Medical Image Segmentation

Objective: To develop a robust and compact deep learning model for automated knee cartilage segmentation on point-of-care ultrasound (POCUS) devices. Methods: We propose MonoUNet, a novel, highly compact segmentation model consisting of (i) an aggressively reduced U-Net backbone, (ii) a trainable monogenic block that extracts multi-scale local phase features from the input, and (iii) a gating mechanism that injects these features into the encoder stages to reduce sensitivity to variations in ultrasound image appearance. MonoUNet segmentation performance was evaluated on a multi-site, multi-device knee cartilage ultrasound dataset using Dice score and mean average surface distance (MASD). Agreement between MonoUNet and manual cartilage outcomes (thickness and echo intensity) was assessed using Bland-Altman analysis with 95% limits of agreement, and reliability was assessed using intraclass correlation coefficient (ICC$_{2,k}$). Results: Overall, MonoUNet outperformed existing lightweight segmentation models, with average Dice scores ranging from 92.62% to 94.82% and MASD values between 0.133 mm and 0.254 mm. MonoUNet reduces the number of parameters by 10x--700x and computational cost by 14x--2000x relative to existing lightweight models. MonoUNet cartilage outcomes showed excellent reliability and agreement with the manual outcomes: intraclass correlation coefficients (ICC$_{2,k})$=0.96 and bias=2.00% (0.047 mm) for average thickness, and ICC$_{2,k}$=0.99 and bias=0.80% (0.328 a.u.) for echo intensity. Conclusion: Incorporating trainable local phase features improves the robustness of highly compact neural networks for knee cartilage segmentation across varying acquisition settings and could support scalable ultrasound-based assessment and monitoring of knee osteoarthritis using POCUS devices. The code is publicly available at https://github.com/alvinkimbowa/monounet.

Domain generalization is a technique aimed at enabling models to maintain high accuracy when applied to new environments or datasets (unseen domains) that differ from the datasets used in training. Generally, the accuracy of models trained on a specific dataset (source domain) often decreases significantly when evaluated on different datasets (target domain). This issue arises due to differences in domains caused by varying environmental conditions such as imaging equipment and staining methods. Therefore, we undertook two initiatives to perform segmentation that does not depend on domain differences. We propose a method that separates category information independent of domain differences from the information specific to the source domain. By using information independent of domain differences, our method enables learning the segmentation targets (e.g., blood vessels and cell nuclei). Although we extract independent information of domain differences, this cannot completely bridge the domain gap between training and test data. Therefore, we absorb the domain gap using the quantum vectors in Stochastically Quantized Variational AutoEncoder (SQ-VAE). In experiments, we evaluated our method on datasets for vascular segmentation and cell nucleus segmentation. Our methods improved the accuracy compared to conventional methods.

Kidney stone disease ranks among the most prevalent conditions in urology, and understanding the composition of these stones is essential for creating personalized treatment plans and preventing recurrence. Current methods for analyzing kidney stones depend on postoperative specimens, which prevents rapid classification before surgery. To overcome this limitation, we introduce a new approach called the Urinary Stone Segmentation and Classification Network (USCNet). This innovative method allows for precise preoperative classification of kidney stones by integrating Computed Tomography (CT) images with clinical data from Electronic Health Records (EHR). USCNet employs a Transformer-based multimodal fusion framework with CT-EHR attention and segmentation-guided attention modules for accurate classification. Moreover, a dynamic loss function is introduced to effectively balance the dual objectives of segmentation and classification. Experiments on an in-house kidney stone dataset show that USCNet demonstrates outstanding performance across all evaluation metrics, with its classification efficacy significantly surpassing existing mainstream methods. This study presents a promising solution for the precise preoperative classification of kidney stones, offering substantial clinical benefits. The source code has been made publicly available: https://github.com/ZhangSongqi0506/KidneyStone.

