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Woof W, de Guimarães TAC, Al-Khuzaei S, Varela MD, Sen S, Bagga P, Mendes B, Shah M, Burke P, Parry D, Lin S, Naik G, Ghoshal B, Liefers B, Fu DJ, Georgiou M, Nguyen Q, da Silva AS, Liu Y, Fujinami-Yokokawa Y, Kabiri N, Sumodhee D, Patel P, Furman J, Moghul I, Sallum J, De Silva SR, Lorenz B, Holz F, Fujinami K, Webster AR, Mahroo O, Downes SM, Madhusuhan S, Balaskas K, Michaelides M, Pontikos N. Quantification of Fundus Autofluorescence Features in a Molecularly Characterized Cohort of More Than 3000 Inherited Retinal Disease Patients from the United Kingdom. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.24.24304809. [PMID: 38585957 PMCID: PMC10996753 DOI: 10.1101/2024.03.24.24304809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Purpose To quantify relevant fundus autofluorescence (FAF) image features cross-sectionally and longitudinally in a large cohort of inherited retinal diseases (IRDs) patients. Design Retrospective study of imaging data (55-degree blue-FAF on Heidelberg Spectralis) from patients. Participants Patients with a clinical and molecularly confirmed diagnosis of IRD who have undergone FAF 55-degree imaging at Moorfields Eye Hospital (MEH) and the Royal Liverpool Hospital (RLH) between 2004 and 2019. Methods Five FAF features of interest were defined: vessels, optic disc, perimacular ring of increased signal (ring), relative hypo-autofluorescence (hypo-AF) and hyper-autofluorescence (hyper-AF). Features were manually annotated by six graders in a subset of patients based on a defined grading protocol to produce segmentation masks to train an AI model, AIRDetect, which was then applied to the entire imaging dataset. Main Outcome Measures Quantitative FAF imaging features including area in mm 2 and vessel metrics, were analysed cross-sectionally by gene and age, and longitudinally to determine rate of progression. AIRDetect feature segmentation and detection were validated with Dice score and precision/recall, respectively. Results A total of 45,749 FAF images from 3,606 IRD patients from MEH covering 170 genes were automatically segmented using AIRDetect. Model-grader Dice scores for disc, hypo-AF, hyper-AF, ring and vessels were respectively 0.86, 0.72, 0.69, 0.68 and 0.65. The five genes with the largest hypo-AF areas were CHM , ABCC6 , ABCA4 , RDH12 , and RPE65 , with mean per-patient areas of 41.5, 30.0, 21.9, 21.4, and 15.1 mm 2 . The five genes with the largest hyper-AF areas were BEST1 , CDH23 , RDH12 , MYO7A , and NR2E3 , with mean areas of 0.49, 0.45, 0.44, 0.39, and 0.34 mm 2 respectively. The five genes with largest ring areas were CDH23 , NR2E3 , CRX , EYS and MYO7A, with mean areas of 3.63, 3.32, 2.84, 2.39, and 2.16 mm 2 . Vessel density was found to be highest in EFEMP1 , BEST1 , TIMP3 , RS1 , and PRPH2 (10.6%, 10.3%, 9.8%, 9.7%, 8.9%) and was lower in Retinitis Pigmentosa (RP) and Leber Congenital Amaurosis genes. Longitudinal analysis of decreasing ring area in four RP genes ( RPGR, USH2A, RHO, EYS ) found EYS to be the fastest progressor at -0.18 mm 2 /year. Conclusions We have conducted the first large-scale cross-sectional and longitudinal quantitative analysis of FAF features across a diverse range of IRDs using a novel AI approach.
