Towards Investigating Residual Hearing Loss: Quantification of Fibrosis in a Novel Cochlear OCT Dataset
Authors: Julia Dietlmeier, Benjamin Greenberg, Wenxuan He, Teresa Wilson, Rubing Xing, Jordan Hill, Adrienne Fettig, Madeline Otto, Teyhana Rounsavill, Lina A. J. Reiss, Jingang Yi, Noel E. O'Connor, George W. S. Burwood
Organizations: Insight Research Ireland Centre for Data Analytics, Dublin City University, Ireland · Rutgers University, New Jersey, USA · Oregon Health & Science University (OHSU), Oregon Hearing Research Center (OHRC), Portland, Oregon, USA
Objective: Cochlear implants (CIs) are bionic prostheses that restores hearing via electrical stimulation of the auditory nerve. Hybrid CIs, which use electroacoustic stimulation (EAS), combine residual low-frequency acoustic hearing with CI electrical stimulation. Intracochlear fibrosis, which forms in response to the presence of the implant, may impede residual hearing function and gradually reduce the efficacy of EAS. It is therefore a translational objective to study the formation of cochlear fibrosis in rodents, with the goal of reducing fibrotic burden and improving outcomes for CI patients. Methods: We generate and annotate a novel dataset of optical coherence tomography (OCT) images from chronically implanted guinea pigs as part of an ongoing study focused on implant induced fibrosis. Objectively assessing fibrotic burden in this model, with high resolution and repeatability, presents an obvious use case for computer vision methods. Results: We present the results of several state-of-the-art semantic segmentation models and compare their efficacy for identifying cochlear fibrosis and other relevant annotations, using a new library of manually segmented OCT images. Conclusions: We find that the best performance is achieved by using a modified version of the well-known UNET architecture (which we term 2D-OCT-UNET) that operates on the upscaled OCT input resolution. Significance: For the first time, we have successfully applied computer vision techniques to an OCT dataset of implanted cochleae with fibrosis. Using this deep learning model, the cochlear fibrotic burden calculation can be reliably carried out as we verify in our experimental section. The dataset and the project code are available at: https://github.com/juliadietlmeier/CF-OCT-segmentation
Figures & tables
Fig. 1: Cochlear OCT dataset samples and the corresponding ground truth annotations from five annotated volumes. The CI/Track class is depicted in red, the Fibrosis class in green and the ST/Free Space class in blue.
Fig. 2: Block diagram of the proposed 2D-OCT-UNET architecture for the multiclass OCT segmentation used in this work. The very deep 2D-OCT-UNET processes two-dimensional OCT slices and consists of seven encoder-decoder blocks with skip connections. The numbers above the encoder, bottleneck and decoder blocks indicate the number of filters in the convolutional Conv2D layers. GN stands for Group Normalization layers with the number of groups parameter ng=2 . The input resolution of the UNET is set to be 1024 × 1024 pixels. We include Dropout (0.1) layers only in the decoder. The number of filters in the last Conv2D layer is equal to the nc=4 (number of classes).
Fig. 3: Schematic of the residual unit in the decoder block of the UEfficientNet model.
Fig. 4: Quantitative results from benchmarking different models are provided for each class. Average quantitative results are given in Table I .
Model
Accuracy
Precision
Recall
Dice (DSC)
Jaccard
parameters
model size
Proposed 2D-OCT-UNET
99.09 %
89.70%
88.78 %
0.8874
0.8158
34,623,099
132.08MB
VGG16-UNET [ 30 ]
99.06%
89.87 %
87.47%
0.8788
0.8061
25,862,532
98.66MB
UEfficientNet [ 33 ]
99.03%
89.52%
87.38%
0.8783
0.8029
113,890,355
434.46MB
Segment Anything Model (SAM, with adapters) [ 39 ]
98.71%
84.90%
85.24%
0.8402
0.7541
94,008,145
358.614MB
MST-DeepLabv3+ [ 36 ]
98.57%
88.99%
78.07%
0.8085
0.7204
6,407,940
24.44MB
SegFormer [ 35 ]
98.60%
85.66%
79.34%
0.8080
0.7101
3,715,684
14.17MB
TABLE I: Quantitative results averaged over all four classes. Models are ranked according to the DSC metric. Our own 2D-OCT-UNET model outperforms other state-of-the-art semantic segmentation models
Fig. 5: Samples from qualitative results are provided for each volume. First two rows: OCTV1L, Third row: OCTV7L, Fourth row: OCTV9L, Fifth row: OCTV10L and the Sixth row: OCTV11L. By comparing to the Ground Truth (GT) it can be inferred that the 2D-OCT-UNET model performed the best and the SAM (prompt-free auto-mode implementation with adapters [ 40 ] ) model qualitatively performed the worst. As previously, the CI/Track class is depicted in red, the Fibrosis class in green and the ST/Free Space class in blue.