In semantic segmentation, the creation of pixel-level labels for training data incurs significant costs. To address this problem, semi-supervised learning, which utilizes a small number of labeled images alongside unlabeled images to enhance the performance, has gained attention. A conventional semi-supervised learning method, ClassMix, pastes class labels predicted from unlabeled images onto other images. However, since ClassMix performs operations using pseudo-labels obtained from unlabeled images, there is a risk of handling inaccurate labels. Additionally, there is a gap in data quality between labeled and unlabeled images, which can impact the feature maps. This study addresses these two issues. First, we propose a method where class labels from labeled images, along with the corresponding image regions, are pasted onto unlabeled images and their pseudo-labeled images. Second, we introduce a method that trains the model to make predictions on unlabeled images more similar to those on labeled images. Experiments on the Chase and COVID-19 datasets demonstrated an average improvement of 2.07% in mIoU compared to conventional semi-supervised learning methods.

Deep learning has been widely applied to 3D medical image segmentation tasks. However, due to the diversity of imaging modalities, the high-dimensional nature of the data, and the heterogeneity of anatomical structures, achieving both segmentation accuracy and computational efficiency in multi-organ segmentation remains a challenge. This study proposed GPAFormer, a lightweight network architecture specifically designed for 3D medical image segmentation, emphasizing efficiency while keeping high accuracy. GPAFormer incorporated two core modules: the multi-scale attention-guided stacked aggregation (MASA) and the mutual-aware patch graph aggregator (MPGA). MASA utilized three parallel paths with different receptive fields, combined through planar aggregation, to enhance the network's capability in handling structures of varying sizes. MPGA employed a graph-guided approach to dynamically aggregate regions with similar feature distributions based on inter-patch feature similarity and spatial adjacency, thereby improving the discrimination of both internal and boundary structures of organs. Experiments were performed on public whole-body CT and MRI datasets including BTCV, Synapse, ACDC, and BraTS. Compared to the existed 3D segmentation networkd, GPAFormer using only 1.81 M parameters achieved overall highest DSC on BTCV (75.70%), Synapse (81.20%), ACDC (89.32%), and BraTS (82.74%). Using consumer level GPU, the inference time for one validation case of BTCV spent less than one second. The results demonstrated that GPAFormer balanced accuracy and efficiency in multi-organ, multi-modality 3D segmentation tasks across various clinical scenarios especially for resource-constrained and time-sensitive clinical environments.

Large volumes of medical data remain underutilized because centralizing distributed data is often infeasible due to strict privacy regulations and institutional constraints. In addition, models trained in centralized settings frequently fail to generalize across clinical sites because of heterogeneity in imaging protocols and continuously evolving data distributions arising from differences in scanners, acquisition parameters, and patient populations. Federated learning offers a promising solution by enabling collaborative model training without sharing raw data. However, incorporating differential privacy into federated learning, while essential for privacy guarantees, often leads to degraded accuracy, unstable convergence, and reduced generalization. In this work, we propose an adaptive differentially private federated learning (ADP-FL) framework for medical image segmentation that dynamically adjusts privacy mechanisms to better balance the privacy-utility trade-off. The proposed approach stabilizes training, significantly improves Dice scores and segmentation boundary quality, and maintains rigorous privacy guarantees. We evaluated ADP-FL across diverse imaging modalities and segmentation tasks, including skin lesion segmentation in dermoscopic images, kidney tumor segmentation in 3D CT scans, and brain tumor segmentation in multi-parametric MRI. Compared with conventional federated learning and standard differentially private federated learning, ADP-FL consistently achieves higher accuracy, improved boundary delineation, faster convergence, and greater training stability, with performance approaching that of non-private federated learning under the same privacy budgets. These results demonstrate the practical viability of ADP-FL for high-performance, privacy-preserving medical image segmentation in real-world federated settings.