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Charng J, Escalona IAV, Turpin A, McKendrick AM, Mackey DA, Alonso-Caneiro D, Chen FK. Nonlinear Reduction in Hyperautofluorescent Ring Area in Retinitis Pigmentosa. Ophthalmol Retina 2024; 8:298-306. [PMID: 37743021 DOI: 10.1016/j.oret.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/27/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
PURPOSE To report baseline dimension of the autofluorescent (AF) ring in a large cohort of retinitis pigmentosa (RP) patients and to evaluate models of ring progression. DESIGN Cohort study. PARTICIPANTS Four hundred and forty-five eyes of 224 patients with clinical diagnosis of RP. METHODS Autofluorescent rings from near-infrared AF (NIRAF) and short-wavelength AF (SWAF) imaging modalities in RP eyes were segmented with ring area and horizontal extent extracted from each image for cross-sectional and longitudinal analyses. In longitudinal analysis, for each eye, ring area, horizontal extent, and natural logarithm of the ring area were assessed as the best dependent variable for linear regression by evaluating R2 values. Linear mixed-effects modeling was utilized to account for intereye correlation. MAIN OUTCOME MEASURES Autofluorescent ring size characteristics at baseline and ring progression rates. RESULTS A total of 439 eyes had SWAF imaging at baseline with the AF ring observed in 206 (46.9%) eyes. Mean (95% confidence interval) of ring area and horizontal extent were 7.85 (6.60 to 9.11) mm2 and 3.35 (3.10 to 3.60) mm, respectively. In NIRAF, the mean ring area and horizontal extent were 7.74 (6.60 to 8.89) mm2 and 3.26 (3.02 to 3.50) mm, respectively in 251 out of 432 eyes. Longitudinal analysis showed mean progression rates of -0.57 mm2/year and -0.12 mm/year in SWAF using area and horizontal extent as the dependent variable, respectively. When ln(Area) was analyzed as the dependent variable, mean progression was -0.07 ln(mm2)/year, which equated to 6.80% decrease in ring area per year. Similar rates were found in NIRAF (area: -0.59 mm2/year, horizontal extent: -0.12 mm/year and ln(Area): -0.08 ln(mm2)/year, equated to 7.75% decrease in area per year). Analysis of R2 showed that the dependent variable ln(Area) provided the best linear model for ring progression in both imaging modalities, especially in eyes with large overall area change. CONCLUSIONS Our data suggest that using an exponential model to estimate progression of the AF ring area in RP is more appropriate than the models assuming linear decrease. Hence, the progression estimates provided in this study should provide more accurate reference points in designing clinical trials in RP patients. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Jason Charng
- Centre of Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Western Australia; Department of Optometry, School of Allied Health, The University of Western Australia, Perth, Australia
| | - Ignacio A V Escalona
- Contact Lens and Visual Optics Laboratory, Centre for Vision and Eye Research, School of Optometry and Vision Science, Queensland University of Technology (QUT), Kelvin Grove, Australia
| | - Andrew Turpin
- Centre of Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Western Australia; School of Population Health, Curtin University, Perth, Australia
| | - Allison M McKendrick
- Centre of Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Western Australia; Department of Optometry, School of Allied Health, The University of Western Australia, Perth, Australia
| | - David A Mackey
- Centre of Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Western Australia
| | - David Alonso-Caneiro
- Contact Lens and Visual Optics Laboratory, Centre for Vision and Eye Research, School of Optometry and Vision Science, Queensland University of Technology (QUT), Kelvin Grove, Australia; School of Science, Technology and Engineering, University of Sunshine Coast, Petrie, Queensland, Australia
| | - Fred K Chen
- Centre of Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Western Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Victoria, Australia; Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia; Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.
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Sabharwal J, Liu TYA, Antonio-Aguirre B, Abousy M, Patel T, Cai CX, Jones CK, Singh MS. Automated identification of fleck lesions in Stargardt disease using deep learning enhances lesion detection sensitivity and enables morphometric analysis of flecks. Br J Ophthalmol 2024:bjo-2023-323592. [PMID: 38408857 DOI: 10.1136/bjo-2023-323592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 01/20/2024] [Indexed: 02/28/2024]
Abstract
PURPOSE To classify fleck lesions and assess artificial intelligence (AI) in identifying flecks in Stargardt disease (STGD). METHODS A retrospective study of 170 eyes from 85 consecutive patients with confirmed STGD. Fundus autofluorescence images were extracted, and flecks were manually outlined. A deep learning model was trained, and a hold-out testing subset was used to compare with manually identified flecks and for graders to assess. Flecks were clustered using K-means clustering. RESULTS Of the 85 subjects, 45 were female, and the median age was 37 years (IQR 25-59). A subset of subjects (n=41) had clearly identifiable fleck lesions, and an AI was successfully trained to identify these lesions (average Dice score of 0.53, n=18). The AI segmentation had smaller (0.018 compared with 0.034 mm2, p<0.001) but more numerous flecks (75.5 per retina compared with 40.0, p<0.001), but the total size of flecks was not different. The AI model had higher sensitivity to detect flecks but resulted in more false positives. There were two clusters of flecks based on morphology: broadly, one cluster of small round flecks and another of large amorphous flecks. The per cent frequency of small round flecks negatively correlated with subject age (r=-0.31, p<0.005). CONCLUSIONS AI-based detection of flecks shows greater sensitivity than human graders but with a higher false-positive rate. With further optimisation to address current shortcomings, this approach could be used to prescreen subjects for clinical research. The feasibility and utility of quantifying fleck morphology in conjunction with AI-based segmentation as a biomarker of progression require further study.
