Publications

PiPViT: Patch-based Visual Interpretable Prototypes for retinal image analysis

M. Oghbaie, T. Araújo, G. S. Reiter, H. Bogunović

Biomedical Signal Processing and Control, 117, 109545, 2026.

PINN-EM: Physics-Guided Disease Progression Model of Geographic Atrophy

D. Lachinov, T. Pinetz, H. Bogunovic

IEEE Transactions on Biomedical Engineering, 73(10), 3555-3566, 2026.

SD-RetinaNet: Topologically Constrained Semi-Supervised Retinal Lesion and Layer Segmentation in OCT

B. Fazekas, G. Aresta, P. Seeböck, J. Mai, U. Schmidt-Erfurth, H. Bogunović

IEEE Transactions on Medical Imaging, 45(3), 945-959, 2026.

Predictive Value of Perilesional Fundus Autofluorescence Patterns and OCT-Based Ellipsoid Zone/Retinal Pigment Epithelium Loss Ratios in Geographic Atrophy Growth Rates

J. Mai, G. S. Reiter, S. Riedl, +6, H. Bogunovic, U. Schmidt-Erfurth

Ophthalmology Science, 6(9), 101306, 2026.

ROQUS: a retinal OCT quality and usability score

G. Aresta, T. Araújo, G. Faustmann, H. Bogunović

Biomedical Optics Express, 16(7), 2972, 2025.

Quality assessment of optical coherence tomography angiography images with Relative-distance-based Patch Distribution Modeling (R-PaDiM)

M. Esengönül, T. F. Araújo, N. Jeremic, A. Zarghami, H. Bogunović, U. Schmidt-Erfurth

Computer Methods and Programs in Biomedicine, 271, 108955, 2025.

SD-LayerNet: Robust and label-efficient retinal layer segmentation via anatomical priors

B. Fazekas, G. Aresta, D. Lachinov, S. Riedl, J. Mai, U. Schmidt-Erfurth, H. Bogunović

Computer Methods and Programs in Biomedicine, 261, 108586, 2025.

Shape Prior for Quality Assessment in OCTA via Denoising Autoencoders at the Segmentation Level

H. Jebril, T. Pinetz, H. Bogunović

IEEE Access, 13, 187467-187476, 2025.

Multimodal foundation model and benchmark for comprehensive retinal OCT image analysis

J. Morano, B. Fazekas, E. Sükei, R. Fecso, T. Emre, +1, G. Faustmann, M. Oghbaie, +1, H. Bogunović

npj Digital Medicine, 8(1), 2025.

Disease Activity and Therapeutic Response to Pegcetacoplan for Geographic Atrophy Identified by Deep Learning-Based Analysis of OCT

U. Schmidt-Erfurth, J. Mai, G. S. Reiter, +6, H. Bogunovic

Ophthalmology, 132(2), 181-193, 2025.

A Novel Management Challenge in Age-Related Macular Degeneration

G. S. Reiter, D. Lachinov, W. Bühl, G. Weigert, C. Grechenig, J. Mai, H. Bogunović, U. Schmidt-Erfurth

Ophthalmology Retina, 9(5), 421-430, 2025.

Anomaly Detection in Retinal OCT Images With Deep Learning-Based Knowledge Distillation

G. Aresta, T. Araújo, U. Schmidt-Erfurth, H. Bogunović

Translational Vision Science & Technology, 14(3), 26, 2025.

An Automated Comparative Analysis of the Exudative Biomarkers in Neovascular Age-Related Macular Degeneration, The RAP Study: Report 6

B. Haj Najeeb, B. S. Gerendas, G. G. Deak, O. Leingang, H. Bogunovic, U. Schmidt-Erfurth

American Journal of Ophthalmology, 264, 53-65, 2024.

Anomaly Detection in Optical Coherence Tomography Angiography (OCTA) with a Vector-Quantized Variational Auto-Encoder (VQ-VAE)

H. Jebril, M. Esengönül, H. Bogunović

Bioengineering, 11(7), 682, 2024.

Pretraining of 3D image segmentation models for retinal OCT using denoising-based self-supervised learning

A. Rivail, T. Araújo, U. Schmidt-Erfurth, H. Bogunović

Biomedical Optics Express, 15(9), 5025, 2024.

VLFATRollout: Fully transformer-based classifier for retinal OCT volumes

M. Oghbaie, T. Araújo, U. Schmidt-Erfurth, H. Bogunović

Computerized Medical Imaging and Graphics, 118, 102452, 2024.

RRWNet: Recursive Refinement Network for effective retinal artery/vein segmentation and classification

J. Morano, G. Aresta, H. Bogunović

Expert Systems with Applications, 256, 124970, 2024.

Interactive Deep Learning-Based Retinal OCT Layer Segmentation Refinement by Regressing Translation Maps

G. Aresta, T. Araújo, B. Fazekas, J. Mai, U. Schmidt-Erfurth, H. Bogunović

IEEE Access, 12, 47009-47023, 2024.

