Uncertainty Quantification for Distribution-to-Distribution Flow Matching in Scientific Imaging

Distribution-to-distribution generative models support scientific imaging tasks ranging from modeling cellular perturbation responses to translating medical images across conditions. Trustworthy generation requires both reliability (generalization across labs, devices, and experimental conditions) and accountability (detecting out-of-distribution cases where predictions may be unreliable). Uncertainty quantification (UQ) based approaches serve as promising candidates for these tasks, yet UQ for distribution-to-distribution generative models remains underexplored. We present a unified UQ framework, Bayesian Stochastic Flow Matching (BSFM), that disentangles aleatoric and epistemic uncertainty. The Stochastic Flow Matching (SFM) component augments deterministic flows with a diffusion term to improve model generalization to unseen scenarios. For UQ, we develop a scalable Bayesian approach -- MCD-Antithetic -- that combines Monte Carlo Dropout with sample-efficient antithetic sampling to produce effective anomaly scores for out-of-distribution detection. Experiments on cellular imaging (BBBC021, JUMP) and brain fMRI (Theory of Mind) across diverse scenarios show that SFM improves reliability while MCD-Antithetic enhances accountability.

6D Robotic OCT Scanning of Curved Tissue Surfaces

Optical coherence tomography (OCT) is a non-invasive volumetric imaging modality with high spatial and temporal resolution. For imaging larger tissue structures, OCT probes need to be moved to scan the respective area. For handheld scanning, stitching of the acquired OCT volumes requires overlap to register the images. For robotic scanning and stitching, a typical approach is to restrict the motion to translations, as this avoids a full hand-eye calibration, which is complicated by the small field of view of most OCT probes. However, stitching by registration or by translational scanning are limited when curved tissue surfaces need to be scanned. We propose a marker for full six-dimensional hand-eye calibration of a robot mounted OCT probe. We show that the calibration results in highly repeatable estimates of the transformation. Moreover, we evaluate robotic scanning of two phantom surfaces to demonstrate that the proposed calibration allows for consistent scanning of large, curved tissue surfaces. As the proposed approach is not relying on image registration, it does not suffer from a potential accumulation of errors along a scan path. We also illustrate the improvement compared to conventional 3D-translational robotic scanning.

MERIT: Multi-domain Efficient RAW Image Translation

RAW images captured by different camera sensors exhibit substantial domain shifts due to varying spectral responses, noise characteristics, and tone behaviors, complicating their direct use in downstream computer vision tasks. Prior methods address this problem by training domain-specific RAW-to-RAW translators for each source-target pair, but such approaches do not scale to real-world scenarios involving multiple types of commercial cameras. In this work, we introduce MERIT, the first unified framework for multi-domain RAW image translation, which leverages a single model to perform translations across arbitrary camera domains. To address domain-specific noise discrepancies, we propose a sensor-aware noise modeling loss that explicitly aligns the signal-dependent noise statistics of the generated images with those of the target domain. We further enhance the generator with a conditional multi-scale large kernel attention module for improved context and sensor-aware feature modeling. To facilitate standardized evaluation, we introduce MDRAW, the first dataset tailored for multi-domain RAW image translation, comprising both paired and unpaired RAW captures from five diverse camera sensors across a wide range of scenes. Extensive experiments demonstrate that MERIT outperforms prior models in both quality (5.56 dB improvement) and scalability (80% reduction in training iterations).

When Minor Edits Matter: LLM-Driven Prompt Attack for Medical VLM Robustness in Ultrasound

Ultrasound is widely used in clinical practice due to its portability, cost-effectiveness, safety, and real-time imaging capabilities. However, image acquisition and interpretation remain highly operator dependent, motivating the development of robust AI-assisted analysis methods. Vision-language models (VLMs) have recently demonstrated strong multimodal reasoning capabilities and competitive performance in medical image analysis, including ultrasound. However, emerging evidence highlights significant concerns about their trustworthiness. In particular, adversarial robustness is critical because Med-VLMs operate via natural-language instructions, rendering prompt formulation a realistic and practically exploitable point of vulnerability. Small variations (typos, shorthand, underspecified requests, or ambiguous wording) can meaningfully shift model outputs. We propose a scalable adversarial evaluation framework that leverages a large language model (LLM) to generate clinically plausible adversarial prompt variants via "humanized" rewrites and minimal edits that mimic routine clinical communication. Using ultrasound multiple-choice question answering benchmarks, we systematically assess the vulnerability of SOTA Med-VLMs to these attacks, examine how attacker LLM capacity influences attack success, analyze the relationship between attack success and model confidence, and identify consistent failure patterns across models. Our results highlight realistic robustness gaps that must be addressed for safe clinical translation. Code will be released publicly following the review process.