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Affiliation(s)
| | | | | | - Mya Abousy
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Tapan Patel
- Johns Hopkins Wilmer Eye Institute, Baltimore, Maryland, USA
| | - Cindy X Cai
- Johns Hopkins Wilmer Eye Institute, Baltimore, Maryland, USA
| | - Craig K Jones
- The Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, Maryland, USA
| | - Mandeep S Singh
- Johns Hopkins Wilmer Eye Institute, Baltimore, Maryland, USA
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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Mishra Z, Wang Z, Xu E, Xu S, Majid I, Sadda SR, Hu ZJ. Recurrent and Concurrent Prediction of Longitudinal Progression of Stargardt Atrophy and Geographic Atrophy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.11.24302670. [PMID: 38405807 PMCID: PMC10888984 DOI: 10.1101/2024.02.11.24302670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Stargardt disease and age-related macular degeneration are the leading causes of blindness in the juvenile and geriatric populations, respectively. The formation of atrophic regions of the macula is a hallmark of the end-stages of both diseases. The progression of these diseases is tracked using various imaging modalities, two of the most common being fundus autofluorescence (FAF) imaging and spectral-domain optical coherence tomography (SD-OCT). This study seeks to investigate the use of longitudinal FAF and SD-OCT imaging (month 0, month 6, month 12, and month 18) data for the predictive modelling of future atrophy in Stargardt and geographic atrophy. To achieve such an objective, we develop a set of novel deep convolutional neural networks enhanced with recurrent network units for longitudinal prediction and concurrent learning of ensemble network units (termed ReConNet) which take advantage of improved retinal layer features beyond the mean intensity features. Using FAF images, the neural network presented in this paper achieved mean (± standard deviation, SD) and median Dice coefficients of 0.895 (± 0.086) and 0.922 for Stargardt atrophy, and 0.864 (± 0.113) and 0.893 for geographic atrophy. Using SD-OCT images for Stargardt atrophy, the neural network achieved mean and median Dice coefficients of 0.882 (± 0.101) and 0.906, respectively. When predicting only the interval growth of the atrophic lesions with FAF images, mean (± SD) and median Dice coefficients of 0.557 (± 0.094) and 0.559 were achieved for Stargardt atrophy, and 0.612 (± 0.089) and 0.601 for geographic atrophy. The prediction performance in OCT images is comparably good to that using FAF which opens a new, more efficient, and practical door in the assessment of atrophy progression for clinical trials and retina clinics, beyond widely used FAF. These results are highly encouraging for a high-performance interval growth prediction when more frequent or longer-term longitudinal data are available in our clinics. This is a pressing task for our next step in ongoing research.
