Lesion

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.

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.

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.

Recent segmentation models have demonstrated promising efficiency by aggressively reducing parameter counts and computational complexity. However, these models often struggle to accurately delineate fine lesion boundaries and texture patterns essential for early skin cancer diagnosis and treatment planning. In this paper, we propose MambaLiteUNet, a compact yet robust segmentation framework that integrates Mamba state space modeling into a U-Net architecture, along with three key modules: Adaptive Multi-Branch Mamba Feature Fusion (AMF), Local-Global Feature Mixing (LGFM), and Cross-Gated Attention (CGA). These modules are designed to enhance local-global feature interaction, preserve spatial details, and improve the quality of skip connections. MambaLiteUNet achieves an average IoU of 87.12% and average Dice score of 93.09% across ISIC2017, ISIC2018, HAM10000, and PH2 benchmarks, outperforming state-of-the-art models. Compared to U-Net, our model improves average IoU and Dice by 7.72 and 4.61 points, respectively, while reducing parameters by 93.6% and GFLOPs by 97.6%. Additionally, in domain generalization with six unseen lesion categories, MambaLiteUNet achieves 77.61% IoU and 87.23% Dice, performing best among all evaluated models. Our extensive experiments demonstrate that MambaLiteUNet achieves a strong balance between accuracy and efficiency, making it a competitive and practical solution for dermatological image segmentation. Our code is publicly available at: https://github.com/maklachur/MambaLiteUNet.

The expanding ecosystem of pathology foundation models has produced powerful but fragmented tile-level representations, limiting their use in clinical tasks that require unified slide-level reasoning and interpretable linkage to clinically meaningful information. We present ASTRA, a pan-cancer framework that integrates heterogeneous foundation-model representations into a shared slide-level representation space and semantically grounds that space using structured pathology annotation fields, including classification category, cancer type, and anatomic site. ASTRA combines sparse mixture-of-experts contextualization, masked multi-model reconstruction, and contrastive alignment to structured pathology prompts to learn slide representations that support 4-category classification, 3-class solid tumor typing, 16-class cancer typing, and text-guided tumor localization without pixel-level supervision. Developed on a CHTN cohort of 10,359 whole-slide images (WSIs) spanning 16 tumor types, ASTRA consistently improves pan-cancer classification across four pathology foundation-model backbones, achieving up to 97.8% macro-AUC for 4-category classification, 99.7% for 3-class solid tumor typing, and 99.2% for 16-class cancer typing. For tumor localization, ASTRA achieves a mean Dice of 0.897 on an annotated in-domain CHTN subset (n = 380) spanning 16 cancer types and 0.738 on an external TCGA cohort (n = 1,686) spanning four cancer types. These results demonstrate that minimal structured pathology annotation fields derived from slide-level metadata can provide effective semantic supervision for unified slide representation learning, enabling both pan-cancer prediction and weakly supervised tumor localization within a single framework.

Automated 3D segmentation of prostate lesions from biparametric MRI (bp-MRI) is essential for reliable algorithmic analysis, but achieving high precision remains challenging. Volumetric methods must combine multiple modalities while ensuring anatomical consistency, but current models struggle to integrate cross-modal information reliably. While vision-language models (VLMs) are replacing the currently used architectural designs, they still lack the fine-grained, lesion-level semantics required for effective localized guidance. To address these limitations, we propose a new multi-encoder U-Net architecture incorporating three key innovations: (1) an alignment loss that enhances foreground text-image similarity to inject lesion semantics; (2) a heatmap loss that calibrates the similarity map and suppresses spurious background activations; and (3) a final-stage, confidence-gated multi-head cross-attention refiner that performs localized boundary edits in high-confidence regions. A phase-scheduled training regime stabilizes the optimization of these components. Our method consistently outperforms prior approaches, establishing a new state-of-the-art on the PI-CAI dataset through enhanced multi-modal fusion and localized text guidance. Our code is available at https://github.com/NUBagciLab/Prostate-Lesion-Segmentation.

Large segmentation foundation models such as the Segment Anything Model (SAM) have reshaped promptable segmentation in natural images, and recent efforts have extended these models to medical images and volumetric settings. However, directly transferring a 3D SAM-style model to lesion segmentation remains challenging due to (i) weak spatial representational capacity for small, irregular targets in intermediate features, and (ii) extreme foreground-background imbalance in 3D volumes.We propose SGP-SAM, a self-gated prompting framework for efficient and effective transfer to 3D lesion segmentation. Our key component, the Self-Gated Prompting Module (SGPM), performs conditional multi-scale spatial enhancement: a lightweight multi-channel gating unit predicts whether the current features require additional multi-scale fusion, and only then activates a Multi-Scale Feature Fusion Block to enrich spatial context. To further address small-lesion learning, we design a Zoom Loss that up-weights lesion-focused supervision by combining Dice and a voxel-balanced focal term.Experiments on MSD Liver Tumor and MSD Brain Tumor (enhancing tumor) show consistent gains over strong transfer baselines based on SAM-Med3D. On MSD Liver Tumor, SGP-SAM improves mDice by 7.3% over fine-tuning.