Medical image segmentation driven by free-text clinical instructions is a critical frontier in computer-aided diagnosis. However, existing multimodal and foundation models struggle with the semantic ambiguity of clinical reports and fail to disambiguate complex anatomical overlaps in low-contrast scans. Furthermore, fully fine-tuning these massive architectures on limited medical datasets invariably leads to severe overfitting. To address these challenges, we propose a novel Semantic-Topological Graph Reasoning (STGR) framework for language-guided pulmonary screening. Our approach elegantly synergizes the reasoning capabilities of large language models (LLaMA-3-V) with the zero-shot delineation of vision foundation models (MedSAM). Specifically, we introduce a Text-to-Vision Intent Distillation (TVID) module to extract precise diagnostic guidance. To resolve anatomical ambiguity, we formulate mask selection as a dynamic graph reasoning problem, where candidate lesions are modeled as nodes and edges capture spatial and semantic affinities. To ensure deployment feasibility, we introduce a Selective Asymmetric Fine-Tuning (SAFT) strategy that updates less than 1% of the parameters. Rigorous 5-fold cross-validation on the LIDC-IDRI and LNDb datasets demonstrates that our framework establishes a new state-of-the-art. Notably, it achieves an 81.5% Dice Similarity Coefficient (DSC) on LIDC-IDRI, outperforming leading LLM-based tools like LISA by over 5%. Crucially, our SAFT strategy acts as a powerful regularizer, yielding exceptional cross-fold stability (0.6% DSC variance) and paving the way for robust, context-aware clinical deployment.

Automatic diagnosis of canine pneumothorax is challenged by data scarcity and the need for trustworthy models. To address this, we first introduce a public, pixel-level annotated dataset to facilitate research. We then propose a novel diagnostic paradigm that reframes the task as a synergistic process of signal localization and spectral detection. For localization, our method employs a Vision-Language Model (VLM) to guide an iterative Flow Matching process, which progressively refines segmentation masks to achieve superior boundary accuracy. For detection, the segmented mask is used to isolate features from the suspected lesion. We then apply Random Matrix Theory (RMT), a departure from traditional classifiers, to analyze these features. This approach models healthy tissue as predictable random noise and identifies pneumothorax by detecting statistically significant outlier eigenvalues that represent a non-random pathological signal. The high-fidelity localization from Flow Matching is crucial for purifying the signal, thus maximizing the sensitivity of our RMT detector. This synergy of generative segmentation and first-principles statistical analysis yields a highly accurate and interpretable diagnostic system (source code is available at: https://github.com/Pu-Wang-alt/Canine-pneumothorax).

Distribution shift in medical imaging remains a central bottleneck for the clinical translation of medical AI. Failure to address it can lead to severe performance degradation in unseen environments and exacerbate health inequities. Existing methods for domain adaptation are inherently limited by exhausting predefined possibilities through simulated shifts or pseudo-supervision. Such strategies struggle in the open-ended and unpredictable real world, where distribution shifts are effectively infinite. To address this challenge, we introduce an empirical law called Rank Stability of Positive Regions'', which states that the relative rank of predicted probabilities for positive voxels remains stable under distribution shift. Guided by this principle, we propose CRISP, a parameter-free and model-agnostic framework requiring no target-domain information. CRISP is the first framework to make segmentation based on rank rather than probabilities. CRISP simulates model behavior under distribution shift via latent feature perturbation, where voxel probability rankings exhibit two stable patterns: regions that consistently retain high probabilities (destined positives according to the principle) and those that remain low-probability (can be safely classified as negatives). Based on these patterns, we construct high-precision (HP) and high-recall (HR) priors and recursively refine them under perturbation. We then design an iterative training framework, making HP and HR progressively squeeze'' to the final segmentation. Extensive evaluations on multi-center cardiac MRI and CT-based lung vessel segmentation demonstrate CRISP's superior robustness, significantly outperforming state-of-the-art methods with striking HD95 reductions of up to 0.14 (7.0% improvement), 1.90 (13.1% improvement), and 8.39 (38.9% improvement) pixels across multi-center, demographic, and modality shifts, respectively.