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Affiliation(s)
- Zubin Mishra
- Doheny Image Analysis Laboratory, Doheny Eye Institute, Pasadena, CA, 91103, USA
- Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ziyuan Wang
- Doheny Image Analysis Laboratory, Doheny Eye Institute, Pasadena, CA, 91103, USA
- The University of California, Los Angeles, CA, 90095, USA
| | - Emily Xu
- Doheny Image Analysis Laboratory, Doheny Eye Institute, Pasadena, CA, 91103, USA
| | - Sophia Xu
- Doheny Image Analysis Laboratory, Doheny Eye Institute, Pasadena, CA, 91103, USA
| | - Iyad Majid
- Doheny Image Analysis Laboratory, Doheny Eye Institute, Pasadena, CA, 91103, USA
| | - SriniVas R. Sadda
- Doheny Image Analysis Laboratory, Doheny Eye Institute, Pasadena, CA, 91103, USA
- The University of California, Los Angeles, CA, 90095, USA
| | - Zhihong Jewel Hu
- Doheny Image Analysis Laboratory, Doheny Eye Institute, Pasadena, CA, 91103, USA
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Abousy M, Antonio-Aguirre B, Aziz K, Hu MW, Qian J, Singh MS. Multimodal Phenomap of Stargardt Disease Integrating Structural, Psychophysical, and Electrophysiologic Measures of Retinal Degeneration. OPHTHALMOLOGY SCIENCE 2024; 4:100327. [PMID: 37869022 PMCID: PMC10585476 DOI: 10.1016/j.xops.2023.100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 10/24/2023]
Abstract
Objective To cluster the diverse phenotypic features of Stargardt disease (STGD) using unsupervised clustering of multimodal retinal structure and function data. Design Retrospective cross-sectional study. Subjects Eyes of subjects with STGD and fundus autofluorescence (FAF), OCT, electroretinography (ERG), and microperimetry (MP) data available within 1 year of the baseline evaluation. Methods A total of 46 variables from FAF, OCT, ERG, and MP results were recorded for subjects with STGD as defined per published criteria. Factor analysis of mixed data identified the most informative variables. Unsupervised hierarchical clustering and silhouette analysis identified the optimal number of clusters to classify multimodal phenotypes. Main Outcome Measures Phenotypic clusters of STGD subjects and the corresponding cluster features. Results We included 52 subjects and 102 eyes with a mean visual acuity (VA) at the time of multimodal testing of 0.69 ± 0.494 logarithm of minimum angle of resolution (20/63 Snellen). We identified 4 clusters of eyes. Compared to the other clusters, cluster 1 (n = 16) included younger subjects, VA greater than that of clusters 2 and 3, normal or moderately low total macular volume (TMV), greater preservation of scotopic and photopic ERG responses and fixation stability, less atrophy, and fewer flecks. Cluster 2 (n = 49) differed from cluster 1 mainly with less atrophy and relatively stable fixation. Cluster 3 (n = 10) included older subjects than clusters 1 and 2 and showed the lowest VA, TMV, ERG responses, and fixation stability, with extensive atrophy. Cluster 4 (n = 27) showed better VA, TMV similar to clusters 1 and 2, moderate ERG activity, stable fixation, and moderate-high atrophy and flecks. Conclusions Reflecting the phenotypic complexity of STGD, an unsupervised clustering approach incorporating phenotypic measures can be used to categorize STGD eyes into distinct clusters. The clusters exhibit differences in structural and functional measures including quantity of flecks, extent of retinal atrophy, visual fixation accuracy, and ERG responses, among other features. If novel pharmacologic, gene, or cell therapy modalities become available in the future, the multimodal phenomap approach may be useful to individualize treatment decisions, and its utility in aiding prognostication requires further evaluation. Financial Disclosures Proprietary or commercial disclosure may be found after the references.
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Affiliation(s)
- Mya Abousy
- Wilmer Eye Institute, Johns Hopkins Hospital, Baltimore, Maryland
| | | | - Kanza Aziz
- Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Ming-Wen Hu
- Wilmer Eye Institute, Johns Hopkins Hospital, Baltimore, Maryland
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Jiang Qian
- Wilmer Eye Institute, Johns Hopkins Hospital, Baltimore, Maryland
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Mandeep S. Singh
- Wilmer Eye Institute, Johns Hopkins Hospital, Baltimore, Maryland
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
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Daich Varela M, Sen S, De Guimaraes TAC, Kabiri N, Pontikos N, Balaskas K, Michaelides M. Artificial intelligence in retinal disease: clinical application, challenges, and future directions. Graefes Arch Clin Exp Ophthalmol 2023; 261:3283-3297. [PMID: 37160501 PMCID: PMC10169139 DOI: 10.1007/s00417-023-06052-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 05/11/2023] Open
Abstract
Retinal diseases are a leading cause of blindness in developed countries, accounting for the largest share of visually impaired children, working-age adults (inherited retinal disease), and elderly individuals (age-related macular degeneration). These conditions need specialised clinicians to interpret multimodal retinal imaging, with diagnosis and intervention potentially delayed. With an increasing and ageing population, this is becoming a global health priority. One solution is the development of artificial intelligence (AI) software to facilitate rapid data processing. Herein, we review research offering decision support for the diagnosis, classification, monitoring, and treatment of retinal disease using AI. We have prioritised diabetic retinopathy, age-related macular degeneration, inherited retinal disease, and retinopathy of prematurity. There is cautious optimism that these algorithms will be integrated into routine clinical practice to facilitate access to vision-saving treatments, improve efficiency of healthcare systems, and assist clinicians in processing the ever-increasing volume of multimodal data, thereby also liberating time for doctor-patient interaction and co-development of personalised management plans.
