Medical Image Segmentation

INTRODUCTION | Fully supervised 3D segmentation of high-resolution ex vivo MRI is limited by the prohibitive cost of volumetric annotation, forcing reliance on sparse 2D slices. Weakly supervised Sparse-to-Dense frameworks bridge this gap, but guidelines remain ambiguous regarding human-centric visual enhancements and transferring optimization strategies across dimensions. We analyze divergent regularization needs for multi-class segmentation of high-resolution ex vivo spinal cord MRI. METHODS | We used 9.4T MRI of multiple sclerosis spinal cords (>104,000 slices) with sparse annotations (428 slices). A 2D Teacher trained on sparse slices generated dense pseudo-labels to train a 3D Student. We systematically evaluated the impact of human-centric preprocessing, spatial augmentation, and soft-label regularization on both architectures. RESULTS | We identified a critical divergence in training dynamics. The 2D Teacher required strong spatial augmentation and soft-labeling to overcome data scarcity, improving White Matter Lesion Dice scores by >11 points. However, propagating these techniques to the 3D Student degraded its performance. Furthermore, human-centric preprocessing (e.g., CLAHE) disrupted global statistical cues, dropping Gray Matter Lesion Dice scores by ~25 points. DISCUSSION | Our study highlights a perception divergence (human-centric contrast enhancement harms machine models) and a regularization conflict across dimensions. 3D architectures trained on dense pseudo-labels exhibit fundamentally different optimization landscapes than 2D counterparts and require distinct, conservative regularization. Code and models: https://github.com/ivadomed/model_seg_sc-gm-lesion_human_ms_exvivo_t2star.

Semantic segmentation is essential for analysing anatomical features in biomedical research, yet a performance gap remains for Vision Transformers (ViTs) in the field, particularly for sparse, fine-structured, and low signal-to-noise targets. We attribute this challenge in part to the lightweight pixel decoders commonly used in promptable ViT models, who may lack the local inductive bias needed for high-precision biomedical masks. We bridge this gap by introducing ViTC-UNet, which conditions a UNet on frozen pre-trained ViT representations through learnable tokens and a two-way attention decoder. This combines ViT global visual priors with the local inductive bias and high-resolution decoding capacity of UNets, while avoiding end-to-end ViT fine-tuning even in cross-domain settings. ViTC-UNet outperforms baseline results in semantic segmentation tasks across MRI and CT modalities, demonstrating that structure-conditioned UNet decoding can efficiently adapt large-scale visual priors to high-complexity biomedical segmentation.

Unsupervised segmentation of pulmonary pathologies in CT remains an open challenge due to the absence of annotated multi pathology cohorts and the failure of existing diffusion-based methods to exploit the quantitative Hounsfield Unit (HU) signal that physically distinguishes tissue classes. To address this, we propose DiffSegLung,a framework that introduces Diffusion Radiomic Distillation, in which handcrafted radiomic descriptors serve as a physics grounded teacher to shape the bottleneck of a 3D diffusion U-Net via a contrastive objective, transferring pathology discriminative structure into the learned representation without any annotations. At inference, the teacher is discarded and multitimestep bottleneck features are clustered by a Gaussian Mixture Model with HU-guided label assignment, followed by Sobel Diffusion Fusion for boundary refinement. Evaluated on 190 expert annotated axial slices drawn from four heterogeneous CT cohorts, Diff-SegLung improves segmentation across all four pathology classes over unsupervised baselines and improves generation fidelity over prior CT diffusion models.

Accurate medical image segmentation is an integral part of the medical image analysis pipeline that requires the ability to merge local and global information. While vision transformers are able to capture global interactions using vanilla self-attention, their quadratic computational complexity in the input size remains a struggle for medical image segmentation tasks. Motivated by the dispersion property of vanilla self-attention and recent development of Mamba form of attention, Scalable and Efficient Mamba like Attention (SEMA) utilizes token localization via local window attention to avoid dispersion and maintain focusing, complemented by theoretically consistent arithmetic averaging to capture global aspect of attention. In this work, we present USEMA, a hybrid UNet architecture that merges the local feature extraction ability of convolutional neural networks (CNNs) with SEMA attention. We conduct experiments with USEMA across a variety of modalities and image sizes, demonstrating improved computational efficiency compared to transformer based models using full self-attention, and superior segmentation performance relative to purely convolution and Mamba-based models.

Cross-domain few-shot medical image segmentation (CD-FSMIS) requires a model to generalise simultaneously to novel anatomical categories and unseen imaging domains from only a handful of annotated examples. Existing prototypical approaches inevitably entangle anatomical structure with domain-specific appearance variations, and thus lack a stable reference for reliable matching under domain shift. We observe that the geometric structure of human anatomy constitutes a reliable, domain-transferable prior that has been overlooked. Building on this insight, we propose GeoProto, a geometry-aware CD-FSMIS framework that enriches prototypical matching with explicit structural priors. The core component, Geometry-Aware Prototype Enrichment (GAPE), augments each local appearance prototype with a learned geometric offset encoding its ordinal position within the organ's interior topology. This offset is derived from an auxiliary Ordinal Shape Branch (OSB) trained under an ordinally consistent objective that enforces monotonic variation of geometric embeddings across interior strata, requiring no annotation beyond standard segmentation masks. Extensive experiments across seven datasets spanning three evaluation settings (cross-modality, cross-sequence, and cross-context) demonstrate that GeoProto achieves state-of-the-art performance.

Split Federated Learning (SplitFed) combines federated and split learning to preserve privacy while reducing client-side computation. However, in medical image segmentation, heterogeneous label quality across clients can significantly degrade performance. We propose SplitFed-CL, a co-learning framework where a global teacher guides local students to detect and refine unreliable annotations. Reliable labels supervise training directly, while unreliable labels are corrected via weighted student--teacher refinement. SplitFed-CL further incorporates consistency regularization for robustness to input perturbations and a trainable weighting module to balance loss terms adaptively. We also introduce a novel difficulty guided strategy to simulate human like boundary centric annotation errors, where the degree of perturbation is governed by shape complexity and the associated annotation difficulty. Experiments on two multiclass segmentation datasets with controlled synthetic noise, together with a binary segmentation dataset containing real-world annotation errors, demonstrate that SplitFed-CL consistently outperforms seven state-of-the-art baselines, yielding improved segmentation quality and robustness.

Data-driven medical AI is traditionally formulated as a discriminative mapping from input $X$ to output $Y$ via a learned function $f$, which does not generalize well across heterogeneous data and modalities encountered in real-world clinical settings. In this work, we propose a fundamentally different, generative paradigm. We model the joint distribution $P(X,Y)$ using diffusion models and reframe inference as a test-time output optimization problem. By guiding the generative process to match observed inputs, our framework enables flexible, gradient-based conditioning at inference time without architectural changes or retraining, effectively supporting arbitrary and previously unseen combinations of observations. Extensive experiments demonstrate strong performance across standard and cross-modality medical image segmentation, few-shot segmentation with only 2 or 4 training samples, degraded-input segmentation, shape completion from sparse and partial observations, and zero-shot application to demonstrate generality. To support these evaluations, we curated and released a large-scale text-shape dataset derived from MedShapeNet. Our results highlight the versatility of generative joint modeling as a foundation for reusable, task-agnostic medical AI systems.

Medical image segmentation models can perform unevenly across subgroups. Most existing fairness methods focus on improving average subgroup performance, implicitly treating each subgroup as internally homogeneous. However, this can hide difficult cases within a subgroup, where high-loss samples are obscured by the subgroup mean. We call this problem \textbf{intra-group hidden failure}. To solve this, we propose \textbf{DuetFair} mechanism, a dual-axis fairness framework that jointly considers inter-subgroup adaptation and intra-subgroup robustness. Based on DuetFair, we introduce \textbf{FairDRO}, which combines distribution-aware mixture-of-experts (dMoE) with subgroup-conditioned distributionally robust optimization (DRO) loss aggregation. This design allows the model to adapt across subgroups while also reducing hidden failures within each subgroup. We evaluate FairDRO on three medical image segmentation benchmarks with varying degrees of within-group heterogeneity. FairDRO achieves the best equity-scaled performance on Harvard-FairSeg and improves worst-case subgroup performance on HAM10000 under both age- and race-based grouping schemes. On the 3D radiotherapy target cohort, FairDRO further improves worst-group Dice by 3.5 points ($\uparrow 6.0\%$) under the tumor-stage grouping and by 4.1 points ($\uparrow 7.4\%$) under the institution grouping over the strongest baseline.

