Medical Image Segmentation

Accurate bladder tumor segmentation and assessment of mus- cle invasion from T2-weighted MRI are important for treatment plan- ning, but developing robust models across institutions is challenging be- cause patient data cannot be centrally pooled and imaging characteristics vary across scanners and acquisition protocols. We propose a federated multi-task learning framework for joint bladder tumor segmentation and MIBC/NMIBC classification across four clinical centers. The proposed Swin Hybrid model combines a ResNet-34 branch for local texture and boundary information with a Swin-Tiny Transformer for global anatomi- cal context. A segmentation-guided classification mechanism further uses tumor localization information to support MIBC prediction. We also investigate several augmentation strategies under both centralized and federated training to improve robustness to multi-center variability. Ex- periments on the FedBCa dataset show that the Swin Hybrid provides the best overall balance between segmentation and classification among the evaluated architectures. Under federated training, Geo+Elastic aug- mentation achieved a DSC of 0.8100 and a patient-level AUC of 0.8931, yielding the highest combined score of 0.8474. These results demonstrate that joint segmentation and classification can be effectively performed across multiple institutions using federated training without centralizing patient data.

Accurate segmentation of the coronary vessel lumen is a prerequisite for quantitative assessment of atherosclerotic plaque and perivascular adipose tissue in coronary computed tomography angiography (CCTA). Cardiologists rely on semi-automated methods for this task because manual vessel tracing and segmentation are labour-intensive. Although many automated methods have been proposed, their validation remains limited by the lack of large, high-quality publicly available datasets. We provide a new dataset of voxel-wise annotations of the vessel lumen and coronary segments, alongside centerlines, and mesh surfaces for 800 scans from the publicly available ImageCAS dataset. Using this dataset, we benchmark established lumen segmentation methods against inter-observer variability, stratifying performance by disease, image quality, coronary dominance, coronary segment, vessel diameter, and lumen attenuation. These labels allow segmentation accuracy to be described in anatomical and clinical context rather than reported as a single aggregate score. The dataset supports the development and validation of methods for lumen segmentation, plaque and perivascular quantification, and haemodynamic modelling.

Automatic cardiac image segmentation is pivotal for diagnosing and treating cardiac diseases. In this work, we introduce MCSeg, a volumetric transformer-based network tailored for multi-modal cardiac segmentation. To overcome the architectural mismatch inherent in existing hybrid networks, we propose a novel Scaling Feature Pyramid (SFP). Unlike conventional skip connections, the SFP effectively bridges the single-scale 3D Vision Transformer (ViT) encoder and the multi-scale CNN decoder by transforming the ViT's output into a hierarchical feature pyramid, ensuring that global contextual information is effectively leveraged. For the training paradigm, the ViT encoder first undergoes self-supervised pre-training via masked image modeling. Subsequently, the network is fine-tuned on downstream tasks, during which a regional mutual information (RMI) loss is integrated to improve boundary segmentation accuracy. In experiments, MCSeg consistently outperforms eleven SOTA methods on CT dataset ImageCHD, multi-modal dataset MM-WHS, MRI dataset HVSMR-2.0 and MSD Heart, highlighting the effectiveness of our MCSeg for multi-modal cardiac segmentation tasks. Furthermore, MCSeg's superior performance in few-shot experiment showcases its significant potential in adapting to limited data scenarios. Codes and pre-trained ViT-B weights are open-sourced at https://openi.pcl.ac.cn/OpenMedIA/MCSeg

Despite rapid advances in MIS, fair and reproducible comparisons of segmentation models remain challenging due to heterogeneous datasets, inconsistent evaluation protocols, and rapidly evolving architectures. In particular, comparisons often implicitly assume that model rankings are invariant to data partitioning, preprocessing, metric aggregation, uncertainty estimation, and computational constraints. The lack of extensible and unified evaluation frameworks further limits systematic investigation of new models, datasets, and training paradigms. We present MEDSEGBENCHMARKER (MSB), a configuration-driven framework for controlled benchmarking of 2D MIS. It integrates duplicate and near-duplicate image detection, group-aware data splitting, YAML study specifications, resumable training, hyperparameter optimization, cross-validation, and checkpoint-based evaluation. Rather than retaining only aggregate performance measures, MSB exports sample- and class-level pixel counts and predictions together with the evaluation context. These elementary artifacts enable post-hoc analyses without repeated inference. We demonstrate MSB in a case study involving three heterogeneous 2D datasets and multiple MIS and general-purpose vision models evaluated at 256- and 512-pixel input resolutions. Reaggregation of identical predictions changes the top-ranked architecture in three of six dataset-resolution settings, despite high rank correlations between aggregation strategies. Increasing input resolution produces model- and dataset-dependent performance gains and losses that must be considered alongside empirically measured inference complexity. These results show that seemingly minor choices in evaluation and experimental setup can affect benchmark conclusions. MSB, available at GitHub, provides a practical and extensible basis for making benchmark conditions and evaluation choices explicit and reproducible.