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Affiliation(s)
- Malena Daich Varela
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, London, UK
| | | | | | | | - Nikolas Pontikos
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, London, UK
| | | | - Michel Michaelides
- UCL Institute of Ophthalmology, London, UK.
- Moorfields Eye Hospital, London, UK.
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Zhao PY, Branham K, Schlegel D, Fahim AT, Jayasundera KT. Automated Segmentation of Autofluorescence Lesions in Stargardt Disease. Ophthalmol Retina 2022; 6:1098-1104. [PMID: 35644472 PMCID: PMC10370158 DOI: 10.1016/j.oret.2022.05.020] [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: 12/27/2021] [Revised: 05/04/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To train a deep learning (DL) algorithm to perform fully automated semantic segmentation of multiple autofluorescence lesion types in Stargardt disease. DESIGN Cross-sectional study with retrospective imaging data. SUBJECTS The study included 193 images from 193 eyes of 97 patients with Stargardt disease. METHODS Fundus autofluorescence images obtained from patient visits between 2013 and 2020 were annotated with ground-truth labels. Model training and evaluation were performed using fivefold cross-validation. MAIN OUTCOMES MEASURES Dice similarity coefficients, intraclass correlation coefficients, and Bland-Altman analyses comparing algorithm-predicted and grader-labeled segmentations. RESULTS The overall Dice similarity coefficient across all lesion classes was 0.78 (95% confidence interval [CI], 0.69-0.86). Dice coefficients were 0.90 (95% CI, 0.85-0.94) for areas of definitely decreased autofluorescence (DDAF), 0.55 (95% CI, 0.35-0.76) for areas of questionably decreased autofluorescence (QDAF), and 0.88 (95% CI, 0.73-1.00) for areas of abnormal background autofluorescence (ABAF). Intraclass correlation coefficients comparing the ground-truth and automated methods were 0.997 (95% CI, 0.996-0.998) for DDAF, 0.863 (95% CI, 0.823-0.895) for QDAF, and 0.974 (95% CI, 0.966-0.980) for ABAF. CONCLUSIONS A DL algorithm performed accurate segmentation of autofluorescence lesions in Stargardt disease, demonstrating the feasibility of fully automated segmentation as an alternative to manual or semiautomated labeling methods.
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Affiliation(s)
- Peter Y Zhao
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan
| | - Kari Branham
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan
| | - Dana Schlegel
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan
| | - Abigail T Fahim
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan
| | - K Thiran Jayasundera
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan.
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Automated segmentation and feature discovery of age-related macular degeneration and Stargardt disease via self-attended neural networks. Sci Rep 2022; 12:14565. [PMID: 36028647 PMCID: PMC9418226 DOI: 10.1038/s41598-022-18785-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/18/2022] [Indexed: 11/09/2022] Open
Abstract
Age-related macular degeneration (AMD) and Stargardt disease are the leading causes of blindness for the elderly and young adults respectively. Geographic atrophy (GA) of AMD and Stargardt atrophy are their end-stage outcomes. Efficient methods for segmentation and quantification of these atrophic lesions are critical for clinical research. In this study, we developed a deep convolutional neural network (CNN) with a trainable self-attended mechanism for accurate GA and Stargardt atrophy segmentation. Compared with traditional post-hoc attention mechanisms which can only visualize CNN features, our self-attended mechanism is embedded in a fully convolutional network and directly involved in training the CNN to actively attend key features for enhanced algorithm performance. We applied the self-attended CNN on the segmentation of AMD and Stargardt atrophic lesions on fundus autofluorescence (FAF) images. Compared with a preexisting regular fully convolutional network (the U-Net), our self-attended CNN achieved 10.6% higher Dice coefficient and 17% higher IoU (intersection over union) for AMD GA segmentation, and a 22% higher Dice coefficient and a 32% higher IoU for Stargardt atrophy segmentation. With longitudinal image data having over a longer time, the developed self-attended mechanism can also be applied on the visual discovery of early AMD and Stargardt features.