Precise localization and delineation of brain tumors using magnetic resonance imaging (MRI) are essential for planning therapy and guiding surgical decisions. To address this, we propose LoGSAM, a parameter-efficient, detection-driven framework that transforms radiologist dictation into text prompts for foundation-model-based localization and segmentation. Radiologist speech is first transcribed and translated using a pretrained Whisper ASR model, followed by negation-aware clinical NLP to extract tumor-specific textual prompts. These prompts guide text-conditioned tumor localization via a LoRA-adapted vision-language detection model, Grounding DINO (GDINO). The predicted bounding boxes are used as prompts for MedSAM to generate pixel-level tumor masks without any additional fine-tuning. On BRISC 2025, LoGSAM attains a Dice score of 80.32%, reaching 98.6% of a fully fine-tuned GDINO + MedSAM baseline while training fewer than 5% of its parameters, indicating a favorable accuracy/parameter trade-off. In addition, we evaluate the full pipeline using German dictations from a board-certified radiologist on unseen MRI scans, achieving 91.7% case-level class-extraction accuracy. These results highlight the feasibility of constructing a modular speech-to-segmentation pipeline from pretrained foundation models with minimal parameter updates.

Delineating the clinical target volume (CTV) in radiotherapy involves complex margins constrained by tumor location and anatomical barriers. While deep learning models automate this process, their rigid reliance on expert-annotated data requires costly retraining whenever clinical guidelines update. To overcome this limitation, we introduce OncoAgent, a novel guideline-aware AI agent framework that seamlessly converts textual clinical guidelines into three-dimensional target contours in a training-free manner. Evaluated on esophageal cancer cases, the agent achieves a zero-shot Dice similarity coefficient of 0.842 for the CTV and 0.880 for the planning target volume, demonstrating performance highly comparable to a fully supervised nnU-Net baseline. Notably, in a blinded clinical evaluation, physicians strongly preferred OncoAgent over the supervised baseline, rating it higher in guideline compliance, modification effort, and clinical acceptability. Furthermore, the framework generalizes zero-shot to alternative esophageal guidelines and other anatomical sites (e.g., prostate) without any retraining. Beyond mere volumetric overlap, our agent-based paradigm offers near-instantaneous adaptability to alternative guidelines, providing a scalable and transparent pathway toward interpretability in radiotherapy treatment planning.

Accurate longitudinal analysis of brain MRI is often hindered by evolving lesions, which bias automated neuroimaging pipelines. While deep generative models have shown promise in inpainting these lesions, most existing methods operate cross-sectionally or lack 3D anatomical continuity. We present a novel pseudo-3D longitudinal inpainting framework based on Denoising Diffusion Probabilistic Models (DDPM). Our approach utilizes multi-channel conditioning to incorporate longitudinal context from distinct visits (t_1, t_2) and extends Region-Aware Diffusion (RAD) to the medical domain, focusing the generative process on pathological regions without altering surrounding healthy tissue. We evaluated our model against state-of-the-art baselines on longitudinal brain MRI from 93 patients. Our model significantly outperforms the leading baseline (FastSurfer-LIT) in terms of perceptual fidelity, reducing the Learned Perceptual Image Patch Similarity (LPIPS) distance from 0.07 to 0.03 while effectively eliminating inter-slice discontinuities. Furthermore, our model demonstrates high longitudinal stability with a Temporal Fidelity Index of 1.024, closely approaching the ideal value of 1.0 and substantially narrowing the gap compared to LIT's TFI of 1.22. Notably, the RAD mechanism provides a substantial gain in efficiency; our framework achieves an average processing time of 2.53 min per volume, representing approximately 10x speedup over the 24.30 min required by LIT. By leveraging longitudinal priors and region-specific denoising, our framework provides a highly reliable and efficient preprocessing step for the study of progressive neurodegenerative diseases. A derivative dataset consisting of 93 pre-processed scans used for testing will be available upon request after acceptance. Code will be released upon acceptance.