Instance segmentation of overlapping cells in microscopy remains challenging due to semi-transparent structures that produce weak boundaries and mixed visual evidence in overlap regions. Existing methods address this through local regions of interest or shape priors but lack global reasoning across overlapping objects. We present QCell, a novel query-based model that de-overlaps cell instances in microscopy scenes. Our approach combines (i) an instance recombination module that decomposes and recombines query representations in latent space, enabling the model to reason about complete object structure under overlap, and (ii) a contrastive query alignment objective that combines distinctive instance feature learning and separation of overlapping cell queries. We additionally introduce a new Organoid dataset benchmark for overlapping cell segmentation. We show that QCell outperforms state-of-the-art methods across multiple benchmarks, achieving +2.2 AP and +2.7 AJI on ISBI2014. Code is available at https://github.com/SlavkoPrytula/QCell

Late gadolinium enhancement (LGE) cardiac magnetic resonance (MR) imaging is the modality of choice to assess myocardial infarction (MI) lesions. Nowadays MI volume quantification is not performed routinely in clinical practice. Numerous deep learning (DL) methods have been developed to automate the segmentation of the myocardium and infarct regions. However, most studies rely on relatively small datasets which typically undergo pre-processing steps to standardize images and focus on a specific phase of myocardial infarction following reperfusion therapy. These limitations have impeded the development of models that are generalizable across diverse conditions and thus suitable for routine clinical use. To advance research and establish benchmarks in generalizable learning for myocardial infarct quantification, this paper presents findings from the Myocardial Segmentation with Automated Infarct Quantification (MYOSAIQ) challenge. The dataset set up for the challenge combines 439 CMR volumes from two multicenter clinical trials, with representative data acquired in acute and chronic phases after acute MI. Data were acquired in 16 centers using MRI scanners from three different vendors. Six teams participated until the end of the challenge, employing various baseline models, data augmentation techniques, and confidence strategies. To enhance the significance of this study, we compare the challengers' results with those of fine-tuned foundation models. Our results indicate that well-designed UNet-based techniques outperform fully automatic foundation models for LGE MR segmentation. While the best methods achieve high-quality and stable delineations of the left ventricle and myocardium under various conditions, they remain improvable in accurately segmenting infarct regions.

Optic disc (OD) segmentation is essential for diagnosing ophthalmic pathologies from retinal fundus images. However, prevailing deep learning approaches operate as opaque black boxes, lacking the inference-stage mathematical traceability--a critical requirement for algorithmic auditing and failure analysis in clinical workflows. This paper presents a fully algorithmically traceable and trainable segmentation pipeline that jointly combines superpixel decomposition, hybrid brightness-proximity superpixel scoring, morphological regularization, iterative GrabCut refinement, and elliptical shape fitting. The hyperparameter optimization is formulated as an objective function and solved via Bayesian optimization to eliminate manual parameter tuning. A quantitative evaluation on the Drishti-GS dataset demonstrates that our method achieves a Dice coefficient of 0.9536, matching state-of-the-art performance. By maintaining explicit mathematical transparency across all processing stages, our framework offers a deterministic, traceable alternative to black-box architectures for medical review and debugging.

Robustness of segmentation models is commonly assessed through input-domain perturbations, while dependence on frequency content within learned feature representations remains less understood. We probe this dependence using targeted post-training low-pass interventions on internal representations of three segmentation architectures, ResNet50-UNet (CNN), VM-UNet (SSM), and Swin-UNETR (Transformer), across CVC-ClinicDB and ISIC2018, with headline evaluations performed on untouched held-out test sets. At cutoff $ρ=0.25$, feature-domain low-pass filtering causes severe degradation on CVC: Dice drops by 100%, 73.2%, and 30.9% for CNN, SSM, and Transformer, respectively, compared with 9.4%, 10.3%, and 0.6% on ISIC. The cross-dataset difference is statistically significant for every architecture. Single-stage interventions further show that the most sensitive stage depends on architecture and dataset: the CNN peaks at the 2nd to 3rd encoder block, whereas the SSM peaks at the 1st to 2nd encoder stage. Native feature-domain spectral measurements show an inverse association between high-frequency energy and fragility on CVC; the relationship is only partial on ISIC and is therefore treated as a candidate correlate rather than a proven mechanism. Finally, Fourier augmentation improves robustness to input-space low-pass filtering but leaves feature-domain degradation essentially unchanged. These results show that feature-spectral robustness is strongly dataset-dependent, architecture-specific, and distinct from input-domain spectral robustness.