Improving Image-to-Image Translation via a Rectified Flow Reformulation

In this work, we propose Image-to-Image Rectified Flow Reformulation (I2I-RFR), a practical plug-in reformulation that recasts standard I2I regression networks as continuous-time transport models. While pixel-wise I2I regression is simple, stable, and easy to adapt across tasks, it often over-smooths ill-posed and multimodal targets, whereas generative alternatives often require additional components, task-specific tuning, and more complex training and inference pipelines. Our method augments the backbone input by channel-wise concatenation with a noise-corrupted version of the ground-truth target and optimizes a simple t-reweighted pixel loss. This objective admits a rectified-flow interpretation via an induced velocity field, enabling ODE-based progressive refinement at inference time while largely preserving the standard supervised training pipeline. In most cases, adopting I2I-RFR requires only expanding the input channels, and inference can be performed with a few explicit solver steps (e.g., 3 steps) without distillation. Extensive experiments across multiple image-to-image translation and video restoration tasks show that I2I-RFR generally improves performance across a wide range of tasks and backbones, with particularly clear gains in perceptual quality and detail preservation. Overall, I2I-RFR provides a lightweight way to incorporate continuous-time refinement into conventional I2I models without requiring a heavy generative pipeline.

Ontology-Guided Diffusion for Zero-Shot Visual Sim2Real Transfer

Bridging the simulation-to-reality (sim2real) gap remains challenging as labelled real-world data is scarce. Existing diffusion-based approaches rely on unstructured prompts or statistical alignment, which do not capture the structured factors that make images look real. We introduce Ontology- Guided Diffusion (OGD), a neuro-symbolic zero-shot sim2real image translation framework that represents realism as structured knowledge. OGD decomposes realism into an ontology of interpretable traits -- such as lighting and material properties -- and encodes their relationships in a knowledge graph. From a synthetic image, OGD infers trait activations and uses a graph neural network to produce a global embedding. In parallel, a symbolic planner uses the ontology traits to compute a consistent sequence of visual edits needed to narrow the realism gap. The graph embedding conditions a pretrained instruction-guided diffusion model via cross-attention, while the planned edits are converted into a structured instruction prompt. Across benchmarks, our graph-based embeddings better distinguish real from synthetic imagery than baselines, and OGD outperforms state-of-the-art diffusion methods in sim2real image translations. Overall, OGD shows that explicitly encoding realism structure enables interpretable, data-efficient, and generalisable zero-shot sim2real transfer.

Translating MRI to PET through Conditional Diffusion Models with Enhanced Pathology Awareness

Positron emission tomography (PET) is a widely recognized technique for diagnosing neurodegenerative diseases, offering critical functional insights. However, its high costs and radiation exposure hinder its widespread use. In contrast, magnetic resonance imaging (MRI) does not involve such limitations. While MRI also detects neurodegenerative changes, it is less sensitive for diagnosis compared to PET. To overcome such limitations, one approach is to generate synthetic PET from MRI. Recent advances in generative models have paved the way for cross-modality medical image translation; however, existing methods largely emphasize structural preservation while neglecting the critical need for pathology awareness. To address this gap, we propose PASTA, a novel image translation framework built on conditional diffusion models with enhanced pathology awareness. PASTA surpasses state-of-the-art methods by preserving both structural and pathological details through its highly interactive dual-arm architecture and multi-modal condition integration. Additionally, we introduce a novel cycle exchange consistency and volumetric generation strategy that significantly enhances PASTA's ability to produce high-quality 3D PET images. Our qualitative and quantitative results demonstrate the high quality and pathology awareness of the synthesized PET scans. For Alzheimer's diagnosis, the performance of these synthesized scans improves over MRI by 4%, almost reaching the performance of actual PET. Our code is available at https://github.com/ai-med/PASTA.