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Charng J, Alam K, Swartz G, Kugelman J, Alonso-Caneiro D, Mackey DA, Chen FK. Deep learning: applications in retinal and optic nerve diseases. Clin Exp Optom 2022:1-10. [PMID: 35999058 DOI: 10.1080/08164622.2022.2111201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
Deep learning (DL) represents a paradigm-shifting, burgeoning field of research with emerging clinical applications in optometry. Unlike traditional programming, which relies on human-set specific rules, DL works by exposing the algorithm to a large amount of annotated data and allowing the software to develop its own set of rules (i.e. learn) by adjusting the parameters inside the model (network) during a training process in order to complete the task on its own. One major limitation of traditional programming is that, with complex tasks, it may require an extensive set of rules to accurately complete the assignment. Additionally, traditional programming can be susceptible to human bias from programmer experience. With the dramatic increase in the amount and the complexity of clinical data, DL has been utilised to automate data analysis and thus to assist clinicians in patient management. This review will present the latest advances in DL, for managing posterior eye diseases as well as DL-based solutions for patients with vision loss.
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Affiliation(s)
- Jason Charng
- Centre of Ophthalmology and Visual Science (incorporating Lions Eye Institute), University of Western Australia, Perth, Australia.,Department of Optometry, School of Allied Health, University of Western Australia, Perth, Australia
| | - Khyber Alam
- Department of Optometry, School of Allied Health, University of Western Australia, Perth, Australia
| | - Gavin Swartz
- Department of Optometry, School of Allied Health, University of Western Australia, Perth, Australia
| | - Jason Kugelman
- School of Optometry and Vision Science, Queensland University of Technology, Brisbane, Australia
| | - David Alonso-Caneiro
- Centre of Ophthalmology and Visual Science (incorporating Lions Eye Institute), University of Western Australia, Perth, Australia.,School of Optometry and Vision Science, Queensland University of Technology, Brisbane, Australia
| | - David A Mackey
- Centre of Ophthalmology and Visual Science (incorporating Lions Eye Institute), University of Western Australia, Perth, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia.,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Fred K Chen
- Centre of Ophthalmology and Visual Science (incorporating Lions Eye Institute), University of Western Australia, Perth, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia.,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.,Department of Ophthalmology, Royal Perth Hospital, Western Australia, Perth, Australia
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A Systematic Review of Artificial Intelligence Applications Used for Inherited Retinal Disease Management. Medicina (B Aires) 2022; 58:medicina58040504. [PMID: 35454342 PMCID: PMC9028098 DOI: 10.3390/medicina58040504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/15/2022] Open
Abstract
Nowadays, Artificial Intelligence (AI) and its subfields, Machine Learning (ML) and Deep Learning (DL), are used for a variety of medical applications. It can help clinicians track the patient’s illness cycle, assist with diagnosis, and offer appropriate therapy alternatives. Each approach employed may address one or more AI problems, such as segmentation, prediction, recognition, classification, and regression. However, the amount of AI-featured research on Inherited Retinal Diseases (IRDs) is currently limited. Thus, this study aims to examine artificial intelligence approaches used in managing Inherited Retinal Disorders, from diagnosis to treatment. A total of 20,906 articles were identified using the Natural Language Processing (NLP) method from the IEEE Xplore, Springer, Elsevier, MDPI, and PubMed databases, and papers submitted from 2010 to 30 October 2021 are included in this systematic review. The resultant study demonstrates the AI approaches utilized on images from different IRD patient categories and the most utilized AI architectures and models with their imaging modalities, identifying the main benefits and challenges of using such methods.