We describe the submission of team FME to the MAMA-MIA Challenge, which evaluated primary tumor segmentation and prediction of pathological complete response (pCR) from pretreatment dynamic contrast-enhanced breast MRI on an external multi-country cohort. For segmentation, we trained a five-fold residual-encoder nnU-Net ensemble using only the first post-contrast minus pre-contrast image, combined with mirroring test-time augmentation and largest-connected-component filtering. For pCR prediction, we ensembled 25 pretrained 3D video classifiers trained on lesion-centred crops from the pre-contrast and first two post-contrast volumes. FME ranked second in both tasks. The segmentation method achieved a combined performance-fairness score of 0.882, with Dice 0.713 and normalized Hausdorff distance 0.099. The pCR method achieved a combined score of 0.664, balanced accuracy of 0.541, and equalized-odds disparity of 0.212. The results indicate that subtraction-based input and ensembling support robust tumor segmentation under cross-site domain shift, whereas pCR prediction from baseline DCE-MRI alone remains limited. For the submission repository, see https://github.com/FraunhoferMEVIS/MAMA-MIA-Challenge-FME

We present an anatomy-aware, promptable model for whole-body lesion segmentation in FDG and PSMA PET/CT, developed for the AUTOPET V challenge. The proposed method is built as family of nnU-Net-based models and trained in two stages: i) a pre-training stage that produces a strong initial segmentation, and ii) an online interactive stage that learns to exploit scribble prompts, refining the prediction over successive interactions. Anatomical context is incorporated through organ supervision using a single shared head that predicts lesions and organs from the same features, which reduces false positives arising from physiological uptake. Also as the tracer (i.e., FDG/PSMA) is not provided at inference, we add a tracer classifier based on image processing and a random forest over coronal MIP features, routing each study to a combined FDG+PSMA model or to a PSMA-specific model. Across four-fold cross-validation the organ-supervised model achieves the best and most stable performance, the interactive stage improves the Dice score monotonically with each prompt, and PSMA-specific training yields the strongest tracer-wise results.

Accurate segmentation of interstitial lung disease (ILD) patterns is essential for quantitative disease assessment and longitudinal monitoring. However, existing approaches remain limited by relying on dense annotations and producing static predictions that cannot be refined, motivating interactive approaches. While promptable models show promise in interactive segmentation, their adaptation to ILDs remains largely unexplored. To address this gap, we investigate prompt-guided foundation models for ILD refinement and present, to the best of our knowledge, the first adaptation of MedSAM2 for interactive 3D ILD segmentation on thoracic CT. We investigate three fine-tuning strategies and multiple clinically motivated prompts: bounding-boxes (BBox), point, lasso, and scribble. On a dataset spanning seven ILD patterns and healthy lung tissue, full model fine-tuning performed best, improving the average Dice score by 4.7 percentage points over MedSAM2.While BBox prompts achieve the strongest performance, non-native MedSAM2 interactions such as lasso and scribble prompts also prove effective. Finally, we present and evaluate a proof-of-concept end-to-end workflow in which MedSAM2 is initialized from an automatic segmentation prior and subsequently refined using radiologist prompts. Model weights and plug-ins made available at: https://github.com/AIHNlab/ILD-SemiSegTool.

Deep learning segmentation models are often evaluated using geometric metrics such as Dice, HD95, and ASD, yet it remains unclear to what extent improvements in these metrics translate into clinically meaningful changes in downstream decision-making. The metric-to-decision gap is examined using radiological Peritoneal Cancer Index (rPCI) region segmentation on contrast-enhanced CT, where a consensus definition provides anatomically grounded 3D regions and the clinically used PCI 20 threshold enables decision-level evaluation. Inter-observer variability is quantified across four experts on ten abdominal CT scans, and a published nnU-Net based rPCI segmentation model is benchmarked against this human reference using Dice, HD95, and ASD across all 13 regions. To relate geometric differences to clinical impact, a probabilistic peritoneal metastasis simulation is implemented on majority-vote rPCI maps, propagating region-boundary variability into variability of derived (r)PCI scores and classification at the PCI 20 cutoff. Observers showed high agreement (mean Dice $0.87$), while the model matched human performance in most regions but deviated more in regions 4, 8, and the small-bowel regions (9-12). Across simulations, score differences were typically small (mean $Δ$rPCI $\approx 0.3$-$0.6$) for both observers and the model, and decision flips occurred predominantly when the reference score was near 20. These results suggest that rPCI-derived scoring is generally robust to typical segmentation variability, while highlighting borderline cases as the main setting where expert review remains essential.