Expert-annotated training data remains the critical bottleneck for AI in histopathology, particularly for rare pathologies where even dozens of cases may be unavailable. While data augmentation offers a solution, existing methods fail to generate sufficiently realistic lesion morphologies that preserve tissue-specific architectures. Here we present PathoGen, a diffusion-based generative model enabling controllable, high-fidelity lesion inpainting into benign histopathology images. We validate PathoGen across four datasets representing kidney, skin, breast, and prostate pathology. Quantitative assessment confirms PathoGen outperforms state-of-the-art baselines in image fidelity and distributional similarity. Evaluation by six expert pathologists revealed that synthetic images by PathoGen were only marginally distinguished from real tissue image slightly above chance (57.75% accuracy), demonstrating strong perceptual realism of PathoGen-generated lesions. PathoGen achieved the highest win rate (35.4%) when pathologists ranked generation quality against all baselines. Crucially, augmenting training sets with PathoGen-synthesized lesions improves segmentation Dice scores by up to 0.18 compared to traditional augmentations, with maximum benefit in data-scarce regimes. By simultaneously generating realistic morphology and pixel-level annotations, PathoGen effectively addresses both data scarcity and annotation cost, two critical bottlenecks in computational pathology development.

While foundation models in radiology are expected to be applied to various clinical tasks, computational cost constraints remain a major challenge when training on 3D-CT volumetric data. In this study, we propose TotalFM, a radiological foundation model that efficiently learns the correspondence between 3D-CT images and linguistic expressions based on the concept of organ separation, utilizing a large-scale dataset of 140,000 series. By automating the creation of organ volume and finding-sentence pairs through segmentation techniques and Large Language Model (LLM)-based radiology report processing, and by combining self-supervised pre-training via VideoMAE with contrastive learning using volume-text pairs, we aimed to balance computational efficiency and representation capability. In zero-shot organ-wise lesion classification tasks, the proposed model achieved higher F1 scores in 83% (5/6) of organs compared to CT-CLIP and 64% (9/14) of organs compared to Merlin. These results suggest that the proposed model exhibits high generalization performance in a clinical evaluation setting using actual radiology report sentences. Furthermore, in zero-shot finding-wise lesion classification tasks, our model achieved a higher AUROC in 83% (25/30) of finding categories compared to Merlin. We also confirmed performance comparable to existing Vision-Language Models (VLMs) in radiology report generation tasks. Our results demonstrate that the organ-separated learning framework can serve as a realistic and effective design guideline for the practical implementation of 3D-CT foundation models. The source code and pretrained models are publicly available at https://github.com/jichi-labo/TotalFM.

Choroidal nevi are common benign pigmented lesions in the eye, with a small risk of transforming into melanoma. Early detection is critical to improving survival rates, but misdiagnosis or delayed diagnosis can lead to poor outcomes. Despite advancements in AI-based image analysis, diagnosing choroidal nevi in colour fundus images remains challenging, particularly for clinicians without specialized expertise. Existing datasets often suffer from low resolution and inconsistent labelling, limiting the effectiveness of segmentation models. This paper addresses the challenge of achieving precise segmentation of fundus lesions, a critical step toward developing robust diagnostic tools. While deep learning models like U-Net have demonstrated effectiveness, their accuracy heavily depends on the quality and quantity of annotated data. Previous mathematical/clustering segmentation methods, though accurate, required extensive human input, making them impractical for medical applications. This paper proposes a novel approach that combines mathematical/clustering segmentation models with insights from U-Net, leveraging the strengths of both methods. This hybrid model improves accuracy, reduces the need for large-scale training data, and achieves significant performance gains on high-resolution fundus images. The proposed model achieves a Dice coefficient of 89.7% and an IoU of 80.01% on 1024*1024 fundus images, outperforming the Attention U-Net model, which achieved 51.3% and 34.2%, respectively. It also demonstrated better generalizability on external datasets. This work forms a part of a broader effort to develop a decision support system for choroidal nevus diagnosis, with potential applications in automated lesion annotation to enhance the speed and accuracy of diagnosis and monitoring.

This paper outlines the specifications and design approach used to construct a full body imaging scanner capable of capturing skin lesions at a dermatoscopic level using cameras mounted on the end-effectors of four UR10 manipulators. The system possesses a view-planning algorithm capable of appropriately selecting the best camera position to acquire images of moles, a high-level controller to allow the manipulators to work simultaneously and a collision-detector that halts the manipulators when they make contact with an object or a person. We evaluate the system through real-patient full-body scans, comparing acquired images against contact dermoscopy and an existing total-body photography system (Vectra) across clinically relevant lesion features, and quantify true optical resolving power using a USAF 1951 resolution target, yielding a smallest resolvable feature size of 22.1 microns for our scanner compared to 8.8 microns for contact dermoscopy. Results show the scanner consistently outperforms Vectra across most clinically relevant features and achieves comparable performance to contact dermoscopy for the majority of features assessed. By acquiring dermatoscopic-quality images automatically and without contact, and without requiring a separate manual dermoscopic examination, the scanner closes part of the gap between total-body photography and handheld dermoscopy, suggesting potential for future integration into screening workflows.