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Rodríguez-Bocanegra E, Biarnés M, Garcia M, Ferraro LL, Fischer MD, Monés J. Kinetics of Heterogeneous Background in Stargardt’s Disease over Time. Life (Basel) 2022; 12:life12030381. [PMID: 35330133 PMCID: PMC8953836 DOI: 10.3390/life12030381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/24/2022] Open
Abstract
Stargardt’s disease (STGD1) is caused by mutations in the ABCA4 gene. Different lesions characterised by decreased autofluorescence levels are found in fundus autofluorescence (FAF) from STGD1 patients and could be used as outcome indicators for disease progression. We investigated the fate of foci with reduced autofluorescence (FRA) within the heterogeneous background of STGD1 patients using FAF imaging. Genetically confirmed STGD1 patients presenting heterogeneous background autofluorescence on high-quality FAF images at a minimum of two visits at least 12 months apart were chosen. A grid centred on the fovea was used to define five different zones. Within each zone, five FRA were randomly selected for each eye. The eccentricity of foci was determined at different time points for each patient. Analysis of 175 randomly chosen FRA showed consistent centrifugal displacement over time, most notably in eyes showing areas with definitely decreased autofluorescence. Interestingly, FRA did not leave an area of hypo-autofluorescence on FAF in locations where they were previously located. These findings may help to better understand STGD1 progression, improve FAF interpretation, and shed light on the nature of heterogeneous background.
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Affiliation(s)
- Eduardo Rodríguez-Bocanegra
- Barcelona Macula Foundation: Research for Vision, 08022 Barcelona, Spain; (M.B.); (M.G.); (L.L.F.); (J.M.)
- Centre for Ophthalmology, University Hospital Tübingen, University Eye Hospital, 72076 Tübingen, Germany;
- Centre for Ophthalmology, Institute for Ophthalmic Research, University Hospital Tübingen, 72076 Tübingen, Germany
- Correspondence:
| | - Marc Biarnés
- Barcelona Macula Foundation: Research for Vision, 08022 Barcelona, Spain; (M.B.); (M.G.); (L.L.F.); (J.M.)
- Institut de la Màcula, Hospital Quirón Teknon, 08022 Barcelona, Spain
| | - Míriam Garcia
- Barcelona Macula Foundation: Research for Vision, 08022 Barcelona, Spain; (M.B.); (M.G.); (L.L.F.); (J.M.)
- Institut de la Màcula, Hospital Quirón Teknon, 08022 Barcelona, Spain
| | - Lucía Lee Ferraro
- Barcelona Macula Foundation: Research for Vision, 08022 Barcelona, Spain; (M.B.); (M.G.); (L.L.F.); (J.M.)
- Institut de la Màcula, Hospital Quirón Teknon, 08022 Barcelona, Spain
| | - Manuel Dominik Fischer
- Centre for Ophthalmology, University Hospital Tübingen, University Eye Hospital, 72076 Tübingen, Germany;
- Centre for Ophthalmology, Institute for Ophthalmic Research, University Hospital Tübingen, 72076 Tübingen, Germany
- Oxford Eye Hospital, Oxford University NHS Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Jordi Monés
- Barcelona Macula Foundation: Research for Vision, 08022 Barcelona, Spain; (M.B.); (M.G.); (L.L.F.); (J.M.)
- Institut de la Màcula, Hospital Quirón Teknon, 08022 Barcelona, Spain
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12
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Huang D, Heath Jeffery RC, Aung-Htut MT, McLenachan S, Fletcher S, Wilton SD, Chen FK. Stargardt disease and progress in therapeutic strategies. Ophthalmic Genet 2021; 43:1-26. [PMID: 34455905 DOI: 10.1080/13816810.2021.1966053] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: Stargardt disease (STGD1) is an autosomal recessive retinal dystrophy due to mutations in ABCA4, characterized by subretinal deposition of lipofuscin-like substances and bilateral centrifugal vision loss. Despite the tremendous progress made in the understanding of STGD1, there are no approved treatments to date. This review examines the challenges in the development of an effective STGD1 therapy.Materials and Methods: A literature review was performed through to June 2021 summarizing the spectrum of retinal phenotypes in STGD1, the molecular biology of ABCA4 protein, the in vivo and in vitro models used to investigate the mechanisms of ABCA4 mutations and current clinical trials.Results: STGD1 phenotypic variability remains an challenge for clinical trial design and patient selection. Pre-clinical development of therapeutic options has been limited by the lack of animal models reflecting the diverse phenotypic spectrum of STDG1. Patient-derived cell lines have facilitated the characterization of splice mutations but the clinical presentation is not always predicted by the effect of specific mutations on retinoid metabolism in cellular models. Current therapies primarily aim to delay vision loss whilst strategies to restore vision are less well developed.Conclusions: STGD1 therapy development can be accelerated by a deeper understanding of genotype-phenotype correlations.