Accurate boundary delineation of brain tumors in Magnetic Resonance Imaging (MRI) is a critical yet formidable challenge in neuro-oncology due to inherent scanner noise, complex anatomical structures, and uneven illumination. Traditional edge detection algorithms, while computationally lightweight and mathematically interpretable, frequently fail to capture the diffuse, localized boundaries of edema when relying solely on global preprocessing and manual parameter tuning. To overcome these limitations, we propose a hybrid automated edge detection pipeline. Our approach integrates an optimally configured Contrast-Limited Adaptive Histogram Equalization (CLAHE) layer into a comprehensive morphological preprocessing framework, followed by a deterministic sequential parameter sweep to fully automate threshold selection. The proposed hybrid model demonstrated enhancement in detecting critical anatomical structures in a publicly available benchmark database from Kaggle. By intelligently amplifying localized gradients without overwhelming the image with background noise, our method achieved higher Recall (Sensitivity). Consequently, the overall F1-Score elevated, and the Structural Similarity Index (SSIM) improved, all while maintaining a highly efficient execution. This establishes our optimized pipeline as a highly practical and near real-time operational model for clinical diagnostics, offering a compelling alternative to computationally heavy deep learning approaches.

Segmentation models can surpass radiologists, classification models, and vision-language models in tumor detection. Importantly, segmentation models outline tumors, allowing radiologists to better verify and trust the AI output. Their main limitation is the scarcity of tumor masks: creating one 3D tumor mask takes up to 30 minutes, so most public CT datasets contain only a few hundred masks, and even the largest private datasets contain only a couple of thousand. Tumor masks are not produced in clinical routine, but radiology reports are. Public datasets contain tens of thousands of CT-Report pairs, and hospitals contain hundreds of thousands. These reports describe tumors in detail, providing large-scale, informative training data. Here, we introduce Report Supervision (R-Super), a training framework that uses reports to directly supervise and improve tumor segmentation. R-Super introduces new loss functions that teach segmentation models to segment tumors that match report descriptions of tumor count, sizes, and locations. Reports are only used for training. We evaluated R-Super on kidney and pancreatic tumor segmentation, exploring diverse training data sizes, up to 41,418 CT-Report plus 3,488 pancreatic tumor CT-Mask pairs. On external validation, R-Super increased tumor detection F1-Score and segmentation DSC by up to +15% with respect to mask-only training. It also surpassed alternative methods such as CLIP and multi-task learning. Leveraging numerous readily available reports to supplement scarce masks, R-Super strongly improves AI performance when very few training masks are available (e.g., 50), and when many masks are available (e.g., 3,488), unlocking scale in tumor segmentation.

Prenatal ultrasound examination is crucial for assessing fetal limb development and detecting congenital anomalies. However, existing artificial intelligence models often overlook fetal lethal skeletal dysplasias due to the lack of high-quality annotated data and a unified framework for multiple long bones. Moreover, generic segmentation models struggle with the inherent noise and semantic gaps in ultrasound images. To address these challenges, we construct the Fetal Limb Bones (FLB) dataset, comprising high-quality annotations for the humerus, femur, tibia-fibula, and radius-ulna. Furthermore, we propose UniFLM (United Segmentation and Measurement on Fetal Limb Ultrasonic Image), a unified framework for automatic cross-plane segmentation and measurement. UniFLM incorporates a Semantic Alignment Skip Connection (SASC) module to bridge the semantic gap between encoder and decoder features, and a Positive Sampling (PoSamp) strategy to filter noise and extract essential semantic information. Finally, a Point Regression Mapping (PRM) module is introduced to learn clinician annotation patterns for precise bone length measurement. Extensive experiments conducted on the FLB dataset and the public FetalP5 benchmark demonstrate that UniFLM achieves competitive performance with consistent generalization across four bone categories and external multi-center data, supported by comprehensive statistical validation including Bland-Altman agreement analysis and bootstrap confidence intervals. The source code is publicly available at https://github.com/chosen1203/UniFLM.