Medical image segmentation is a critical task in computer-aided diagnosis and treatment planning. However, deep learning models often struggle to generalize across datasets due to domain shifts arising from variations in imaging protocols, scanner types, and patient populations. Traditional domain generalization (DG) methods utilize causal feature learning, adversarial consistency, and style augmentation to improve segmentation robustness. While effective, these approaches rely on explicit feature alignment, adversarial objectives, or handcrafted augmentations, which may not fully exploit the capabilities of foundation models. Recently, the Segment Anything Model (SAM) has demonstrated strong generalization capabilities in segmentation tasks. SAM-based DG methods attempt to improve medical image segmentation. However, these approaches primarily operate in the spatial domain and overlook frequency-based discrepancies that significantly affect model robustness. In this work, we propose Frequency-based Domain Generalization with SAM (FSAM), a novel framework that integrates Low-Rank Adaptation (LoRA) for efficient fine-tuning and a frequency adapter to incorporate frequency-domain representations for single-source domain generalization. FSAM enhances SAM's segmentation robustness by extracting domain-invariant high-frequency features, mitigating frequency-related domain shifts. Experimental results on fundus and prostate datasets demonstrate that FSAM outperforms existing traditional DG and SAM-based DG approaches in domain generalization. Codes and pre-trained models will be made available on GitHub.

Modern computer vision systems increasingly encounter performance limitations in data-scarce domains, where collecting large-scale, high-quality labeled data is costly or impractical. While controllable diffusion models enable scalable synthetic image generation, directly applying synthetic augmentation often leads to unstable performance gains due to dataset-level quality issues and insufficient feedback mechanisms. In this work, we present a Real-Calibrated Synthetic-First Data Engine, a modular data engineering framework that combines controllable diffusion generation and multi-stage curation/filtering within a unified pipeline, with optional support for uncertainty-driven selection and human verification. Instead of introducing new generative algorithms, our approach focuses on systematic dataset construction for improving the practical reliability of synthetic augmentation in low-data regimes. The framework is implemented as a modular CLI-based pipeline, where generation, filtering, selection, and validation components can be independently configured and replaced. This design emphasizes reproducibility, flexibility, and practical deployment in real-world data workflows. Through empirical evaluation centered on human pose estimation, we show that synthetic data improves a real-data baseline when used as near-zero-human-annotation-cost augmentation alongside real anchors, while synthetic-only training remains substantially below real-only performance. Supplementary segmentation diagnostics show the same domain-gap pattern. These results highlight the practical value of data-centric orchestration for low-data augmentation.

Multiple Sclerosis (MS) is a chronic autoimmune disease that can significantly reduce the quality of life of a patient. Existing treatment options can only help slow down the progression of the disease. Therefore, early detection and precise monitoring of disease progression are important. Deep learning offers state-of-the-art models for detecting and segmenting MS lesions in brain MRI scans. However, most of these models are evaluated using the Dice score, without accounting for lesion-wise detection and segmentation performance or other metrics that quantify model performance in cases that are complex or confusing for human annotators, or in cases that are essential for disease detection and progression monitoring. In this paper, we highlight the need to rethink the evaluation of MS lesion segmentation models. In this context, we first present problem fingerprinting in detail to highlight what neurologists look for in brain MRI scans for MS detection and progression monitoring, and which metrics are required to properly quantify model performance in these contexts. Additionally, we present an analysis of state-of-the-art models on two open-source datasets using these metrics to highlight their usability for real-world deployment in hospitals.

While U-Net architectures remain the gold standard for medical image segmentation, their deployment in resource-constrained environments demands aggressive model compression. However, finding an optimally efficient configuration is computationally prohibitive, typically requiring exhaustive train-and-evaluate cycles to find the smallest model that maintains peak performance. In this paper, we introduce a training-free selection framework to automatically identify ultralightweight, dataset-specific U-Net configurations directly at initialization. We observe that systematically scaling down U-Net channel width induces a sharp transition from a stable performance plateau to representational capacity collapse. To pinpoint this boundary without training, we propose a Jacobian-based sensitivity metric that scores discrete, width-capped U-Net variants using a small set of unlabeled images. By analyzing the total variation of this sensitivity curve, we isolate the smallest stable configuration, which we denote as XTinyU-Net. Evaluated across six diverse medical datasets within the nnU-Net framework, XTinyU-Net achieves segmentation accuracy comparable to the heavy nnU-Net baseline with 400x-1600x fewer parameters, and outperforms contemporary lightweight architectures while utilizing 5x-72x fewer parameters. Code is publicly accessible on https://github.com/alvinkimbowa/nntinyunet.git.

Accurate skin lesion segmentation is vital for dermoscopic Computer-Aided Diagnosis. However, visual ambiguity and morphological irregularity often defeat spatial modeling, necessitating multi-domain architectures. Existing paradigms frequently overlook the active use of prediction uncertainty, leading to deterministic frameworks that suffer from blind cross-domain fusion and overfit to label noise. To address these issues, we propose the Uncertainty-Guided Dual-Domain Network (UGDD-Net). UGDD-Net introduces a novel "Glance-and-Gaze" mechanism to transform uncertainty into an active guiding signal. Specifically, the Uncertainty-Guided Bi-directional Feature Fusion (UGBFF) module uses pixel-level uncertainty to modulate spatial-spectral interactions. The Uncertainty-Guided Graph Refinement (UGGR) module constructs a topology-aware graph to propagate reliable semantic consensus and refine uncertain nodes. Finally, the Uncertainty-Guided Margin-Adaptive Loss (UGML) enforces strict constraints on confident pixels while relaxing penalties on uncertain ones to improve statistical calibration. Extensive experiments on ISIC2017, ISIC2018, PH2, and HAM10000 datasets demonstrate that UGDD-Net achieves state-of-the-art performance, especially on "Hard Samples". Our uncertainty maps align with expert inter-observer variability, providing robust interpretability for human-machine collaborative diagnosis.

Segmentation is a fundamental vision task underlying numerous downstream applications. Recent promptable segmentation models, such as Segment Anything Model 3 (SAM3), extend segmentation from category-agnostic mask prediction to concept-guided localization conditioned on high-level textual prompts. However, existing benchmarks primarily evaluate mask accuracy or object presence, leaving unclear whether these models faithfully ground the queried concept or instead rely on visually salient but semantically misleading cues. We introduce CAFE: \textbf{C}ounterfactual \textbf{A}ttribute \textbf{F}actuality \textbf{E}valuation, a novel benchmark for evaluating concept-faithful segmentation in promptable segmentation models. Our \textbf{CAFE} is built on attribute-level counterfactual manipulation: the target region and ground-truth mask are preserved, while attributes such as surface appearance, context, or material composition are modified to introduce misleading semantic cues. The benchmark contains 2,146 paired test samples, each consisting of a target image, a ground-truth mask, a positive prompt, and a misleading negative prompt. These samples cover three counterfactual categories: Superficial Mimicry (\textbf{SM}), Context Conflict (\textbf{CC}), and Ontological Conflict (\textbf{OC}). We evaluate various model types and sizes on our CAFE. Experiments reveal a systematic gap between localization quality and concept discrimination: models often generate accurate masks even for misleading prompts, suggesting that strong mask prediction does not necessarily imply faithful semantic grounding. Our CAFE provides a controlled benchmark for diagnosing whether promptable segmentation models perform concept-faithful grounding rather than shortcut-driven mask retrieval.

Purpose: To develop and evaluate cross-sequence transfer learning for automatic femoral cartilage segmentation, testing bidirectional transfer between dual-echo steady-state (DESS) and sagittal proton density-weighted 3D fast spin-echo (Cube) sequences. Materials and Methods: We optimized a modified 2D U-Net on 507 DESS images from the Osteoarthritis Initiative (OAI). We then established same-sequence baselines using subject-level cross-validation on a subset of 44 OAI DESS images and 44 Cube images acquired at the Istituto Ortopedico Rizzoli, Bologna, Italy. Each subset included 22 non-lesioned and 22 lesioned subjects. Finally, we performed transfer learning across sequences by fine-tuning the pretrained models on the target sequence with increasing training set sizes to study convergence, while keeping validation and test sets fixed. Segmentations were evaluated using Dice similarity coefficient (DSC) and average surface distance (ASD). Lesion effects were assessed with two-sided Mann-Whitney U tests with Bonferroni correction. Results: Same-sequence training yielded higher accuracy on DESS than Cube (DSC, $0.900$ vs $0.830$; $P < .001$). Cube-to-DESS transfer matched DESS performance (DSC, $0.903 \pm 0.032$ vs $0.900 \pm 0.027$), reaching a performance plateau at 9 training subjects. DESS-to-Cube yielded a lower combined DSC ($0.802 \pm 0.049$ vs $0.830 \pm 0.042$), reaching a plateau at 24 training subjects. Lesions did not affect DESS ($P \ge .39$) but reduced Cube accuracy (DSC, $0.805$ vs $0.856$; $P < .001$). Conclusion: Transfer learning across sequences can substantially reduce target-sequence annotation requirements for femoral cartilage segmentation, but performance is direction- and sequence-dependent, and the effects of lesions on segmentation may vary across MRI sequences.