Optical Coherence Tomography (OCT) layer segmentation faces challenges due to annotation scarcity and heterogeneous label granularities across datasets. While semi-supervised learning helps alleviate label scarcity, existing methods typically assume a fixed granularity, failing to fully exploit cross-granularity supervision. This paper presents LUMOS, a semi-supervised universal OCT retinal layer segmentation framework based on a Dual-Decoder Network with a Hierarchical Prompting Strategy (DDN-HPS) and Reliable Progressive Multi-granularity Learning (RPML). DDN-HPS combines a dual-branch architecture with a multi-granularity prompting strategy to effectively suppress pseudo-label noise propagation. Meanwhile, RPML introduces region-level reliability weighing and a progressive training approach that guides the model from easier to more difficult tasks, ensuring the reliable selection of cross-granularity consistency targets, thereby achieving stable cross-granularity alignment. Experiments on six OCT datasets demonstrate that LUMOS largely outperforms existing methods and exhibits exceptional cross-domain and cross-granularity generalization capability.

Automated analysis of optical coherence tomography (OCT) and OCT angiography (OCTA) images is critical for robust ophthalmic diagnosis. Existing mainstream methods trained from scratch rely heavily on massive data and model scale, thereby hindering their practical deployment in resource-constrained clinical settings. Although transfer learning based on foundation models (FMs) is promising, it still faces significant challenges: domain shift and task misalignment. To address these, we propose TAPE: A Two-stage Adaptation Framework via Parameter-Efficient Fine-tuning, which strategically decouples adaptation into domain alignment and task fitting for downstream segmentation. The domain adaptation stage notably applies parameter-efficient fine-tuning (PEFT) in the context of masked image modeling for medical image domain adaptation, a novel approach to the best of our knowledge. Applying TAPE to retinal layer segmentation on both universal (masked auto-encoder, MAE) and specialized (RETFound) FMs, it demonstrates superior parameter efficiency and achieves state-of-the-art generalization performance across diverse pathologies.

Microcalcification (MC) analysis is clinically important in screening mammography because clustered puncta can be an early sign of malignancy, yet dense MC segmentation remains challenging: targets are extremely small and sparse, dense pixel-level labels are expensive and ambiguous, and cross-site shift often induces texture-driven false positives and missed puncta in dense tissue. We propose MC-GenRef, a real dense-label-free framework that combines high-fidelity synthetic supervision with test-time generative posterior refinement (TT-GPR). During training, real negative mammogram patches are used as backgrounds, and physically plausible MC patterns are injected through a lightweight image formation model with local contrast modulation and blur, yielding exact image-mask pairs without real dense annotation. Using only these synthetic labeled pairs, MC-GenRef trains a base segmentor and a seed-conditioned rectified-flow (RF) generator that serves as a controllable generative prior. During inference, TT-GPR treats segmentation as approximate posterior inference: it derives a sparse seed from the current prediction, forms seed-consistent RF projections, converts them into case-specific surrogate targets through the frozen segmentor, and iteratively refines the logits with overlap-consistent and edge-aware regularization. On INbreast, the synthetic-only initializer achieved the best Dice without real dense annotations, while TT-GPR improved miss-sensitive performance to Recall and FNR, with strong class-balanced behavior (Bal.Acc., G-Mean). On an external private Yonsei cohort ( n=50 ), TT-GPR consistently improved the synthetic-only initializer under cross-site shift, increasing Dice and Recall while reducing FNR. These results suggest that test-time generative posterior refinement is a practical route to reduce MC misses and improve robustness without additional real dense labeling.