Deep Multimodal Fusion of Data With Heterogeneous Dimensionality via Projective Networks

J. Morano, G. Aresta, C. Grechenig, U. Schmidt-Erfurth, H. Bogunović

IEEE Journal of Biomedical and Health Informatics, 28(4), 2235-2246, 2024.

3DTINC: Time-Equivariant Non-Contrastive Learning for Predicting Disease Progression From Longitudinal OCTs

T. Emre, A. Chakravarty, A. Rivail, D. Lachinov, +8, H. Bogunović

IEEE Transactions on Medical Imaging, 43(9), 3200-3210, 2024.

Learning Spatio-Temporal Model of Disease Progression With NeuralODEs From Longitudinal Volumetric Data

D. Lachinov, A. Chakravarty, C. Grechenig, U. Schmidt-Erfurth, H. Bogunović

IEEE Transactions on Medical Imaging, 43(3), 1165-1179, 2024.

Morph-SSL: Self-Supervision With Longitudinal Morphing for Forecasting AMD Progression From OCT Volumes

A. Chakravarty, T. Emre, O. Leingang, +7, H. Bogunović

IEEE Transactions on Medical Imaging, 43(9), 3224-3239, 2024.

Anomaly guided segmentation: Introducing semantic context for lesion segmentation in retinal OCT using weak context supervision from anomaly detection

P. Seeböck, J. I. Orlando, M. Michl, J. Mai, U. Schmidt-Erfurth, H. Bogunović

Medical Image Analysis, 93, 103104, 2024.

Deep Learning-Based Prediction of Individual Geographic Atrophy Progression from a Single Baseline OCT

J. Mai, D. Lachinov, G. S. Reiter, S. Riedl, C. Grechenig, H. Bogunovic, U. Schmidt-Erfurth

Ophthalmology Science, 4(4), 100466, 2024.

Deep Neural Networks for Automated Outer Plexiform Layer Subsidence Detection on Retinal OCT of Patients With Intermediate AMD

G. Aresta, T. Araujo, G. S. Reiter, +6, H. Bogunovic

Translational Vision Science & Technology, 13(6), 7, 2024.

Automated inter-device 3D OCT image registration using deep learning and retinal layer segmentation

D. Rivas-Villar, A. R. Motschi, M. Pircher, C. K. Hitzenberger, M. Schranz, P. K. Roberts, U. Schmidt-Erfurth, H. Bogunović

Biomedical Optics Express, 14(7), 3726, 2023.

Deep survival modeling of longitudinal retinal OCT volumes for predicting the onset of atrophy in patients with intermediate AMD

A. Rivail, W. D. Vogl, S. Riedl, +6, H. Bogunović

Biomedical Optics Express, 14(6), 2449, 2023.

Therapeutic response in the HAWK and HARRIER trials using deep learning in retinal fluid volume and compartment analysis

U. Schmidt-Erfurth, Z. Mulyukov, B. S. Gerendas, G. S. Reiter, D. Lorand, G. Weissgerber, H. Bogunović

Eye, 37(6), 1160-1169, 2023.

Segmentation of Bruch's Membrane in Retinal OCT With AMD Using Anatomical Priors and Uncertainty Quantification

B. Fazekas, D. Lachinov, G. Aresta, J. Mai, U. Schmidt-Erfurth, H. Bogunovic

IEEE Journal of Biomedical and Health Informatics, 27(1), 41-52, 2023.

Progression Dynamics of Early versus Later Stage Atrophic Lesions in Nonneovascular Age-Related Macular Degeneration Using Quantitative OCT Biomarker Segmentation

L. M. Coulibaly, G. S. Reiter, P. Fuchs, D. Lachinov, O. Leingang, W. D. Vogl, H. Bogunovic, U. Schmidt-Erfurth

Ophthalmology Retina, 7(9), 762-770, 2023.

Few-shot out-of-distribution detection for automated screening in retinal OCT images using deep learning

T. Araújo, G. Aresta, U. Schmidt-Erfurth, H. Bogunović

Scientific Reports, 13(1), 2023.

Linking Function and Structure with ReSensNet

P. Seeböck, W. D. Vogl, S. M. Waldstein, +5, H. Bogunović, U. Schmidt-Erfurth

Ophthalmology Retina, 6(6), 501-511, 2022.

Reducing image variability across OCT devices with unsupervised unpaired learning for improved segmentation of retina

D. Romo-Bucheli, P. Seeböck, J. I. Orlando, B. S. Gerendas, S. M. Waldstein, U. Schmidt-Erfurth, H. Bogunović

Biomedical Optics Express, 11(1), 346, 2020.

End-to-End Deep Learning Model for Predicting Treatment Requirements in Neovascular AMD From Longitudinal Retinal OCT Imaging

D. Romo-Bucheli, U. S. Erfurth, H. Bogunovic

IEEE Journal of Biomedical and Health Informatics, 24(12), 3456-3465, 2020.

REFUGE Challenge: A unified framework for evaluating automated methods for glaucoma assessment from fundus photographs

J. I. Orlando, H. Fu, J. Barbosa Breda, +27, H. Bogunović

Medical Image Analysis, 59, 101570, 2020.