Open-vocabulary semantic segmentation requires adapting image-level vision-language models such as CLIP to dense pixel-level prediction, which is challenging due to the mismatch between hierarchical structure and semantic alignment in the embedding space. While recent works leverage hyperbolic geometry to model hierarchical relationships, they align embeddings across hierarchical levels but overlook semantic misalignment among embeddings within the same level. In this work, we propose HyRo, a hyperbolic fine-tuning framework that decouples hierarchical and semantic alignment in the Poincaré ball model. HyRo aligns hierarchical levels by adjusting the hyperbolic radius and refines semantic relationships through angular alignment using an orthogonal transformation that theoretically preserves the hyperbolic radius. Experiments on standard open-vocabulary semantic segmentation benchmarks demonstrate that HyRo achieves state-of-the-art performance over prior methods.

Uncertainty quantification complements model predictions by characterizing their reliability, which is essential for high-stakes decision making such as medical image segmentation. However, most existing methods reduce uncertainty to a scalar confidence estimate, leaving its spatial distribution semantically underconstrained. In this work, we focus on uncertainty interpretability, namely, whether estimated uncertainty behaves in a human-understandable manner with respect to sources of ambiguity. We identify three perception-aligned principles requiring the spatial distribution of uncertainty to reflect: (1) image contrast between structures, (2) severity of image corruption, and (3) geometric complexity in anatomical structures. Accordingly, we develop a principle-guided uncertainty supervision framework (PriUS) based on evidential learning, in which the corresponding supervision objectives are explicitly enforced during training. We further introduce quantitative metrics to measure the consistency between predicted uncertainty and image attributes that induce ambiguity. Experiments on ACDC, ISIC, and WHS datasets showed that, compared with state-of-the-art methods, PriUS produced more consistent uncertainty estimates while maintaining competitive segmentation performance.

Multiple sclerosis (MS) expresses substantial clinical and radiological heterogeneity, which poses significant challenges for automatic lesion segmentation. The current deep learning-based SOTA is highly susceptible to changes in both distribution, e.g., changes in scanner; as well as the structure of inputs, evident in the current divide between cross-sectional and longitudinal approaches. We introduce TimeLesSeg, a unified contrast-agnostic framework designed to segment MS lesions regardless of the presence of a temporal dimension in its inputs, with a single convolutional neural network. Our approach models pathological priors through lesion masks, which are processed together with the current scan. Cross-sectional processing is enabled by exposing the model to training cases where no prior information is available, which are modeled with an empty mask, allowing it to operate seamlessly in both scenarios. To overcome the scarcity and inconsistency of longitudinal datasets, we propose a novel generative pipeline in which patterns of lesion evolution are simulated by stochastically deforming each individual lesion with morphological operations, producing realistic prior timepoints. In parallel, we achieve contrast agnosticism through Gaussian mixture model-based domain randomization, enabling the network to experience a wide spectrum of intensity profiles. Results on three publicly available and two in-house datasets show that TimeLesSeg outperforms the contrast-agnostic state of the art on single-modality inputs across overlap- and distance-based metrics. In longitudinal processing, our method outperforms SAMSEG, and captures lesion load dynamics more accurately than both the former and LST-AI. All source code related to the development of TimeLesSeg is available at https://github.com/NeuroADaS-Lab/TimeLesSeg.

Non-alcoholic fatty pancreas disease (NAFPD) is an underdiagnosed condition associated with metabolic syndrome, insulin resistance, and increased risk of pancreatic cancer. Diagnosis typically relies on subjective visual assessment of ultrasound images by clinicians. We propose an end-to-end framework for automatically classifying normal versus fatty pancreas from abdominal ultrasound images. Our method employs a TransUNet-based segmentation architecture with a ResNet encoder and transformer bottleneck to delineate the pancreas and the splenic vein, followed by anatomically-guided patch extraction and patient-level classification through pairwise texture comparison. The feature engineering mimics clinical reasoning by comparing the echogenicity of peri-venous fat to the pancreatic parenchyma, providing an interpretable signal for classification. The segmentation models are initialized via domain-specific transfer learning from a liver segmentation task. We validate the full pipeline on a clinical dataset of 214 abdominal ultrasound images with 107 expert-labeled cases using 5-fold cross-validation. SVM with RBF kernel achieves a mean cross-validated accuracy of 89.7%,$\pm$,1.8% and F1 of 0.898,$\pm$,0.019, while the unsupervised K-Means baseline reaches 87.8% accuracy, demonstrating that the proposed features capture the relevant clinical signal even without labeled training data. To our knowledge, this is the first end-to-end automated framework for fatty pancreas classification from ultrasound using segmentation-guided texture analysis.

Semantic segmentation of large-scale 3D point clouds is crucial for applications such as autonomous driving and urban digital twins. However, the sparse sampling pattern of LiDAR and the view-dependent geometric distortion in image observations complicate cross-modal alignment and hinder stable fusion. Inspired by the fact that 2D images captured by cameras are representations of the 3D world, we recognize that the features learned from 2D and 3D segmentation share some common semantics, while other aspects remain modality-specific. This insight motivates a unified multimodal framework for joint 2D-3D semantic segmentation. We combine a SAM-based vision encoder with a SPTNet-based geometric encoder to extract complementary semantic and geometric representations. The resulting features from both modalities are explicitly decomposed into shared and private subspaces, where the shared components summarize semantic factors common to both domains, and the private components preserve properties that are unique to each modality. A lightweight attention-based fusion module aggregates the shared features into a consistent cross-modal representation, and a regularized training objective ensures both semantic alignment and subspace independence. Experiments on the SemanticKITTI and nuScenes benchmarks demonstrate consistent improvements in segmentation accuracy over representative multimodal baselines, accompanied by competitive computational efficiency. Cross-domain evaluation on nuScenes USA-Singapore shows stable performance under distribution shifts, demonstrating strong generalization. The implementation code is publicly available at: https://github.com/shuaizhang69/UniD-Shift.

Adapting foundation models to medical segmentation typically requires either backbone fine-tuning or high-capacity task-specific decoders, both of which are difficult to fit reliably when annotations are scarce. We show that frozen DINOv3 features already contain useful structural and boundary cues for medical segmentation, and that the main bottleneck lies in how these features are read out. We propose DINO-MVR, a Multi-View Readout framework for annotation-efficient medical segmentation. DINO-MVR trains only lightweight MLP probes on features from the final three transformer blocks of a frozen DINOv3 backbone, without updating the backbone itself. At inference, each input is interpreted through complementary resolutions and test-time augmentations, whose probability maps are combined by entropy-weighted fusion and refined with simple spatial regularization. For volumetric inputs, Gaussian z-axis smoothing further improves inter-slice consistency. Under fixed evaluation protocols on endoscopy, dermoscopy, and MRI benchmarks, DINO-MVR achieves strong readout-only performance, including 0.895 Dice on Kvasir-SEG, 0.897 Dice on ISIC 2018, and 0.908 Dice on BraTS FLAIR whole-tumor segmentation. With only five annotated BraTS patients, it recovers 98.4% of the performance obtained by the 40-patient BraTS reference run. These results suggest that frozen self-supervised vision backbones can support accurate medical segmentation when paired with an effective multi-view readout.

Recent advances in learned image compression (LIC) have enabled practical deployments, spurring active research into image compression for machines and progressive coding schemes. However, their integration remains under-explored: prior works on progressive machine codec predominantly target sample-level difficulty adaptation (i.e., easy-to-hard), without considering semantic-level scalability. In this work, we introduce a semantic hierarchy-aware progressive codec that enables semantic scalability (i.e., coarse-to-fine) from a single bitstream. We first systematically categorize ImageNet-1K classes into CLIP embedding-based semantic hierarchies. Based on a channel-wise autoregressive framework, we decompose latent representations into hierarchically ordered channel blocks, each explicitly optimized for a corresponding semantic hierarchy. Extensive experiments demonstrate that our approach substantially improves coarse-level recognition at low bitrates while maintaining fine-grained accuracy at higher bitrates. By reframing progressive transmission through the lens of semantic scalability, our work provides an efficient and interpretable solution for task-adaptive image coding, outperforming existing progressive codecs under hierarchical evaluation.

Deep learning-based organs/structures-at-risk(OARs) auto-contouring models can improve radiotherapy workflows, but models trained on adult data often underperform in pediatric patients. Developing robust pediatric-specific models is hindered by data scarcity and fragmentation across centers. Federated learning (FL) enables privacy-preserving collaborative training without the need for data sharing. We evaluated the feasibility and performance of FL for developing pediatric-specific OAR segmentation models across two European medical centers. Computed tomography (CT) images from pediatric patients from Utrecht and Heidelberg with a renal tumor or abdominal neuroblastoma were retrospectively collected and locally processed. An nnU-Net-based framework segmented 19 OARs using local and FL schemes. FL was implemented with secure weight exchange on a cloud storage across institutional firewalls. Performance was assessed using the Dice similarity coefficient (DSC), 95th percentile Hausdorff distance, and mean surface distance. Robustness to patient orientation, false-positive segmentation of surgically removed kidneys, and failure cases were identified. A total of 310 postoperative CTs from 272 patients (105 renal tumors, 167 neuroblastomas) were included. Local models performed well on their respective center data but showed significantly reduced cross-center performance for four to seven of the nine evaluated OARs (DSC). In contrast, the FL model matched local performance for at least seven of nine OARs and achieved the best cross-center results across three metrics, with DSC gains of 0.003-0.007 over local models. FL also maintained stable performance across patient orientations and reduced false-positive kidney segmentations. Real-world FL improves cross-center robustness of CT-based OAR segmentation models in pediatric upper abdominal tumors.