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Affiliation(s)
- Di Huang
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Rachael C Heath Jeffery
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia.,Department of Ophthalmology, Perth Children's Hospital, Nedlands, Western Australia, Australia
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13
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Heath Jeffery RC, Chen FK. Stargardt disease: Multimodal imaging: A review. Clin Exp Ophthalmol 2021; 49:498-515. [PMID: 34013643 PMCID: PMC8366508 DOI: 10.1111/ceo.13947] [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: 05/11/2021] [Accepted: 05/15/2021] [Indexed: 12/20/2022]
Abstract
Stargardt disease (STGD1) is an autosomal recessive retinal dystrophy, characterised by bilateral progressive central vision loss and subretinal deposition of lipofuscin-like substances. Recent advances in molecular diagnosis and therapeutic options are complemented by the increasing recognition of new multimodal imaging biomarkers that may predict genotype and disease progression. Unique non-invasive imaging features of STDG1 are useful for gene variant interpretation and may even provide insight into the underlying molecular pathophysiology. In addition, pathognomonic imaging features of STGD1 have been used to train neural networks to improve time efficiency in lesion segmentation and disease progression measurements. This review will discuss the role of key imaging modalities, correlate imaging signs across varied STGD1 presentations and illustrate the use of multimodal imaging as an outcome measure in determining the efficacy of emerging STGD1 specific therapies.
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Affiliation(s)
- Rachael C. Heath Jeffery
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
- Department of OphthalmologyRoyal Perth HospitalPerthWestern AustraliaAustralia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute)The University of Western AustraliaNedlandsWestern AustraliaAustralia
- Department of OphthalmologyRoyal Perth HospitalPerthWestern AustraliaAustralia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and PhysicsSir Charles Gairdner HospitalPerthWestern AustraliaAustralia
- Department of OphthalmologyPerth Children's HospitalNedlandsWestern AustraliaAustralia
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14
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Next-Generation Sequencing Applications for Inherited Retinal Diseases. Int J Mol Sci 2021; 22:ijms22115684. [PMID: 34073611 PMCID: PMC8198572 DOI: 10.3390/ijms22115684] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a collection of phenotypically and genetically diverse conditions. IRDs phenotype(s) can be isolated to the eye or can involve multiple tissues. These conditions are associated with diverse forms of inheritance, and variants within the same gene often can be associated with multiple distinct phenotypes. Such aspects of the IRDs highlight the difficulty met when establishing a genetic diagnosis in patients. Here we provide an overview of cutting-edge next-generation sequencing techniques and strategies currently in use to maximise the effectivity of IRD gene screening. These techniques have helped researchers globally to find elusive causes of IRDs, including copy number variants, structural variants, new IRD genes and deep intronic variants, among others. Resolving a genetic diagnosis with thorough testing enables a more accurate diagnosis and more informed prognosis and should also provide information on inheritance patterns which may be of particular interest to patients of a child-bearing age. Given that IRDs are heritable conditions, genetic counselling may be offered to help inform family planning, carrier testing and prenatal screening. Additionally, a verified genetic diagnosis may enable access to appropriate clinical trials or approved medications that may be available for the condition.
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15
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Perepelkina T, Fulton AB. Artificial Intelligence (AI) Applications for Age-Related Macular Degeneration (AMD) and Other Retinal Dystrophies. Semin Ophthalmol 2021; 36:304-309. [PMID: 33764255 DOI: 10.1080/08820538.2021.1896756] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Artificial intelligence (AI), with its subdivisions (machine and deep learning), is a new branch of computer science that has shown impressive results across a variety of domains. The applications of AI to medicine and biology are being widely investigated. Medical specialties that rely heavily on images, including radiology, dermatology, oncology and ophthalmology, were the first to explore AI approaches in analysis and diagnosis. Applications of AI in ophthalmology have concentrated on diseases with high prevalence, such as diabetic retinopathy, retinopathy of prematurity, age-related macular degeneration (AMD), and glaucoma. Here we provide an overview of AI applications for diagnosis, classification, and clinical management of AMD and other macular dystrophies.
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Affiliation(s)
- Tatiana Perepelkina
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, United States
| | - Anne B Fulton
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, United States
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