Fig. 6: Example of fibrosis quantification using our 2D-OCT-UNET model. First row shows outcome of human (red curve) and AI-computed (blue curve) segmentation of fibrosis for OCTV1L and OCTV7L volumes. Fibrotic burden is expressed as a function of Z position within the OCT scan. The AI-computed segmentation was trained upon the more sparse human-computed segmentation and applied to all sections from the top of the ST to the point where depth within the preparation reduced Signal-to-Noise-Ratio (SNR) and therefore confidence in segmentation by the human segmenters. The AI performance was excellent and provided a high resolution assessment of the amount of fibrosis in the ST. The second row shows quantitative prediction error analysis plots. Prediction error is defined as a difference between the human-computed (GT) fibrosis and the AI-computed fibrosis. The correlation statistics for the absolute error are as follows: OCTV1L ρ=−0.1088 , p=0.3464 , OCTV7L ρ=0.0374 , p=0.8723 where ρ is the Pearson’s correlation coefficient and p is the two-sided p-value. The correlation statistics for the signed error are as follows: OCTV1L ρ=−0.0857 , p=0.4585 , OCTV7L ρ=−0.1343 , p=0.5616 . We identified an outlier in the ground truth of the OCTV7L volume. We do not include this outlier in our formal analysis and plot this datapoint (marked with an asterisk) separately from the error lines. The annotations for the outlier slice are shown in Fig. 7 .
Fig. 7: First row depicts ground truth and the second row depicts corresponding 2D-OCT-UNET predictions for the OCTV7L volume. An outlier in the ground truth annotations can be seen in the middle slice in the first row. This human mistake in the annotation would cause a significant p -value of 0.0050 if included in the formal error analysis.
Medical image segmentation delineates organs, lesions, and other structures in scans to support measurement, diagnosis, treatment planning, and research.
Robotic cochlear-implant (CI) insertion requires precise prediction and regulation of contact forces to minimize intracochlear trauma and prevent failure modes such as locking and buckling. Aligned with the integration of advanced medical imaging and robotics for autonomous, precision interventions, this paper presents a unified CT-to-simulation pipeline for contact-aware insertion planning and validation. We develop a low-dimensional, differentiable Cosserat-rod model of the electrode array coupled with frictional contact and pseudo-dynamics regularization to ensure continuous stick-slip transitions. Patient-specific cochlear anatomy is reconstructed from CT imaging and encoded via an analytic parametrization of the scala-tympani lumen, enabling efficient and differentiable contact queries through closest-point projection. Based on a differentiated equilibrium-constraint formulation, we derive an online direction-update law under an RCM-like constraint that suppresses lateral insertion forces while maintaining axial advancement. Simulations and benchtop experiments validate deformation and force trends, demonstrating reduced locking/buckling risk and improved insertion depth. The study highlights how CT-based imaging enhances modeling, planning, and safety capabilities in robot-assisted inner-ear procedures.
Color fundus photography (CFP) is the mainstay of large-scale retinal screening, but its diagnostic capacity is limited by the lack of depth-resolved structure, which optical coherence tomography (OCT) provides yet is less accessible at population scale. We present EyeMVP, a cross-modal retinal foundation model that uses paired CFP--OCT pretraining to learn OCT-informed CFP representations while requiring only CFP at inference. Pretrained on 674,893 same-eye same-day CFP--OCT triples from 112,642 patients across eight hospitals, EyeMVP uses cross-modal masked reconstruction to enrich CFP features with OCT-associated supervision, and combines source-constrained cross-attention with CFP-derived structural masks to accommodate the non-aligned geometry of en-face CFP and cross-sectional OCT. Across 15 dataset-level settings spanning classification and segmentation, under both full-data and few-shot regimes, EyeMVP performs on par with or better than representative retinal foundation models, with consistent gains on macular and optic-nerve tasks; it attains AUROCs of 0.923 for macular edema and 0.867 for myopic macular schisis, two conditions poorly resolved in CFP. In an exploratory reader study, EyeMVP surpasses junior and intermediate ophthalmologists but not seniors on macular edema, while exceeding all groups on myopic macular schisis. These results indicate that cross-modal reconstruction can enrich CFP representations with OCT-associated supervision, offering a practical route to stronger CFP-based screening.
Zhuo Deng, Ruiheng Zhang, Ziheng Zhang +23
Shenzhen International Graduate School, Tsinghua University, Shenzhen, China · Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China · Liangxiang Hospital of Beijing Fangshan District, Capital Medical University, Beijing, China +6
Optical Coherence Tomography (OCT) has become one of the most used imaging modality in ophthalmology. It provides high-resolution, non-invasive visualization of retinal microarchitecture. The automated analysis of OCT images through representation learning has emerged as a central research frontier. This has mainly been driven by the clinical need to process large acquisition volumes. The objective is to reduce the reliance on expert annotation, and improve diagnostic consistency across devices and populations. This survey provides a comprehensive and structured review of representation learning methods for retinal OCT image analysis. It covers the period from early deep learning approaches to the most recent developments in foundation models and vision-language systems. We organize the literature along a principled taxonomy of learning paradigms, encompassing supervised learning with CNN-based and transformer-based architectures, self-supervised and semi-supervised methods, generative approaches, as well as 3D volumetric modeling, multimodal representation learning, and large-scale pretrained foundation models. For each paradigm, we analyze the core methodological contributions, identify persistent limitations, and trace the connections between successive approaches. We further provide a structured overview of publicly available OCT datasets, discuss evaluation protocol considerations, and present a unified problem formulation that situates each learning paradigm within a common mathematical framework. Building on this analysis, we identify and discuss the most pressing open research directions emerging in the literature. This includes volumetric foundation model pretraining, uncertainty-aware representation learning, federated and privacy-preserving training, fairness and bias mitigation, concept-based interpretability,...
Hedi Tabia, Désiré Sidibé, Nawres Khlifa +6
IBISC Univ. Evry Université Paris-Saclay · University of Tunis El Manar · ESIEE Paris - Université Gustave Eiffel +2