Semantic segmentation is a core component of discourse analysis, yet existing models are primarily developed and evaluated on high-resource written text, limiting their effectiveness on low-resource spoken varieties. In particular, dialectal Arabic exhibits informal syntax, code-switching, and weakly marked discourse structure that challenge standard segmentation approaches. In this paper, we introduce a new multi-genre benchmark (more than 1000 samples) for semantic segmentation in conversational Arabic, focusing on dialectal discourse. The benchmark covers transcribed casual telephone conversations, code-switched podcasts, broadcast news, and expressive dialogue from novels, and was annotated and validated by native Arabic annotators. Using this benchmark, we show that segmentation models performing well on MSA news genres degrade on dialectal transcribed speech. We further propose a segmentation model that targets local semantic coherence and robustness to discourse discontinuities, consistently outperforming strong baselines on dialectal non-news genres. The benchmark and approach generalize to other low-resource spoken languages.

Curating fully annotated datasets for medical image segmentation is labour-intensive and expertise-demanding. To alleviate this problem, prior studies have explored scribble annotations for weakly supervised segmentation. Existing solutions mainly compute losses on annotated areas and generate pseudo labels by propagating annotations to adjacent regions. However, these methods often suffer from inaccurate and unrealistic segmentations due to insufficient supervision and incomplete shape information. In contrast, we first investigate the principle of good scribble annotations, which leads to efficient scribble forms via supervision maximization and randomness simulation. We further introduce regularization terms to encode the spatial relationship and the shape constraints, where the EM algorithm is utilized to estimate the mixture ratios of label classes. These ratios are critical in identifying the unlabeled pixels for each class and correcting erroneous predictions, thus the accurate estimation lays the foundation for the incorporation of spatial prior. Finally, we integrate the efficient scribble supervision with the prior into a framework, referred to as ZScribbleSeg, and apply it to multiple scenarios. Leveraging only scribble annotations, ZScribbleSeg achieves competitive performance on six segmentation tasks including ACDC, MSCMRseg, BTCV, MyoPS, Decathlon-BrainTumor and Decathlon-Prostate. Our code will be released via https://github.com/DLwbm123/ZScribbleSeg.

Continual learning (CL) is essential for deploying medical image segmentation models in clinical environments where imaging domains, anatomical targets, and diagnostic tasks evolve over time. However, continual segmentation still faces three main challenges. First, the scenarios for this task remain insufficiently standardized for real-world clinical settings. Second, existing research has been primarily focused on mitigating forgetting, overlooking the other essential properties such as plasticity. Third, a benchmark work with comprehensive evaluation on existing methods is stll desirable. To address these gaps, we present such benchmark study of continual medical image segmentation. We first define three clinically motivated scenarios, namely Domain-CL, Class-CL, and Organ-CL, to respectively capture the cross-center domain shift, the incremental anatomical structure segmentation, and the cross-organ segmentation. We then introduce an evaluation framework that measures not only general performance and forgetting, but also plasticity, forward generalizability, parameter efficiency, and replay burden. The results, from extensive experiments with representative CL methods, showed that it was still challenging to develop a model that could satisfy all the requirements simultaneously. Nevertheless, these studies also suggested that the replay-based methods achieve the best overall balance between stability and plasticity, the parameter-isolation methods should be effective at reducing forgetting, though at the cost of increased model size, and the forward generalizability remain a significantly understudied aspect of this research field. Finally, we discuss related learning paradigms and outline future directions for continual medical image segmentation.

Segment Anything Model 2 (SAM2) demonstrated impressive zero-shot capabilities on natural images but faces challenges in biomedical segmentation due to significant domain shifts and prompt dependency. To address these limitations, we propose a prompt-free, parameter-efficient fine-tuning framework designed for multi-class segmentation on variable-sized inputs. We introduce a convolutional Positional Encoding Generator to adapt effectively to arbitrary aspect ratios and present a dual-adapter strategy: High-Performance Adapter utilizing deformable convolutions for precise boundary modeling and Lightweight Adapter employing structural re-parameterization to minimize inference latency. Experiments on ISBI 2012, Kvasir-SEG, Synapse, and ACDC datasets demonstrate that our approach significantly outperforms strong adaptation baselines. Specifically, our method improved segmentation accuracy by up to 19.66% over the vanilla SAM2, while reducing computational costs by approximately 87% compared to heavyweight medical SAM adaptations, establishing a superior trade-off between accuracy and efficiency.

We report the design and results of the third autoPET challenge (MICCAI 2024), which benchmarked automated lesion segmentation in whole-body PET/CT under a compositional generalization setting. Training data comprised 1,014 [18F]-FDG PET/CT studies from the University Hospital Tübingen and 597 [18F]/[68Ga]-PSMA PET/CT studies from the LMU University Hospital Munich, constituting the largest publicly available annotated PSMA PET/CT dataset to date. The held-out test set of 200 studies covered four tracer-center combinations, two of which represented unseen compositional pairings. A complementary data-centric award category isolated the contribution of data handling strategies by restricting participants to a fixed baseline model. Seventeen teams submitted 27 algorithms, predominantly nnU-Net-based 3D networks with PET/CT channel concatenation. The top-ranked algorithm achieved a mean DSC of 0.66, FNV of 3.18 mL, and FPV of 2.78 mL across all four test conditions, improving DSC by 8% and reducing the false-negative volume by 5 mL relative to the provided baseline. Ranking was stable across bootstrap resampling and alternative ranking schemes for the top tier. Beyond the benchmark, we provide an in-depth analysis of segmentation performance at the patient and lesion level. Three main conclusions can be drawn: (1) in-domain multitracer PET/CT segmentation is sufficient and probably approaching reader agreement; (2) compositional generalization to unseen tracer-center combinations remains an open problem mainly driven by systematic volume overestimation; (3) heterogeneity and case difficulty drive performance variation substantially more than the choice of algorithm among top-ranked teams.

Rheumatoid arthritis (RA) assessment from hand radiographs requires multi-level analysis and modeling of anatomical structures and fine-grained local pathological changes. However, existing public resources do not support such unified multi-level analysis, often lacking full-hand coverage, fine-grained annotations, and consistent integration with clinical scoring systems. In particular, annotations that enable quantitative analysis of bone erosion (BE) remain scarce. RAM-H1200 contains 1,200 hand radiographs collected from six medical centers, with multi-level annotations including (i) whole-hand bone structure instance segmentation, (ii) pixel-level BE masks, (iii) SvdH-defined joint regions of interest, and (iv) joint-level SvdH scores for both BE and joint space narrowing (JSN). It is designed to evaluate whether models can jointly capture anatomical structure, localized erosive pathology, and clinically standardized RA severity from hand radiographs. The proposed BE masks enable, for the first time, quantitative BE analysis beyond coarse categorical grading by providing explicit spatial supervision for lesion extent and morphology. To our knowledge, RAM-H1200 is the first public large-scale benchmark that jointly supports whole-hand bone structure instance segmentation, pixel-level BE delineation, and clinically grounded joint-level SvdH scoring for both BE and JSN. Results across benchmark tasks show that anatomical modeling is substantially more mature than quantitative BE analysis: whole-hand bone segmentation achieves strong performance, whereas BE segmentation remains a major open challenge. By unifying anatomical structure modeling, quantitative lesion analysis, and clinically grounded SvdH scoring, RAM-H1200 provides a single benchmark for comprehensive RA analysis on hand radiographs.

Although self-supervised pretraining is expected to learn broadly transferable representations, its effectiveness across imaging modalities substantially different from the pretraining domain, and on complex tumor-segmentation tasks, remains understudied. Evaluating CT-pretrained transformers on MRI rectal cancer segmentation, we identified two interacting failure modes in CT-to-MRI transfer: (a) inefficient token usage caused by zero-padding to match pretrained input dimensions, and (b) ineffective feature adaptation. We investigated these vulnerabilities using two primary CT-pretrained hierarchical shifted-window transformer backbones, SMIT and Swin UNETR, together with VoCo as a large-scale-pretrained supporting benchmark; these models differ in pretraining objectives and datasets. Mechanistic analysis leveraged an attention dilution index (ADI), an entropy-based metric quantifying attention diverted toward uninformative padding tokens, and centered kernel alignment (CKA) to measure feature reuse during MRI adaptation. ADI increased with zero-padding, while high feature reuse did not necessarily translate to improved downstream accuracy. To mitigate these issues, we introduced two interventions: a tumor-aware augmentation strategy to expand tumor appearance heterogeneity coverage, and an anisotropic cropping strategy to restore token efficiency. Fine-tuning with these strategies on identical rectal MRI datasets yielded detection rates of 91.1% (225/247) and 88.7% (219/247) for the primary SMIT and Swin UNETR backbones, with the supporting VoCo benchmark reaching 90.3% (223/247), demonstrating significantly improved robustness under CT-to-MRI transfer. This study is among the first to examine when pretrained transformers fail to transfer across imaging modalities and demonstrates how targeted mitigation strategies can systematically overcome cross-modality transfer limitations.

