OPTARI: An open-source software framework for clinical translation of optoacoustic imaging

Ultrasound images vary widely across scanners, operators, and anatomical targets, which often causes models trained in one setting to generalize poorly to new hospitals and clinical conditions. The Foundation Model Challenge for Ultrasound Image Analysis (FMC-UIA) reflects this difficulty by requiring a single model to handle multiple tasks, including segmentation, detection, classification, and landmark regression across diverse organs and datasets. We propose a unified multi-task framework based on a transformer visual encoder from the Qwen3-VL family. Intermediate token features are projected into spatial feature maps and fused using a lightweight multi-scale feature pyramid, enabling both pixel-level predictions and global reasoning within a shared representation. Each task is handled by a small task-specific prediction head, while training uses task-aware sampling and selective loss balancing to manage heterogeneous supervision and reduce task imbalance. Our method is designed to be simple to optimize and adaptable across a wide range of ultrasound analysis tasks. The performance improved from 67% to 85% on the validation set and achieved an average score of 81.84% on the official test set across all tasks. The code is publicly available at: https://github.com/saitejalekkala33/FMCUIA-ISBI.git

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,...

Optical coherence tomography (OCT) offers compact, contactless, micron-scale imaging suitable for intraoperative guidance, but native OCT volumes are discretely sampled, anisotropic, and currently inefficient for downstream geometric reasoning and robot integration. We present OCTN (pronounced "octane"), an implicit neural representation framework that converts volumetric OCT scans into a continuous, differentiable, and spatially faithful tissue-intensity field. OCTN uses a two-stage hybrid training strategy that combines supervision from acquired voxels with inter-slice interpolations, preserving B-scan fidelity while improving continuity in sparsely sampled regions. For versatility, we first show that OCTN enables fast volumetric reasoning by storing the learned tissue representation natively on the GPU, supporting intensity-based spatial queries with up to 43x speedup over conventional CPU processing. We then demonstrate OCTN-enabled OCT-guided robotic laser surgery where the continuous tissue representation supports implicit surface discovery and surface-constrained path planning via multiple optimization strategies, including Newton- and SGD-based optimization. Next, OCTN enables reconstruction of dense volumetric structure from sparsely acquired B-scans, while reducing acquisition time by 4x and preserving clinically relevant structures. Across the newly generated Duke TissueOCT dataset and public OCT datasets, OCTN achieves robust, high-fidelity reconstruction with PSNR > 30 dB and training time < 10 s, while preserving surface consistency within 10 $μ$m Chamfer distance relative to baseline reconstruction. The TissueOCT dataset and code are publicly available at raprakashvi.github.io/octn