Application of Automated Quantification of Fluid Volumes to Anti–VEGF Therapy of Neovascular Age-Related Macular Degeneration

U. Schmidt-Erfurth, W. D. Vogl, L. M. Jampol, H. Bogunović

Ophthalmology, 127(9), 1211-1219, 2020.

Automated Quantification of Photoreceptor alteration in macular disease using Optical Coherence Tomography and Deep Learning

J. I. Orlando, B. S. Gerendas, S. Riedl, +4, H. Bogunović, U. Schmidt-Erfurth

Scientific Reports, 10(1), 2020.

FunPiQ: A New Benchmark for Pixel-Level Quality Assessment in Fundus Images

P. Wang, J. Morano, V. Mares, H. Bogunović

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 109-119, 2026.

Quantification of Uncertainty with Adversarial Models in Medical Image Segmentation

H. Jebril, T. Pinetz, G. Klambauer, H. Bogunović

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 447-456, 2026.

Test-Time Adaptation in Optical Coherence Tomography Using Trajectory-Aligned Time-Independent Flow

V. Hucke, T. Pinetz, G. Reiter, U. Schmidt-Erfurth, H. Bogunović

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 545-555, 2026.

Automatic Detection and Prediction of nAMD Activity Change in Retinal OCT Using Siamese Networks and Wasserstein Distance for Ordinality

T. Emre, T. Araújo, M. Oghbaie, D. Lachinov, G. Aresta, H. Bogunović

MARIO Challenge, MICCAI 2024 (Image-Based Prediction of Retinal Disease Progression), 106-117, 2025.

RetFiner: A Vision-Language Refinement Scheme for Retinal Foundation Models

R. Fecso, J. Morano, U. Schmidt-Erfurth, H. Bogunović

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 541-551, 2025.

GARD: Gamma-Based Anatomical Restoration and Denoising for Retinal OCT

B. Fazekas, T. Pinetz, G. Aresta, T. Emre, H. Bogunović

Ophthalmic Medical Image Analysis (OMIA), 32-42, 2025.

Forecasting Disease Progression with Parallel Hyperplanes in Longitudinal Retinal OCT

A. Chakravarty, T. Emre, D. Lachinov, A. Rivail, +6, H. Bogunović

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 273-283, 2024.

Learning Temporally Equivariance for Degenerative Disease Progression in OCT by Predicting Future Representations

T. Emre, A. Chakravarty, D. Lachinov, A. Rivail, U. Schmidt-Erfurth, H. Bogunović

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 196-206, 2024.

Comparative Analysis of Data Augmentation for Retinal OCT Biomarker Segmentation

M. Unterdechler, B. Fazekas, G. Aresta, H. Bogunović

Ophthalmic Medical Image Analysis (OMIA), 94-103, 2024.

Self-supervised Learning via Inter-modal Reconstruction and Feature Projection Networks for Label-Efficient 3D-to-2D Segmentation

J. Morano, G. Aresta, D. Lachinov, J. Mai, U. Schmidt-Erfurth, H. Bogunović

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 589-599, 2023.

Transformer-Based End-to-End Classification of Variable-Length Volumetric Data

M. Oghbaie, T. Araújo, T. Emre, U. Schmidt-Erfurth, H. Bogunović

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 358-367, 2023.

Adapting Segment Anything Model (SAM) for Retinal OCT

B. Fazekas, J. Morano, D. Lachinov, G. Aresta, H. Bogunović

Ophthalmic Medical Image Analysis (OMIA), 92-101, 2023.

Pretrained Deep 2.5D Models for Efficient Predictive Modeling from Retinal OCT: A PINNACLE Study Report

T. Emre, M. Oghbaie, A. Chakravarty, A. Rivail, +7, H. Bogunović

Ophthalmic Medical Image Analysis (OMIA), 132-141, 2023.

Deep Dirichlet Uncertainty for Unsupervised Out-of-Distribution Detection of Eye Fundus Photographs in Glaucoma Screening

T. Araojo, G. Aresta, H. Bogunovic

IEEE International Symposium on Biomedical Imaging (ISBI), 1-5, 2022.

SD-LayerNet: Semi-supervised Retinal Layer Segmentation in OCT Using Disentangled Representation with Anatomical Priors

B. Fazekas, G. Aresta, D. Lachinov, S. Riedl, J. Mai, U. Schmidt-Erfurth, H. Bogunović

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 320-329, 2022.

TINC: Temporally Informed Non-contrastive Learning for Disease Progression Modeling in Retinal OCT Volumes

T. Emre, A. Chakravarty, A. Rivail, S. Riedl, U. Schmidt-Erfurth, H. Bogunović

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 625-634, 2022.

Projective Skip-Connections for Segmentation Along a Subset of Dimensions in Retinal OCT

D. Lachinov, P. Seeböck, J. Mai, F. Goldbach, U. Schmidt-Erfurth, H. Bogunovic

Medical Image Computing and Computer-Assisted Intervention (MICCAI), 431-441, 2021.