Accurate analysis of histopathological images is critical for disease diagnosis and treatment planning. Whole-slide images (WSIs), which digitize tissue specimens at gigapixel resolution, are fundamental to this process but require aggregating thousands of patches for slide-level predictions. Multiple Instance Learning (MIL) tackles this challenge with a two-stage paradigm, decoupling tile-level embedding and slide-level prediction. However, most existing methods implicitly embed patch representations in homogeneous Euclidean spaces, overlooking the hierarchical organization and regional heterogeneity of pathological tissues. This limits current models' ability to capture global tissue architecture and fine-grained cellular morphology. To address this limitation, we introduce a hybrid hyperbolic-Euclidean representation that embeds WSI features in dual geometric spaces, enabling complementary modeling of hierarchical tissue structures and local morphological details. Building on this formulation, we develop BatMIL, a WSI classification framework that leverages both geometric spaces. To model long-range dependencies among thousands of patches, we employ a structured state space sequence model (S4) backbone that encodes patch sequences with linear computational complexity. Furthermore, to account for regional heterogeneity, we introduce a chunk-level mixture-of-experts (MoE) module that groups patches into regions and dynamically routes them to specialized subnetworks, improving representational capacity while reducing redundant computation. Extensive experiments on seven WSI datasets spanning six cancer types demonstrate that BatMIL consistently outperforms state-of-the-art MIL approaches in slide-level classification tasks. These results indicate that geometry-aware representation learning offers a promising direction for next-generation computational pathology.

Multi-rater medical image segmentation captures the inherent ambiguity of clinical interpretation, where diagnostic boundaries vary across experts and imaging devices. Existing approaches often reduce this diversity to consensus labels or treat rater differences as noise, resulting in overconfident and poorly calibrated models. We propose a harmonized probabilistic framework that disentangles acquisition artifacts from genuine annotator variability through adaptive feature conditioning and frequency-domain personalization. A lightweight Harmonizer Network implicitly models scanner-specific artifacts and performs dynamic feature modulation to standardize latent representations, ensuring that uncertainty reflects anatomy rather than noise. To represent rater-specific styles, we introduce a novel High-Frequency Prompt Modules that operate in the spectral domain to encode annotator-dependent boundary precision and textural sensitivity. These prompts adaptively modulate harmonized features to produce personalized yet anatomically consistent segmentations. Furthermore, a Generalized Energy Distance based regularization aligns the generative distribution with empirical annotation variability, promoting diversity where experts disagree and consensus where they converge. Experiments on LIDC-IDRI and NPC-170 show SOTA aggregated and individualized segmentation, with notable GED reductions and improved Dice scores, especially on noisy cases. Beyond accuracy, the model exhibits clinically meaningful uncertainty. Confidence rises in agreement regions and declines in ambiguous areas, supporting its use as a reliable and interpretable tool for multi-expert clinical workflows.

Weakly Supervised Semantic Segmentation (WSSS) with image-level labels typically leverages Class Activation Maps (CAMs) to achieve pixel-level predictions. Recently, Contrastive Language-Image Pre-training (CLIP) has been introduced to generate CAMs in WSSS. However, previous WSSS methods solely adopt CLIP's vision-language paired property for dense localization, neglecting its inherently limited dense knowledge across both visual and text modalities, which renders CAM generation suboptimal. In this work, we propose DiCLIP, a novel WSSS framework that leverages the generative diffusion model to enhance CLIP's dense knowledge across two modalities. Specifically, Visual Correlation Enhancement (VCE) and Text Semantic Augmentation (TSA) modules are proposed for dense prediction enhancement. To improve the spatial awareness of visual features, our VCE module utilizes diffusion's reliable spatial consistency to mitigate the over-smoothing issue in CLIP's attention. It designs the Attention Clustering Refinement (ACR) module to reliably extract diverse correlation maps from the diffusion model. The correlation maps act as a diversity bias for CLIP's self-attention, recursively pushing its visual features towards a more discriminative dense distribution. To augment the semantics of text embeddings, our TSA module argues that a single text modality is insufficient to encompass the variability of visual categories. Thus, we leverage diffusion's generative power to maintain a dynamic key-value cache model, shifting CAM generation from a patch-text matching mechanism to a novel visual knowledge retrieval paradigm. With these enhancements, DiCLIP not only outperforms state-of-the-art methods on PASCAL VOC and MS COCO but also significantly reduces training costs. Code is publicly available at https://github.com/zwyang6/DiCLIP.

Attacking semantic segmentation models is significantly harder than image classification models because an attacker must flip thousands of pixel predictions simultaneously. Standard pixel-wise cross-entropy (CE) is ill-suited to this setting: it tends to overemphasize already-misclassified pixels, which slows optimization and overstates model robustness. To address these issues, we introduce TsallisPGD, an adversarial attack built on the Tsallis cross-entropy, a generalization of CE parameterized by $q$, which adaptively reshapes the gradient landscape by controlling gradient concentration across pixels. By varying $q$, we steer the attack toward pixels at different confidence levels. We first show that no single fixed-$q$ is universally optimal, as its effectiveness depends on the dataset, model architecture, and perturbation budget. Motivated by this, we propose a dynamic $q$-schedule that sweeps $q$ during optimization. Extensive experiments on Cityscapes, Pascal VOC, and ADE20K show that TsallisPGD, using a single validation-selected schedule, achieves the best average attack rank across all evaluated settings and improves over CEPGD, SegPGD, CosPGD, JSPGD, and MaskedPGD in reducing accuracy and mIoU on both standard and robust models.

Anatomical mesh segmentation requires models that operate directly on irregular surface geometry while remaining robust to arbitrary patient pose and mesh resolution variation. Existing task-specific mesh and point-cloud methods are not equivariant, and can degrade sharply under test-time perturbation, for example dropping by 25-26 IoU points on intraoral scan segmentation at $40^\circ$ tilt. We present EAMS, an Equivariant Anatomical Mesh Segmentor built on Equivariant Mesh Neural Networks (EMNN), and evaluate it across four clinically distinct tasks spanning edge-, vertex-, and face-level supervision. We combine intrinsic mesh descriptors with anatomy-aware priors, including PCA-derived frames for dental arches and liver surfaces, and augment message passing to provide lightweight global context. Across intracranial aneurysm and intraoral segmentation, EAMS variants are competitive with specialized baselines on unperturbed inputs while remaining stable under geometric perturbations, and on liver surfaces they expose a favorable trade-off between canonical-pose accuracy and rotation robustness. These results show that a lightweight ($<2$M parameters) equivariant framework can deliver robust anatomical mesh segmentation across diverse supervision types without task-specific architectures.

Deep learning-based medical image segmentation is increasingly used to support clinical diagnosis and develop new treatment strategies. However, model performance remains limited by the scarcity of high-quality annotated data and insufficient generalization across imaging protocols. This limitation is particularly evident in MRI and CT, where models are typically trained on a single acquisition sequence and exhibit reduced robustness when applied to unseen sequences or contrasts. Although data augmentation is widely used to improve general robustness on medical images, its impact on cross-modality generalization has not been quantitatively explored. In this work, we study a targeted set of data augmentation techniques designed to improve cross-modality transfer. We train three spine segmentation models, each on a single-modality/sequence dataset, and evaluate them across seven out-of-distribution datasets (spanning CT and MRI), reflecting a realistic single-sequence training and multi-sequence/contrast/modality deployment scenario. Our results demonstrate substantial performance gains on unseen domains (average Dice gain of 155 %) while preserving in-domain accuracy (average Dice decrease of 0.008 %), including effective transfer between CT and MRI. To mitigate the computational cost typically associated with strong data augmentation, we implement GPU-optimized augmentations that maintain, and even improve, training efficiency by approximately 10 %. We release our approach as an open-source toolbox, enabling seamless integration into commonly used frameworks such as nnUNet and MONAI. These augmentations significantly enhance robustness to heterogeneous clinical imaging scenarios without compromising training speed.

Medical experts often manually segment images to obtain diagnostic statistics and discard the resulting annotations. We aim to train segmentation models to alleviate this burden, but constrained to the retained summary statistics (e.g., the area of the annotated region). Empirical results suggest that statistics alone are insufficient for this task, but adding weak information in the form of a few pixels within the area of interest significantly improves performance. We use a novel loss function that combines terms for image reconstruction quality, matching to summary statistics, and overlap between the predicted foreground and the weak supervisory signal. Experiments on standard image, ultrasound (breast cancer), and Computed Tomography (CT) scan (kidney tumors) data demonstrate the utility and potential of the approach.

