OCTCube: A 3D foundation model for optical coherence tomography that improves cross-dataset, cross-disease, cross-device and cross-modality analysis

Optical coherence tomography (OCT) has become critical for diagnosing retinal diseases as it enables 3D images of the retina and optic nerve. OCT acquisition is fast, non-invasive, affordable, and scalable. Due to its broad applicability, massive numbers of OCT images have been accumulated in routine exams, making it possible to train large-scale foundation models that can generalize to various diagnostic tasks using OCT images. Nevertheless, existing foundation models for OCT only consider 2D image slices, overlooking the rich 3D structure. Here, we present OCTCube, a 3D foundation model pre-trained on 26,605 3D OCT volumes encompassing 1.62 million 2D OCT images. OCTCube is developed based on 3D masked autoencoders and exploits FlashAttention to reduce the larger GPU memory usage caused by modeling 3D volumes. OCTCube outperforms 2D models when predicting 8 retinal diseases in both inductive and cross-dataset settings, indicating that utilizing the 3D structure in the model instead of 2D data results in significant improvement. OCTCube further shows superior performance on cross-device prediction and when predicting systemic diseases, such as diabetes and hypertension, further demonstrating its strong generalizability. Finally, we propose a contrastive-self-supervised-learning-based OCT-IR pre-training framework (COIP) for cross-modality analysis on OCT and infrared retinal (IR) images, where the OCT volumes are embedded using OCTCube. We demonstrate that COIP enables accurate alignment between OCT and IR en face images. Collectively, OCTCube, a 3D OCT foundation model, demonstrates significantly better performance against 2D models on 27 out of 29 tasks and comparable performance on the other two tasks, paving the way for AI-based retinal disease diagnosis.

Unsupervised cross domain learning with applications to 7 layer segmentation of OCTs

Unsupervised cross domain adaptation for OCT 7 layer segmentation and other medical applications where labeled training data is only available in a source domain and unavailable in the target domain. Our proposed method helps generalize of deep learning to many areas in the medical field where labeled training data are expensive and time consuming to acquire or where target domains are too novel to have had labelling.