Accurate rectal cancer segmentation from magnetic resonance imaging (MRI) is essential for adaptive radiotherapy and tumor response assessment, but deployment also requires computational efficiency and informative, calibrated uncertainty estimates. We therefore introduce SWIFT, a SWin pretrained model wIth parameter-eFficient and Tumor-aware fine-tuning for rectal cancer segmentation. A Swin V2 encoder pretrained on 10,444 public 3D CT volumes using a DINOv2-style objective was adapted to T2-weighted MRI through four cumulative configurations: full fine-tuning (SWIFT), decoder compression (SWIFTe), low-rank adaptation (SWIFTe-LoRA), and a four-member LoRA-decoder ensemble (SWIFTe-LDE4). Geometric accuracy, tumor detection, radiomic agreement, and probability calibration were evaluated on a held-out 247-case test set from a single-institution cohort acquired using 1.5 or 3 Tesla GE scanners. Compared with SWIFT, SWIFTe reduced total parameters by 70.1% (from 72.8M to 21.8M) and increased tumor detection rate from 89.9% to 93.9%, while achieving a slightly lower median surface DSC (0.61 versus 0.62) and improved radiomic agreement. In a separate SWIFTe ablation, removing tumor-aware augmentation reduced detection from 93.9% to 89.9% but increased surface DSC from 0.61 to 0.64, demonstrating a detection-boundary-agreement trade-off. SWIFTe-LoRA used 14.6% of SWIFTe's trainable parameters while retaining similar segmentation performance. SWIFTe-LDE4 achieved the lowest calibration errors among the four configurations after temperature scaling (expected calibration error, 0.217; Brier score, 0.222), although the absolute expected calibration error indicates residual miscalibration. Similar efficiency-calibration patterns were observed using the public VoCo checkpoint, supporting robustness across pretrained initializations rather than external clinical generalizability.

Age-related macular degeneration (AMD) and diabetic macular edema (DME) are leading causes of vision loss, and optical coherence tomography (OCT) is the standard modality for detecting and monitoring the subtle lesions that drive treatment decisions. Most deep-learning segmentation work for OCT is validated only in-domain, leaving generalization to clinical data collected under different acquisition protocols largely untested. This work develops and systematically ablates four lesion-segmentation pipelines -- 2D and 3D variants for AMD and DME -- reaching Dice scores of 0.76 to 0.82 with strong volumetric and surface calibration (r vol, r surf greater than or equal to 0.97 across all four pipelines) on an in-domain validation set. The ablation process establishes a full-volume, calibration-aware adoption standard that catches mechanisms an ordinary slice-level evaluation would keep, and identifies ensemble composition as the most consistent driver of improvement. To test generalization, the models are evaluated on OLIVES, an external clinical cohort with no lesion-level ground truth, using a proxy-metric framework built around biomarker AUROC, central subfield thickness (CST) correlation, and longitudinal concordance. Predictions track clinical biomarkers outside the training distribution, though less strongly than in-domain -- evidence for, not validation of, automated lesion-burden tracking as a clinical tool.

Although Multimodal Large Language Models (MLLMs) have demonstrated impressive performance in Medical Visual Question Answering (Med-VQA), their reliance on global image features often lacks precise pixel-level grounding, thereby limiting clinical trustworthiness. To bridge the semantic gap between high-level clinical reasoning and spatial localization, we propose MedREAL (Medical REasoning-driven Answering and Localization), a unified framework that seamlessly aligns linguistic reasoning with spatial grounding. Specifically, MedREAL introduces Seg Anchored Reasoning Pooling (SARP) to distill task-relevant semantic evidence directly from [SEG] tokens within the MLLM's hidden states. Furthermore, a Reasoning-to-Visual (R2V) fusion mechanism is proposed to effectively inject these reasoning-aware features into a segmentation pipeline for accurate mask decoding. To facilitate this paradigm, we construct MedRAVS-13K, a comprehensive dataset comprising 13,824 expertly validated samples across four diverse imaging modalities. Extensive experiments demonstrate that MedREAL significantly outperforms state-of-the-arts, achieving 68.49% gIoU and 70.47% cIoU on benchmark evaluations. By generating evidence masks that are strictly consistent with textual diagnoses, MedREAL provides a robust, interpretable framework for reasoning-driven medical image analysis.

Oralscan image segmentation is essential for computer-aided diagnosis and treatment planning in digital dentistry. However, existing visual state space models (SSMs) often rely on manually designed scanning orders to flatten image patches into sequences, which disrupts the semantic spatial continuity and hinders coherent feature extraction from key foreground regions. Moreover, elements such as inconsistent lighting, reflective surfaces, and noise during data acquisition disrupt the frequency distribution by diminishing high-frequency details while enhancing low-frequency components, consequently hindering the accurate localization of boundaries. In response to these challenges, we introduce FU-Mamba, an innovative framework that incorporates dynamic scanning and frequency domain enhancement within the SSM architecture. Specifically, the Dynamic Mamba Block (DMB) adaptively learns sampling offsets via a trainable offset prediction network and performs flexible bilinear interpolation, enabling content-aware scanning that preserves spatial coherence. Furthermore, a frequency domain enhancement block balances spectral components through wavelet-guided decomposition and spectrum pooling, improving robustness under adverse imaging conditions. Experimental findings indicate that FU-Mamba attains a notable enhancement in segmentation accuracy, evidenced by a 1.1% increase in the mean intersection over union (mIoU) metric when evaluated on the dental segmentation dataset. Project page: https://byte2bite.github.io/FU-Mamba/