Organoids are complex, three dimensional, self-organizing cell cultures which manifest organ-like features and represent a powerful platform for studying human disease and developing treatment options. Organoid development is characterized by dynamic morphological and cellular organization, which mimic some aspects of organ development. To study these rapid changes over the course of organoid development, advanced imaging and analytical tools are critical to accurately monitor the trajectory of organoid growth and investigate disease processes. In this work, we focus on computer vision and machine learning techniques to automatically measure the size and shape of developing spheroids derived from pluripotent stem cells (iPSCs), which are typically the starting material for generating organoid cultures. To facilitate this task, we introduce a composite method that combines the Segment Anything Model (SAM), a general-purpose foundation model, with an existing domain-specific tool. This composite method is evaluated together with several existing tools by testing them on organoid image data and comparing with the results of manual image segmentation. We find that no single existing tool is able to segment the test images with sufficient accuracy across all test conditions, but the newly introduced composite method produces consistent and accurate results for all but a very small fraction of the most challenging images. Finally, we compare the accuracy of this method to the variability between manual segmentations by independent annotators (inter-observer variability) and find that by one measure it performs at the level of inter-observer variability and by others it performs very close to it.

Federated Learning enables decentralized training by aggregating model updates across clients without sharing raw data, while Split Federated Learning further partitions the model between clients and a server to reduce computation and communication at the client side. However, decentralized medical institutions rarely operate on a single shared task, making standard Federated and SplitFed collaborations poorly aligned with real clinical workflows. Multi-task FL extends these frameworks by allowing clients to handle different tasks, but often introduces instability and privacy vulnerabilities. This study proposes \textbf{MuCALD-SplitFed}, a multi-task SplitFed framework that integrates causal representation learning and latent diffusion. Experiments show MuCALD-SplitFed consistently improves segmentation, while baseline SplitFed fails to converge. The proposed approach further reduces information leakage at split points, mitigating reconstruction-based and membership inference attacks. Additionally, MuCALD SplitFed outperforms state-of-the-art personalized FL and multi-task FL approaches. The code repository is: https://github.com/ChamaniS/MuCALD_SplitFed.

We present FoR-Net, an efficient semantic segmentation framework that focuses on identifying and enhancing hard regions. Instead of relying on heavy global modeling, FoR-Net adopts an efficient strategy that selectively emphasizes informative regions through a learned importance map and a Top-K activation mechanism. Specifically, a selector module predicts region-wise importance, enabling the model to focus on challenging areas such as thin structures and object boundaries. Multi-scale reasoning is achieved using convolutional branches with different receptive fields, allowing diverse spatial context aggregation. We evaluate FoR-Net on the Cityscapes benchmark under limited computational resources. Despite its efficient design and standard training configuration, FoR-Net achieves competitive performance and exhibits improved attention to difficult regions. These results suggest that selective region-focused reasoning can serve as a practical and efficient alternative for semantic segmentation. This work explores region-focused reasoning under resource-constrained settings and provides insights for developing efficient and region-aware segmentation models.

Tumor segmentation in whole-body PET/CT imaging is crucial for precise disease evaluation and treatment planning. However, it remains challenging due to variability in lesion size, contrast, and anatomical distribution. Relying on manual segmentation makes the process time-consuming and prone to intra- and inter-observer variability. This work presents a whole-body tumor segmentation method developed for the AutoPET III challenge, where the goal is to build models that generalize across tracers and multi-center data. We employ the nnU-Net framework with a ResNet-based encoder as our baseline and systematically investigate the impact of training strategies, including intensity normalization, batch dice optimization, and data augmentation using CraveMix. Our experiments show that these strategies significantly influence model performance, particularly in reducing false positives and improving robustness to lesion variability. The best-performing configuration achieves a Dice score of up to 0.80 on the preliminary test phase, and our method ranked third in the AutoPET III challenge. The code is publicly available here.

Objective: Accurate probability estimates are essential for the safe deployment of medical image segmentation models in clinical decision-making. However, modern deep segmentation networks are often poorly calibrated, a problem exacerbated when multiple expert annotations exhibit substantial disagreement. While inter-rater variability is typically treated as noise, it provides valuable information about intrinsic annotation ambiguity that must be reflected in model confidence. Methods: We improve the probabilistic calibration of medical image segmentation models by reformulating multi-rater supervision as an ordinal learning problem. Voxel-wise annotator agreement is treated as an ordered target, linking predictive confidence to the empirical variability in training data. This formulation allows the use of ordinal-aware scoring rules, such as the Ranked Probability Score ordinal loss, combined with a standard binary objective to preserve discriminative performance. Results: We evaluated the proposed approach across four public segmentation benchmarks spanning ophthalmology, histopathology, and thoracic imaging. Calibration was assessed using a multi-rater extension of expected calibration error. Results consistently show that ordinal-aware training yields substantially improved calibration with respect to inter-rater agreement without degrading segmentation accuracy. Conclusions: Treating multi-rater annotations as ordered information provides a principled and architecture-agnostic route to more reliable probabilistic segmentation models.

Synthetic Aperture Radar (SAR) imagery is widely used for flood monitoring due to its all-weather and day-night imaging capability. However, flood mapping using single-polarization SAR data remains challenging in complex environments where surface and volume scattering coexist. In this paper, we investigate the effectiveness of cross-polarization fusion of VV and VH SAR observations for improved flood mapping. A deep learning-based segmentation framework is employed to jointly exploit complementary information from VV and VH polarizations. To ensure a fair evaluation, three configurations are compared under identical training conditions: VV only, VH only, and fused VV-VH input. Performance is assessed using standard flood mapping metrics, including Intersection over Union (IoU) and F1-score, along with qualitative visual analysis. Experimental results demonstrate that VV-VH fusion consistently outperforms single-polarization models, particularly in vegetated and heterogeneous flood regions, leading to more accurate flood boundary delineation. The findings highlight the importance of cross-polarization SAR fusion for enhancing the reliability of SAR-based flood mapping in disaster monitoring applications.

Active learning (AL) has emerged as a crucial strategy for reducing the prohibitive costs associated with medical image segmentation. However, standard uncertainty-based AL methods typically focus on maximizing performance metrics, ignoring performance disparities or fairness across groups with sensitive attributes. While fair active learning has been explored in classification tasks, its intersection with medical image segmentation remains unaddressed. In this work, we introduced a fairness-aware active learning framework with a Weighted Entropy selection strategy that modulates uncertainty based on current group-specific performance estimates on the labeled set. To decouple true epistemic uncertainty from anatomical volume variances, we further utilized a masked, scaled entropy restricted to the region of interest. The framework was evaluated on synthetic T1-weighted brain MRIs with controlled left caudate bias in both strong and weak bias settings. A 3D U-Net was trained to segment the left caudate under several AL strategies, starting from both demographically balanced and strongly imbalanced initial labeled sets. Experiments demonstrated that our method markedly reduces performance disparities between groups compared to random sampling and standard uncertainty sampling. By prioritizing poorly segmented subgroups during the AL cycles, our method consistently achieved the highest equity-scaled performance and reduced the disparity metric by 75% (strong bias) and 86% (weak bias) relative to standard entropy at the final budget. Overall, this work is among the first studies on fair AL for medical image segmentation, offering an efficient strategy to train more equitable models in resource-constrained environments.

We propose a unified cross-domain transfer learning framework that leverages knowledge from multiple heterogeneous medical imaging datasets to improve performance across segmentation, classification, and object detection tasks. Our approach employs a teacher-student paradigm in which a joint teacher model aggregates domain-invariant representations learned from diverse source datasets, while a task-specific student model is trained via multi-level knowledge distillation. Originally developed for medical image segmentation, the framework is extended to support image-level classification and object-level detection, enabling a general multi-task formulation for medical image analysis. We evaluate our method on a broad suite of datasets, including six segmentation benchmarks, BrainMetShare, ISLES, BraTS (MRI) and Lung MSD, LiTS, KiTS (CT), as well as multiple classification datasets for pulmonary disease and dementia, and detection datasets with native bounding-box annotations. Across all tasks and modalities, the proposed approach yields consistent improvements over strong dataset-specific and multi-head baselines, demonstrating enhanced robustness to distributional shifts and superior generalization. These findings highlight the potential of multi-dataset knowledge distillation as a scalable and task-agnostic approach for enhancing segmentation, classification, and object detection performance across heterogeneous medical imaging domains.

