
- School of Medicine, Wake Forest University, Winston-Salem, NC, United States
- Atrium Health Wake Forest Baptist Medical Center, Winston-Salem, NC, United States
| | - Kevin C. Chan
- Departments of Ophthalmology and Radiology, Neuroscience Institute, NYU Grossman School of Medicine, NYU Langone Health, New York University, New York, NY, United States
- Department of Biomedical Engineering, Tandon School of Engineering, New York University, New York, NY, United States
| |
Collapse
|
7
|
Nadeem MW, Goh HG, Hussain M, Liew SY, Andonovic I, Khan MA. Deep Learning for Diabetic Retinopathy Analysis: A Review, Research Challenges, and Future Directions. SENSORS (BASEL, SWITZERLAND) 2022; 22:s22186780. [PMID: 36146130 PMCID: PMC9505428 DOI: 10.3390/s22186780] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 05/12/2023]
Abstract
Deep learning (DL) enables the creation of computational models comprising multiple processing layers that learn data representations at multiple levels of abstraction. In the recent past, the use of deep learning has been proliferating, yielding promising results in applications across a growing number of fields, most notably in image processing, medical image analysis, data analysis, and bioinformatics. DL algorithms have also had a significant positive impact through yielding improvements in screening, recognition, segmentation, prediction, and classification applications across different domains of healthcare, such as those concerning the abdomen, cardiac, pathology, and retina. Given the extensive body of recent scientific contributions in this discipline, a comprehensive review of deep learning developments in the domain of diabetic retinopathy (DR) analysis, viz., screening, segmentation, prediction, classification, and validation, is presented here. A critical analysis of the relevant reported techniques is carried out, and the associated advantages and limitations highlighted, culminating in the identification of research gaps and future challenges that help to inform the research community to develop more efficient, robust, and accurate DL models for the various challenges in the monitoring and diagnosis of DR.
Collapse
Affiliation(s)
- Muhammad Waqas Nadeem
- Faculty of Information and Communication Technology (FICT), Universiti Tunku Abdul Rahman (UTAR), Kampar 31900, Malaysia
| | - Hock Guan Goh
- Faculty of Information and Communication Technology (FICT), Universiti Tunku Abdul Rahman (UTAR), Kampar 31900, Malaysia
- Correspondence: (H.G.G.); (I.A.)
| | - Muzammil Hussain
- Department of Computer Science, School of Systems and Technology, University of Management and Technology, Lahore 54000, Pakistan
| | - Soung-Yue Liew
- Faculty of Information and Communication Technology (FICT), Universiti Tunku Abdul Rahman (UTAR), Kampar 31900, Malaysia
| | - Ivan Andonovic
- Department of Electronic and Electrical Engineering, Royal College Building, University of Strathclyde, 204 George St., Glasgow G1 1XW, UK
- Correspondence: (H.G.G.); (I.A.)
| | - Muhammad Adnan Khan
- Pattern Recognition and Machine Learning Lab, Department of Software, Gachon University, Seongnam 13557, Korea
- Faculty of Computing, Riphah School of Computing and Innovation, Riphah International University, Lahore Campus, Lahore 54000, Pakistan
| |
Collapse
|
8
|
Gao M, Guo Y, Hormel TT, Tsuboi K, Pacheco G, Poole D, Bailey ST, Flaxel CJ, Huang D, Hwang TS, Jia Y. A Deep Learning Network for Classifying Arteries and Veins in Montaged Widefield OCT Angiograms. OPHTHALMOLOGY SCIENCE 2022; 2:100149. [PMID: 36278031 PMCID: PMC9562370 DOI: 10.1016/j.xops.2022.100149] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/16/2022] [Accepted: 03/28/2022] [Indexed: 01/18/2023]
|
9
|
Ahmed S, Le D, Son T, Adejumo T, Ma G, Yao X. ADC-Net: An Open-Source Deep Learning Network for Automated Dispersion Compensation in Optical Coherence Tomography. Front Med (Lausanne) 2022; 9:864879. [PMID: 35463032 PMCID: PMC9024062 DOI: 10.3389/fmed.2022.864879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/14/2022] [Indexed: 11/23/2022] Open
Abstract
Chromatic dispersion is a common problem to degrade the system resolution in optical coherence tomography (OCT). This study is to develop a deep learning network for automated dispersion compensation (ADC-Net) in OCT. The ADC-Net is based on a modified UNet architecture which employs an encoder-decoder pipeline. The input section encompasses partially compensated OCT B-scans with individual retinal layers optimized. Corresponding output is a fully compensated OCT B-scan with all retinal layers optimized. Two numeric parameters, i.e., peak signal to noise ratio (PSNR) and structural similarity index metric computed at multiple scales (MS-SSIM), were used for objective assessment of the ADC-Net performance and optimal values of 29.95 ± 2.52 dB and 0.97 ± 0.014 were obtained respectively. Comparative analysis of training models, including single, three, five, seven and nine input channels were implemented. The mode with five-input channels was observed to be optimal for ADC-Net training to achieve robust dispersion compensation in OCT.