A Unified Platform and Quality Assurance Framework for 3D Ultrasound Reconstruction with Robotic, Optical, and Electromagnetic Tracking

Three-dimensional (3D) Ultrasound (US) can facilitate diagnosis, treatment planning, and image-guided therapy. However, current studies rarely provide a comprehensive evaluation of volumetric accuracy and reproducibility, highlighting the need for robust Quality Assurance (QA) frameworks, particularly for tracked 3D US reconstruction using freehand or robotic acquisition. This study presents a QA framework for 3D US reconstruction and a flexible open source platform for tracked US research. A custom phantom containing geometric inclusions with varying symmetry properties enables straightforward evaluation of optical, electromagnetic, and robotic kinematic tracking for 3D US at different scanning speeds and insonation angles. A standardised pipeline performs real-time segmentation and 3D reconstruction of geometric targets (DSC = 0.97, FPS = 46) without GPU acceleration, followed by automated registration and comparison with ground-truth geometries. Applying this framework showed that our robotic 3D US achieves state-of-the-art reconstruction performance (DSC-3D = 0.94 +- 0.01, HD95 = 1.17 +- 0.12), approaching the spatial resolution limit imposed by the transducer. This work establishes a flexible experimental platform and a reproducible validation methodology for 3D US reconstruction. The proposed framework enables robust cross-platform comparisons and improved reporting practices, supporting the safe and effective clinical translation of 3D ultrasound in diagnostic and image-guided therapy applications.

TuLaBM: Tumor-Biased Latent Bridge Matching for Contrast-Enhanced MRI Synthesis

Contrast-enhanced magnetic resonance imaging (CE-MRI) plays a crucial role in brain tumor assessment; however, its acquisition requires gadolinium-based contrast agents (GBCAs), which increase costs and raise safety concerns. Consequently, synthesizing CE-MRI from non-contrast MRI (NC-MRI) has emerged as a promising alternative. Early Generative Adversarial Network (GAN)-based approaches suffered from instability and mode collapse, while diffusion models, despite impressive synthesis quality, remain computationally expensive and often fail to faithfully reproduce critical tumor contrast patterns. To address these limitations, we propose Tumor-Biased Latent Bridge Matching (TuLaBM), which formulates NC-to-CE MRI translation as Brownian bridge transport between source and target distributions in a learned latent space, enabling efficient training and inference. To enhance tumor-region fidelity, we introduce a Tumor-Biased Attention Mechanism (TuBAM) that amplifies tumor-relevant latent features during bridge evolution, along with a boundary-aware loss that constrains tumor interfaces to improve margin sharpness. While bridge matching has been explored for medical image translation in pixel space, our latent formulation substantially reduces computational cost and inference time. Experiments on BraTS2023-GLI (BraSyn) and Cleveland Clinic (in-house) liver MRI dataset show that TuLaBM consistently outperforms state-of-the-art baselines on both whole-image and tumor-region metrics, generalizes effectively to unseen liver MRI data in zero-shot and fine-tuned settings, and achieves inference times under 0.097 seconds per image.

EgoForge: Goal-Directed Egocentric World Simulator

Generative world models have shown promise for simulating dynamic environments, yet egocentric video remains challenging due to rapid viewpoint changes, frequent hand-object interactions, and goal-directed procedures whose evolution depends on latent human intent. Existing approaches either focus on hand-centric instructional synthesis with limited scene evolution, perform static view translation without modeling action dynamics, or rely on dense supervision, such as camera trajectories, long video prefixes, synchronized multicamera capture, etc. In this work, we introduce EgoForge, an egocentric goal-directed world simulator that generates coherent, first-person video rollouts from minimal static inputs: a single egocentric image, a high-level instruction, and an optional auxiliary exocentric view. To improve intent alignment and temporal consistency, we propose VideoDiffusionNFT, a trajectory-level reward-guided refinement that optimizes goal completion, temporal causality, scene consistency, and perceptual fidelity during diffusion sampling. Extensive experiments show EgoForge achieves consistent gains in semantic alignment, geometric stability, and motion fidelity over strong baselines, and robust performance in real-world smart-glasses experiments.