Quantifying wound tissue composition is essential for monitoring chronic ulcer progression and guiding treatment decisions. However, pixel-level annotations are costly, and multi-tissue wound datasets remain scarce, particularly for neglected diseases such as leprosy. We introduce LUTSeg, a longitudinal chronic ulcer dataset comprising 141 images from 39 patients with wound masks and five tissue categories annotated by five expert clinicians, including a multi-expert gold-standard subset for inter-rater agreement analysis. To establish an initial benchmark for LUTSeg, we further propose TiSage, a semi-supervised tissue segmentation framework that integrates multi-scale semantic priors from a frozen medical vision-language model within a teacher-student architecture. We evaluate TiSage on LUTSeg and DFUTissue, showing improvements over supervised and semi-supervised baselines in most low-label settings. Code & data: https://github.com/carlosh93/TiSage

Acquiring pixel-level annotations for medical image segmentation is a severe bottleneck. Traditional U-Net architectures, while effective, learn local texture patterns and lack awareness of global anatomical structures, leading to boundary delineation failures in low-data regimes. This research paper proposes utilizing unsupervised Denoising Diffusion Probabilistic Models (DDPMs) to extract anatomical features. We train a DDPM on 21 unlabeled abdominal CT scans to learn structural representations, transferring the encoder weights to a downstream segmentation task evaluated on the BTCV multi-organ dataset. Diffusion pretraining significantly improved liver segmentation: Dice increased from $0.75\pm0.36$ to $0.93\pm0.16$ ($p < 5.33\times10^{-26}$, 0.529 Cohen's d), Average Surface Distance (ASD) decreased by 66%, and 95th-percentile Hausdorff Distance (HD95) reduced by 45%. For kidney segmentation, Dice improved from $0.90\pm0.19$ to $0.95\pm0.10$ ($p < 4.01\times10^{-11}$). Multi-organ pooled performance showed a 68% variance reduction and a 74% improvement in boundary precision (Dice $0.95\pm0.07$). Crucially, frozen encoder models retained > 80% of fine-tuned performance without exposure to segmentation labels, proving the existence of learned anatomical priors. In low-data scenarios, diffusion-pretrained models maintained robust performance with only 50% (Dice: 0.92 liver, 0.94 kidney), 25%, and even 10% (Dice: 0.89 liver, 0.71 kidney) of labeled data. Using unlabeled images for diffusion-based pretraining successfully embeds robust anatomical features prior to human supervision, transforming U-Nets into anatomy-aware systems.

Objective: Diffusion-weighted MRI (DWI-MRI) is the gold standard for visualizing and quantifying acute ischaemic stroke (AIS). Although deep learning methods can accurately segment AIS lesions, the optimal image inputs and model architecture remain uncertain. We evaluated whether accurate AIS lesion segmentation can be achieved using a pragmatic deep learning approach with minimal preprocessing and clinically feasible inference times. Materials and Methods: Self-configured nnU-Net models were trained on 1,744 DWI cases from local, national, and open-access datasets and tested on 436 cases. Four experimental conditions were evaluated using five-fold cross-validation: with or without brain extraction and using either DWI alone or DWI plus apparent diffusion coefficient (ADC) images as inputs. Two architectures were compared: the baseline nnU-Net (base) and a residual encoder nnU-Net (ResEnc). Performance was benchmarked against the DeepISLES ensemble model from the 2022 ISLES challenge. Results: In the test set (n=436), the base model achieved a median (IQR) Dice similarity coefficient (DSC) of 0.84 (0.19). For the base model, only two of six pairwise comparisons between input configurations showed significant differences. ResEnc produced small but significant improvements in DSC compared with the base model for DWI, DWI+brain extraction, and DWI+ADC inputs (all p<0.02), but not for DWI+ADC+brain extraction (p>0.50). The base model significantly outperformed DeepISLES, particularly in patients with smaller infarct volumes (signed-rank test, p<0.01). Conclusions: A baseline nnU-Net trained on DWI alone, without preprocessing, enabled fast and accurate AIS lesion segmentation. This streamlined approach may facilitate clinical research and support acute stroke imaging workflows