Zero-shot vision-language models (VLMs) offer a promptable alternative to task-specific training for gross tumor volume (GTV) delineation in non-small-cell lung cancer (NSCLC), but the prompt dimensions that govern their spatial behavior remain poorly understood. We study this question by probing alignment directions in VoxTell on a held-out internal NSCLC tumor dataset through sub-prompt decomposition into diagnosis, demographic, staging, anatomical, generic, and irrelevant controls; attribute-wise perturbation robustness; specificity ladders; and cross-case prompt swaps, while benchmarking against fine-tuned and zero-shot baselines using the Dice Similarity Coefficient (DSC) with Wilcoxon signed-rank tests and Benjamini-Hochberg correction. Alignment analyses revealed that anatomical location is the dominant driver of VoxTell's spatial attention: 63.4 percent of location perturbations caused catastrophic drops, prompt specificity improved from generic to full descriptions except for diagnosis-only prompts, irrelevant prompts correctly yielded zero segmentation, and cross-case prompt swaps confirmed patient-specific conditioning (matched DSC 0.906 vs. mismatched 0.406). Histology and stage substitutions had minimal effect, indicating that the model prioritizes "where to look" over "what to look for." In this context, VoxTell, operating fully zero-shot, achieved a mean DSC of 0.613, statistically indistinguishable from nnUNet (0.690, adjusted p = 0.156) and Ahmed et al. (0.675, adjusted p = 0.679), while significantly outperforming all other zero-shot models. Together, these findings argue that segmentation VLMs should be evaluated not only by Dice, but also by the prompt dimensions to which they align.

Lissajous confocal laser endomicroscopy (CLE) is a promising solution for high speed in vivo optical biopsy for handheld scenarios. However, Lissajous scanning traces a resonant trajectory and samples only the visited pixels per frame; at high frame rates, many pixels remain unvisited, creating structured holes. In this work, we introduce the first benchmark for high-rate Lissajous CLE, consisting of low-quality video clips paired with high-quality reference images. The reference images are wide-FOV mosaics obtained by stitching stabilized, slow-scan frames of the same tissue, enabling temporally aligned supervision. Using this dataset, we propose MIRA, a lightweight recurrent framework for Lissajous CLE restoration that iteratively aggregates temporal context through feature reuse and displacement alignment. Our experiments demonstrate that MIRA outperforms both lightweight and high-complexity baselines in restoration quality while maintaining a favorable computational efficiency suitable for clinical deployment.

Many machine learning systems make constrained decisions by optimizing factorized objectives, but the context-specific objective is often treated as fixed. We study contextual decision-weight learning: from logged decisions and proxy outputs, learn an optimizer-facing weight vector w(x) over interpretable decision factors z(x,d), rather than a direct policy or generic predictive score. We propose OTSS, an output-targeted soft-segmentation model that deploys the personalized decision-ready weight vector. At the function-class level, the theory highlights a hard-versus-soft distinction. Hard partitions incur an approximation-estimation tradeoff under overlap, while a realizable fixed-K soft class removes the hard-partition approximation floor and attains a parametric rate. We evaluate OTSS in controlled benchmarks with finite evaluation libraries, where the true weight vector and downstream regret can be computed exactly. In the representative overlap setting, OTSS attains the lowest mean regret among the comparators, including EM mixture regression, the strongest soft-mixture baseline in our comparison; it matches EM on coefficient recovery while running about two orders of magnitude faster. In a matched K=5 benchmark, OTSS remains competitive under hard-routed truth and improves as heterogeneity becomes softer and sample size grows. On a fixed Complete Journey retail anchor with real household covariates and action geometry, OTSS again achieves the lowest mean-regret point estimate.

Topological features play an essential role in ensuring geometric plausibility and structural consistency in image analysis tasks such as segmentation and skeletonization. However, integrating topology-preserving learning based on simple points into deep learning tasks remains challenging, as existing simple point detection methods are confined to binary images and are non-differentiable, rendering them incompatible with gradient-based optimization in modern deep learning. Moreover, morphological and purely data-driven approaches often fail to guaranty topological consistency. To address these limitations, we propose a novel method that directly computes simple points on continuous-valued images, enabling differentiable topological inference. Building on this theory, we develop an efficient skeleton extraction algorithm that preserves topological structures in binary and continuous-valued images. Furthermore, we design a variational model that enforces topological constraints by preserving topologically non-removable (i.e., non-simple) points, which can be seamlessly integrated into any deep neural network segmentation with softmax or sigmoid outputs. Experimental results demonstrate that the proposed approach effectively improves topological integrity and structural accuracy across multiple benchmarks. The codes are available in https://github.com/levnsio/CSP.

Accurate lesion segmentation is crucial for clinical diagnosis and treatment planning. However, lesions often resemble surrounding tissues and exhibit ill-defined boundaries, leading to unstable predictions in boundary/transition regions. Moreover, small-lesion cues can be diluted by multi-scale feature extraction, causing under- or over-segmentation. To address these challenges, we propose an Uncertainty-Aware Hypergraph Refinement Network (UHR-Net). First, we introduce an Uncertainty-Oriented Instance Contrastive (UO-IC) pretraining strategy that couples geometry-aware copy-paste augmentation with hard-negative mining of lesion-like background regions to improve instance-level discrimination for small and visually ambiguous lesions. Second, we design an Uncertainty-Guided Hypergraph Refinement (UGHR) block, which derives an entropy-based uncertainty map from a coarse probability map to guide hypergraph refinement. By splitting hyperedge prototypes into foreground and background groups, UGHR decouples higher-order interactions and improves refinement in ambiguous regions. Experiments on five public benchmarks demonstrate consistent gains over strong baselines. Code is available at: https://github.com/CUGfreshman/UHR-Net.

Ultrasound interpretation requires both precise lesion localization and holistic clinical reasoning, yet existing methods typically excel at only one of these capabilities: specialized detectors offer strong localization but limited reasoning, whereas multimodal large language models (MLLMs) provide flexible reasoning but weak grounding in specialized medical domains. We present Echo-α, an agentic multimodal reasoning model for ultrasound interpretation that unifies these strengths within an invoke-and-reason framework. Echo-α is trained to coordinate organ-specific detector outputs, integrate them with global visual context, and convert the resulting evidence into grounded diagnostic decisions beyond detector-only inference. This behavior is established through a nine-task supervised curriculum and then refined by sequential reinforcement learning under different reward trade-offs, yielding Echo-α-Grounding for lesion anchoring and Echo-α-Diagnosis for final diagnosis. On multi-center renal and breast ultrasound benchmarks, Echo-α outperforms competitive baselines on both grounding and diagnosis. In particular, on cross-center test sets, Echo-α-Grounding attains 56.73%/43.78% F1@0.5 and Echo- α-Diagnosis reaches 74.90%/49.20% overall accuracy on renal/breast ultrasound. These results suggest that agentic multimodal reasoning can turn specialized detectors into verifiable clinical evidence, offering a practical route toward ultrasound AI systems that are more accurate, interpretable, and transferable. The repository is at https://github.com/MiliLab/Echo-Alpha.

Peritoneal metastases (PM) are staged using the surgically determined Peritoneal Cancer Index (sPCI), which requires invasive laparoscopic assessment. Although CT is routinely used for preoperative evaluation, imaging-based assessment of PM extent remains challenging and is often less structured than surgical PCI scoring. A recent consensus study defined radiological PCI (rPCI) regions for cross-sectional imaging. We present the first deep learning approach to automatically segment 13 rPCI regions on CT. 62 contrast-enhanced CT scans were retrospectively collected across the full PCI range. Each scan was annotated into non-overlapping rPCI regions by one researcher, reviewed by a second, with disagreements resolved by a radiologist. Using five-fold cross-validation, we compared nnU-Net and Swin UNETR with Dice, 95th-percentile Hausdorff distance (HD95) and Average Surface Distance (ASD). We introduce an anatomically constrained pipeline that trains on merged super-regions and splits them during post-processing using TotalSegmentator landmarks at the hips and the ligament of Treitz. On this 62-scan cohort, the baseline nnU-Net reached an overall Dice of 0.81 and outperformed Swin UNETR (0.76). The proposed pipeline improved the overall Dice to 0.84 and reduced boundary error (HD95 13.7 to 11.8 mm; ASD 4.1 to 3.4 mm), with the largest gains in the small-bowel regions, approaching the interobserver Dice of 0.87. Automated rPCI region segmentation on CT is feasible and approaches interobserver agreement. Encoding anatomical boundary constraints substantially improves segmentation quality in the most challenging regions. This provides a reproducible foundation for non-invasive, imaging-based PCI assessment. The main limitations are the single-center cohort and the small interobserver subset.

In open-world semi-supervised learning (OWSSL), a model learns from labeled data and unlabeled data containing both known and novel classes. In practical OWSSL applications, models are expected to perform rigorous classification by directly selecting the most semantically relevant label from a candidate set for each sample. Existing OWSSL methods fail to achieve this because novel samples are trained without explicit supervision, and these methods lack mechanisms to extract latent semantic information, resulting in predicted labels that have no semantic correspondence to candidate textual labels. To address this, we introduce SEmantic Capture for Open-world Semi-supervised learning (SECOS), which directly predicts textual labels from the candidate set without post-processing, meeting the requirements of practical OWSSL applications. SECOS leverages external knowledge to extract and align semantic representations across modalities for both known and novel classes, providing explicit supervisory signals for training novel classes. Extensive experiments demonstrate that even when existing OWSSL methods are evaluated under the more lenient post-hoc matching setting, SECOS still surpasses them by up to 5.4% without such assistance, highlighting its superior effectiveness. Code is available at https://github.com/ganchi-huanggua/OSSL-Classification.