Collapse
Affiliation(s)
- Shaiban Ahmed
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL, United States
| | - David Le
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL, United States
| | - Taeyoon Son
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL, United States
| | - Tobiloba Adejumo
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL, United States
| | - Guangying Ma
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL, United States
| | - Xincheng Yao
- Department of Biomedical Engineering, University of Illinois Chicago, Chicago, IL, United States
- Department of Ophthalmology and Visual Science, University of Illinois Chicago, Chicago, IL, United States
| |
Collapse
|
10
|
Gao M, Hormel TT, Wang J, Guo Y, Bailey ST, Hwang TS, Jia Y. An Open-Source Deep Learning Network for Reconstruction of High-Resolution OCT Angiograms of Retinal Intermediate and Deep Capillary Plexuses. Transl Vis Sci Technol 2021; 10:13. [PMID: 34757393 PMCID: PMC8590160 DOI: 10.1167/tvst.10.13.13] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/06/2021] [Indexed: 01/27/2023] Open
Abstract
Purpose We propose a deep learning-based image reconstruction algorithm to produce high-resolution optical coherence tomographic angiograms (OCTA) of the intermediate capillary plexus (ICP) and deep capillary plexus (DCP). Methods In this study, 6-mm × 6-mm macular scans with a 400 × 400 A-line sampling density and 3-mm × 3-mm scans with a 304 × 304 A-line sampling density were acquired on one or both eyes of 180 participants (including 230 eyes with diabetic retinopathy and 44 healthy controls) using a 70-kHz commercial OCT system (RTVue-XR; Optovue, Inc., Fremont, California, USA). Projection-resolved OCTA algorithm removed projection artifacts in voxel. ICP and DCP angiograms were generated by maximum projection of the OCTA signal within the respective plexus. We proposed a deep learning-based method, which receives inputs from registered 3-mm × 3-mm ICP and DCP angiograms with proper sampling density as the ground truth reference to reconstruct 6-mm × 6-mm high-resolution ICP and DCP en face OCTA. We applied the same network on 3-mm × 3-mm angiograms to enhance these images further. We evaluated the reconstructed 3-mm × 3-mm and 6-mm × 6-mm angiograms based on vascular connectivity, Weber contrast, false flow signal (flow signal erroneously generated from background), and the noise intensity in the foveal avascular zone. Results Compared to the originals, the Deep Capillary Angiogram Reconstruction Network (DCARnet)-enhanced 6-mm × 6-mm angiograms had significantly reduced noise intensity (ICP, 7.38 ± 25.22, P < 0.001; DCP, 11.20 ± 22.52, P < 0.001), improved vascular connectivity (ICP, 0.95 ± 0.01, P < 0.001; DCP, 0.96 ± 0.01, P < 0.001), and enhanced Weber contrast (ICP, 4.25 ± 0.10, P < 0.001; DCP, 3.84 ± 0.84, P < 0.001), without generating false flow signal when noise intensity lower than 650. The DCARnet-enhanced 3-mm × 3-mm angiograms also reduced noise, improved connectivity, and enhanced Weber contrast in 3-mm × 3-mm ICP and DCP angiograms from 101 eyes. In addition, DCARnet preserved the appearance of the dilated vessels in the reconstructed angiograms in diabetic eyes. Conclusions DCARnet can enhance 3-mm × 3-mm and 6-mm × 6-mm ICP and DCP angiogram image quality without introducing artifacts. Translational Relevance The enhanced 6-mm × 6-mm angiograms may be easier for clinicians to interpret qualitatively.
Collapse
Affiliation(s)
- Min Gao
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Tristan T. Hormel
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jie Wang
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Yukun Guo
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Steven T. Bailey
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Thomas S. Hwang
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Yali Jia
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
11
|
Yu TT, Ma D, Lo J, Ju MJ, Beg MF, Sarunic MV. Effect of optical coherence tomography and angiography sampling rate towards diabetic retinopathy severity classification. BIOMEDICAL OPTICS EXPRESS 2021; 12:6660-6673. [PMID: 34745763 PMCID: PMC8547994 DOI: 10.1364/boe.431992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Optical coherence tomography (OCT) and OCT angiography (OCT-A) may benefit the screening of diabetic retinopathy (DR). This study investigated the effect of laterally subsampling OCT/OCT-A en face scans by up to a factor of 8 when using deep neural networks for automated referable DR classification. There was no significant difference in the classification performance across all evaluation metrics when subsampling up to a factor of 3, and only minimal differences up to a factor of 8. Our findings suggest that OCT/OCT-A can reduce the number of samples (and hence the acquisition time) for a volume for a given field of view on the retina that is acquired for rDR classification.
Collapse
Affiliation(s)
- Timothy T. Yu
- Engineering Science, Simon Fraser University, Burnaby BC V5A1S6, Canada
| | - Da Ma
- Engineering Science, Simon Fraser University, Burnaby BC V5A1S6, Canada
| | - Julian Lo
- Engineering Science, Simon Fraser University, Burnaby BC V5A1S6, Canada
| | - Myeong Jin Ju
- Dept. of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, V5Z 3N9, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V5Z 3N9, Canada
| | - Mirza Faisal Beg
- Engineering Science, Simon Fraser University, Burnaby BC V5A1S6, Canada
| | | |
Collapse
|