Probability calibration aligns model confidence with predictive accuracy, enabling clinicians to identify unreliable segmentation regions. This alignment breaks down under domain shift, where artifacts and unseen protocols produce confident errors. Existing post-hoc methods adapt the correction at test time, conditioning on predictive entropy, the logit pattern, or augmentation response, but each proxy is read from the terminal prediction, the very quantity that shift corrupts. This motivates reliability evidence beyond the terminal prediction, which categorical diffusion provides in two ways. First, a generative shape prior keeps a capacity-limited reference intact when appearance is corrupted, so its disagreement with the primary segmentor highlights primary-model errors. Second, every reverse step yields a class distribution, separating persistent disagreement from transient discrepancy. Aggregated over the trajectory, this disagreement correlates with Dice at 0.788, against 0.521 for a matched discriminative control. We therefore propose CARD (Calibration via Agreement in Reverse Diffusion), which maps the temporal aggregate of this disagreement to a temperature field applied per pixel across all classes, so that confidence changes while the segmentation does not. Across cardiac, prostate and brain MRI shifts, CARD lowers calibration error in 45 of 49 comparisons against the strongest baseline in each setting.

Whole-heart segmentation from CT and MRI is essential for quantitative cardiac image analysis, but remains challenging under multi-center and multi-modality distribution shift. In the CARE whole-heart segmentation task, models must generalize from limited labeled sites to unseen acquisition distributions, where variation in spacing, intensity, reconstruction texture, and anatomy can degrade out-of-distribution performance. We propose a modality-routed 3D cardiac segmentation pipeline that combines TotalSegmentator-initialized nnU-Netv2 models with site-characterized, label-preserving appearance augmentation. We first characterize the available sites using measurable image properties and use this analysis to motivate candidate data-space generalization routes. The final retained recipe applies Bias Field + Bezier appearance augmentation, combining smooth spatial intensity perturbation with nonlinear intensity remapping, followed by lightweight class-wise largest-connected-component cleanup. On the primary held-out-site validation splits, the final configuration improves CT mean Dice from 0.8350 to 0.9135 and MRI mean Dice from 0.7695 to 0.7830, while also reducing HD95. These results suggest that site-motivated appearance augmentation is a practical strategy for improving cross-site robustness in limited-data whole-heart segmentation. Our code can be found in https://github.com/Purdue-M2/Improving-Cross-Site-Whole-Heart-Segmentation

Surgical instrument segmentation (SIS) is fundamental for computer-assisted surgery, where reliable instrument masks enable precise scene understanding and clinical assistance. Recently, adapting foundation models like the Segment Anything Model (SAM) to the surgical domain via prompt-learning has shown encouraging results. However, the performance of these adapted models under challenging surgical conditions is constrained by suboptimal adaptation mechanisms. Specifically, optimizing prompts or prototypes purely via downstream segmentation loss tends to cause them to degenerate into task-specific parameters rather than serving as persistent, stable category memory, thereby degrading their robustness against complex intraoperative variations. Moreover, routing multi-scale visual cues through a single prompt pathway creates a bottleneck that hinders effective scale-matched coupling. To address these limitations, we propose HPMA, a Hierarchical Prototype-Memory Adaptation framework for SAM. Specifically, HPMA constructs a frozen, multi-scale visual prototype memory bank from annotated surgical scenes and integrates it into SAM's feature space using lightweight adapters to preserve stable category evidence. To maximize the utility of multi-scale cues, we introduce a scale-matched coupling mechanism where global prototypes calibrate class-level prompt features, structural prototypes guide decoder object queries, and local prototypes align high-resolution feature maps through a local alignment objective. Extensive experiments on the public EndoVis2017 and EndoVis2018 datasets demonstrate that our approach achieves state-of-the-art performance, outperforming existing foundation model adaptation methods.

Reliable clot-volume quantification and subsequent risk assessment in pulmonary embolism depend on precise segmentation of emboli on computed tomography pulmonary angiography. Deep learning models for this task must be trained on accurate voxel-level labels. The three public datasets that provide such labels were annotated under different protocols, and some of their studies contain unlabeled emboli or labels that are discontinuous across slices. This Data Descriptor presents voxel-level pulmonary embolism annotations for 149 of the 166 studies in these datasets. A primary rater drew all annotations under a single protocol. A thoracic radiologist with more than 20 years of experience reviewed and revised them. Three raters at three different centers independently annotated a subset of 15 studies. The subset was selected by source dataset and embolus location. Technical validation quantifies volumetric agreement with the source annotations, changes in within-mask attenuation, and inter-rater agreement on the subset. The dataset is intended to allow segmentation models to be developed and compared under a common reference standard.