Surgical resection remains the only potentially curative treatment for pancreatic ductal adenocarcinoma (PDAC), and eligibility depends on accurate assessment of vascular invasion (VI), i.e., tumor extension into adjacent critical vessels. Despite its importance for preoperative staging and surgical planning, computational VI assessment remains underexplored. Two major challenges are the lack of public datasets and the diagnostic ambiguity at the tumor-vessel interface, which leads to substantial inter-rater variability even among expert radiologists. To address these limitations, we introduce the CURVAS-PDACVI Dataset and Challenge, an open benchmark for uncertainty-aware AI in PDAC staging based on a densely annotated dataset with five independent expert annotations per scan. We also propose a multi-metric evaluation framework that extends beyond spatial overlap to include probabilistic calibration and VI assessment. Evaluation of six state-of-the-art methods shows that strong global volumetric overlap does not necessarily translate into reliable performance at clinically critical tumor-vessel interfaces. In particular, methods optimized for binary segmentation perform competitively on average overlap metrics, but often degrade in high-complexity cases with low expert consensus, either collapsing in volume or overextending at uncertain boundaries. In contrast, methods that model inter-rater disagreement produce better calibrated probabilistic maps and show greater robustness in these ambiguous cases. The benchmark highlights the limitations of volumetric accuracy as a proxy for localized surgical utility, motivating uncertainty-aware probabilistic models for preoperative decision-making.

Fine-grained RGBT image semantic segmentation is crucial for all-weather unmanned aerial vehicle (UAV) scene understanding. However, UAV RGBT image semantic segmentation faces two coupled challenges: cross-modal spatial misalignment caused by sensor parallax and platform vibration, and severe semantic confusion among fine-grained ground objects under top-down aerial views. To address these issues, we propose a Graph-based Semantic Calibration Network (GSCNet) for unaligned UAV RGBT image semantic segmentation. Specifically, we design a Feature Decoupling and Alignment Module (FDAM) that decouples each modality into shared structural and private perceptual components and performs deformable alignment in the shared subspace, enabling robust spatial correction with reduced modality appearance interference. Moreover, we propose a Semantic Graph Calibration Module (SGCM) that explicitly encodes the hierarchical taxonomy and co-occurrence regularities among ground-object categories in UAV scenes into a structured category graph, and incorporates these priors into graph-attention reasoning to calibrate predictions of visually similar and rare categories. In addition, we construct the Unaligned RGB-Thermal Fine-grained (URTF) benchmark, to the best of our knowledge, the largest and most fine-grained benchmark for unaligned UAV RGBT image semantic segmentation, containing over 25,000 image pairs across 61 semantic categories with realistic cross-modal misalignment. Extensive experiments on URTF demonstrate that GSCNet significantly outperforms state-of-the-art methods, with notable gains on fine-grained categories. The dataset is available at https://github.com/mmic-lcl/Datasets-and-benchmark-code.

Purpose: Rapid and reliable diagnostic tools are crucial for managing respiratory diseases like COVID-19, where chest X-ray analysis coupled with artificial intelligence techniques has proven invaluable. However, most existing works on X-ray images have not considered lung segmentation, raising concerns about their reliability. Additionally, some have employed disproportionate and impractical augmentation techniques, making models less generalized and prone to overfitting. This study presents a critical analysis of both issues and proposes a methodology (SDL-COVID) for more reliable classification of chest X-rays for COVID-19 detection. Methods: We use class activation mapping to obtain a visual understanding of the predictions made by Convolutional Neural Networks (CNNs), validating the necessity of lung segmentation. To analyze the effect of data augmentation, deep learning models are implemented on two levels: one for an augmented dataset and another for a non-augmented dataset. Results: Careful analysis of X-ray images and their corresponding heat maps under expert medical supervision reveals that lung segmentation is necessary for accurate COVID-19 prediction. Regarding data augmentation, test accuracy significantly drops beyond a certain threshold with additional augmented images, indicating model overfitting. Conclusion: Our proposed methodology, SDL-COVID, achieves a precision of 95.21% and a lower false negative rate, ensuring its reliability for COVID-19 detection using chest X-rays.

Vision foundation models (VFMs), such as DINOv3, provide rich semantic representations that are promising for computational pathology. However, many current adaptations pair frozen VFMs with lightweight decoders, creating a capacity mismatch that often limits boundary fidelity for infiltrative tumor bulk segmentation. This paper presents Dino-NestedUNet, a framework that couples a pre-trained DINOv3 encoder with a Nested Dense Decoder. Instead of sparse skip connections and linear upsampling, the proposed decoder forms a dense grid of intermediate pathways to enable continuous feature reuse and multi-scale recalibration, aligning high-level semantics with low-level morphological textures during reconstruction. We evaluate Dino-NestedUNet on three histopathology cohorts (multi-center CHTN, institutional OSU, and CAMELYON16) and observe consistent improvements over UNet++ and standard Dino-UNet variants, particularly under cross-domain shift. To further assess external generalization, we perform zero-shot evaluation by training on CHTN and directly testing on unseen TIGER WSIBULK and OSU CRC cohorts without fine-tuning. These results suggest that dense decoding is a key ingredient for unlocking foundation encoders in boundary-sensitive pathology segmentation.

Text guided 3D medical image segmentation offers a flexible alternative to class based and spatial prompt based models by allowing users to specify regions of interest directly in natural language. This paradigm avoids reliance on predefined label sets, reduces ambiguous outputs, and aligns more naturally with clinical workflows. However, existing text guided frameworks are often computationally expensive, exhibit weak text volume feature alignment, and fail to capture fine anatomical details. We propose ESICA, a lightweight and scalable framework that addresses these challenges through three innovations: (1) a similarity matrix based mask prediction formulation that enhances semantic alignment, (2) an efficient decomposed decoder with adapter modules for accurate volumetric decoding, and (3) a two pass refinement strategy that sharpens boundaries and resolves uncertain regions. To improve training stability and generalization, ESICA adopts a two stage scheme consisting of positive only pretraining followed by balanced fine tuning. On the CVPR BiomedSegFM benchmark spanning five imaging modalities (CT, MRI, PET, ultrasound, and microscopy), ESICA achieves state of the art segmentation accuracy, while the compact ESICA4 Lite variant attains similar segmentation performance with substantially fewer parameters, yielding a superior efficiency accuracy trade off. Our framework advances text guided segmentation toward efficient, scalable, and clinically deployable systems. Code will be made publicly available at https://github.com/mirthAI/ESICA.

Segmentation models such as Segment Anything Model (SAM) and SAM2 achieve strong prompt-driven zero-shot performance. However, their training on natural images limits domain transfer to medical data. Consequently, accurate segmentation typically requires extensive fine-tuning and expert-designed prompts. We propose DiffuSAM, a diffusion-based adaptation of SAM2 for prompt-free medical image segmentation. Our framework synthesizes SAM2-compatible segmentation mask-like embeddings via a lightweight diffusion-prior from off-the-shelf frozen SAM2 image features. The generated embeddings are integrated into SAM2's mask decoder to produce accurate segmentations, thereby eliminating the need for user prompts. The diffusion prior is further conditioned on previously segmented slices, enforcing spatial consistency across volumes. Evaluated on the BTCV and CHAOS datasets for CT and MRI under Source-Free Unsupervised Domain Adaptation (SF-UDA) and Few-Shot settings, DiffuSAM achieves competitive performance with efficient training and inference. Code is available upon request from the corresponding author.

Clinical fusion of Single Photon Emission Computed Tomography Myocardial Perfusion Imaging (SPECT MPI) and Computed Tomography Angiography (CTA) remains limited by cross-modality misregistration and reliance on manual landmarks, which can hinder accurate ischemia localization and lesion-level functional assessment. To address this issue, we propose a registration and fusion framework for SPECT MPI and CTA that integrates functional and structural information for comprehensive cardiac evaluation. The proposed pipeline performs U-Net-based segmentation on both modalities. On SPECT MPI, only the left ventricle (LV) is extracted, and anatomical landmarks are automatically derived from characteristic LV structures. On CTA, both ventricles are segmented, and their spatial relationship is used to automatically define landmarks at the interventricular septal junction. Scale-space consistency preprocessing and landmark-driven coarse registration are applied to mitigate initial misalignment. Based on this initialization, multiple fine registration methods are evaluated on LV epicardial surface point clouds, including ICP, SICP, CPD, CluReg, FFD, and BCPD-plus-plus. The resulting transformations are then propagated to voxel-level resampling for high-precision SPECT-CTA fusion. In a retrospective cohort of 60 patients, the proposed framework preserved sub-millimeter coronary detail from CTA while accurately overlaying quantitative SPECT perfusion. Among the evaluated methods, BCPD-plus-plus achieved the highest accuracy with a mean point cloud distance of 1.7 mm. By combining robust initialization, comparative fine registration, and voxel-level fusion, the proposed approach provides a practical solution for myocardial ischemia localization and functional evaluation of coronary lesions, while remaining independent of any specific fine registration algorithm.