Self-supervised pretraining enables transferable representations for medical imaging, yet most CT encoders remain biased toward coarse semantic understanding, limiting their sensitivity to fine-grained anatomical structures such as vessels or small tumors. In this paper, we introduce Biased Masked Image Modeling (B-MIM), a modification of the iBOT objective that stochastically reduces global semantic alignment to prioritize local patch reconstruction. This bias encourages the encoder to capture high-frequency morphological details and structural continuity. We curate a multi-institutional CT abdominal dataset of 9,955 filtered studies from 17 public sources and pretrain a 3D Swin Transformer backbone using B-MIM. Across inter-dataset experiments on liver vessel segmentation, the proposed encoder improves topological fidelity (clDice) and achieves competitive Dice scores in tumor segmentation, compared to fully fine-tuned baselines, despite updating only a fraction of the parameters. Our results suggest that reducing global semantic pressure during pretraining enhances generalization to intricate anatomical structures.

Segmenting ischemic stroke lesions on T1-weighted (T1w) MRI acquired across different scanners and protocols without intensity standardization is difficult because lesions are subtle and share intensity characteristics with cerebrospinal fluid. Standard deep learning architectures trained across multiple centers plateau around Dice 0.66, with acute lesions ($\le 7$ days post-stroke) performing substantially worse due to severe sample scarcity. We combine a MedNeXt-L ($k=5$) backbone with on-the-fly 3D CarveMix augmentation that pastes real lesion patches into healthy brain regions during training. By generating synthetic lesion placements dynamically within each fold with subject-level split isolation, the model sees more diverse lesion patterns without requiring pre-generated copies on disk. We evaluate on 1,453 native T1w scans from 55 clinical centers in the ISLES 2026 challenge. Our method achieves a mean 5-fold cross-validation Dice of 0.648 at 500 epochs, a +0.018 improvement over the MedNeXt-L backbone at a matched training budget (0.630)

Cardiac cine-MRI serves as a direct visual indicator of cardiovascular hemodynamics by capturing the continuous wall motion of the aorta. Quantifying these dynamic structural changes across the cardiac cycle is essential for measuring aortic distensibility, a primary marker of arterial stiffness. However, standard 2D segmentation networks focus on each frame independently. Consequently, when rapid systolic flow temporarily obscures the aorta's boundaries, this lack of continuous context results in frame-to-frame tracking dropouts and boundary inconsistencies. Spatiotemporal ($2\text{D}+t$) networks can enforce temporal consistency across the sequence but suffer from a scarcity of expert annotations. To address this, we present a semi-supervised spatiotemporal ($2\text{D}$ to $2\text{D}+t$) knowledge distillation framework exploiting the cardiac cycle. The framework distills a spatial teacher's expertise into a spatiotemporal student network by executing a dynamic latent interception, pairing a recurrent spatiotemporal bottleneck with a residual spatial bypass. Our model selection strategy applies a baseline validation threshold ($\text{DSC} \ge 0.50$) prior to selecting the epoch that maximizes anatomical consistency. This strategy enables the spatiotemporal student model to achieve superior surface tracking accuracy ($\text{NSD@1mm} = 92.3\% \pm 0.2\%$) and high structural reliability ($\text{Frac}_{2\text{CC}} = 99.2\% \pm 0.6\%$), reducing population-wide structural anomalies by over 56% compared to a 2D nnU-Net baseline.

Accurate brain tumor segmentation from magnetic resonance imaging (MRI) is essential for diagnosis, treatment planning, surgical guidance, and disease monitoring. However, developing automated segmentation models that generalize across diverse tumor characteristics, imaging protocols, acquisition sites, and patient populations remains challenging. Variations in tumor morphology and imaging distributions can substantially degrade performance outside the training domain. Consequently, improving the robustness and generalization of deep learning-based segmentation models has become a key objective in medical image analysis. To improve segmentation robustness, we propose Multi-Stage Dynamic Prompt nnU-Net, a prompt-conditioned extension of nnU-Net. Three independent dynamic prompt modules are inserted into the deepest encoder stages. Each module contains a learnable bank of ten 256-dimensional prompt vectors and uses globally pooled encoder features to generate image-specific prompt representations. These representations are projected into feature-wise scaling $(γ)$ and shifting $(β)$ parameters that modulate encoder feature maps through Feature-wise Linear Modulation (FiLM), enabling adaptive feature conditioning at multiple semantic levels. Evaluation on the BraTS GOAT validation dataset demonstrated that the proposed Multi-Stage Dynamic Prompt nnU-Net outperformed the baseline nnU Net across the majority of evaluated metrics and tumor subregions. The proposed model achieved average lesion-wise Dice scores of 76.16% (ET), 80.04% (TC), and 86.42% (WT), compared with 74.38%, 78.14% and 84.01% for the baseline model. The results demonstrate that multi-stage dynamic prompt conditioning improves segmentation accuracy and boundary delineation for brain tumor segmentation.