Cardiac magnetic resonance (CMR) is a cornerstone for diagnosing cardiovascular disease. However, it remains underutilized due to complex, time-consuming interpretation across multi-sequences, phases, quantitative measures that heavily reliant on specialized expertise. Here, we present BAAI Cardiac Agent, a multimodal intelligent system designed for end-to-end CMR interpretation. The agent integrates specialized cardiac expert models to perform automated segmentation of cardiac structures, functional quantification, tissue characterization and disease diagnosis, and generates structured clinical reports within a unified workflow. Evaluated on CMR datasets from two hospitals (2413 patients) spanning 7-types of major cardiovascular diseases, the agent achieved an area under the receiver-operating-characteristic curve exceeding 0.93 internally and 0.81 externally. In the task of estimating left ventricular function indices, the results generated by this system for core parameters such as ejection fraction, stroke volume, and left ventricular mass are highly consistent with clinical reports, with Pearson correlation coefficients all exceeding 0.90. The agent outperformed state-of-the-art models in segmentation and diagnostic tasks, and generated clinical reports showing high concordance with expert radiologists (six readers across three experience levels). By dynamically orchestrating expert models for coordinated multimodal analysis, this agent framework enables accurate, efficient CMR interpretation and highlights its potentials for complex clinical imaging workflows. Code is available at https://github.com/plantain-herb/Cardiac-Agent.

Surgical video segmentation is fundamental to computer-assisted surgery. In practice, surgeons need to dynamically specify targets throughout extended procedures, using heterogeneous cues such as visual selections, textual expressions, or audio instructions. However, existing Promptable Video Object Segmentation (PVOS) methods are typically restricted to a single prompt modality and rely on coupled frameworks that cause optimization interference between target initialization and tracking. Moreover, these methods produce hallucinated predictions when the target is absent and suffer from accumulated mask drift without failure recovery. To address these challenges, we present UniSurgSAM, a unified PVOS model enabling reliable surgical video segmentation through visual, textual, or audio prompts. Specifically, UniSurgSAM employs a decoupled two-stage framework that independently optimizes initialization and tracking to resolve the optimization interference. Within this framework, we introduce three key designs for reliability: presence-aware decoding that models target absence to suppress hallucinations; boundary-aware long-term tracking that prevents mask drift over extended sequences; and adaptive state transition that closes the loop between stages for failure recovery. Furthermore, we establish a multi-modal and multi-granular benchmark from four public surgical datasets with precise instance-level masklets. Extensive experiments demonstrate that UniSurgSAM achieves state-of-the-art performance in real time across all prompt modalities and granularities, providing a practical foundation for computer-assisted surgery. Code and datasets will be available at https://jinlab-imvr.github.io/UniSurgSAM.

Few-Shot Medical Image Segmentation (FSMIS) aims to segment novel object classes in medical images using only minimal annotated examples, addressing the critical challenges of data scarcity and domain shifts prevalent in medical imaging. While Diffusion Models (DM) excel in visual tasks, their potential for FSMIS remains largely unexplored. We propose that the rich visual priors learned by large-scale DMs offer a powerful foundation for a more robust and data-efficient segmentation approach. In this paper, we introduce SD-FSMIS, a novel framework designed to effectively adapt the powerful pre-trained Stable Diffusion (SD) model for the FSMIS task. Our approach repurposes its conditional generative architecture by introducing two key components: a Support-Query Interaction (SQI) and a Visual-to-Textual Condition Translator (VTCT). Specifically, SQI provides a straightforward yet powerful means of adapting SD to the FSMIS paradigm. The VTCT module translates visual cues from the support set into an implicit textual embedding that guides the diffusion model, enabling precise conditioning of the generation process. Extensive experiments demonstrate that SD-FSMIS achieves competitive results compared to state-of-the-art methods in standard settings. Surprisingly, it also demonstrated excellent generalization ability in more challenging cross-domain scenarios. These findings highlight the immense potential of adapting large-scale generative models to advance data-efficient and robust medical image segmentation.

Most deep learning pipelines for retinal vessel segmentation resize fundus images to satisfy GPU memory constraints and enable uniform batch processing. However, the impact of this resizing on thin vessel detection remains underexplored. When high resolution images are downsampled, thin vessels are reduced to subpixel structures, causing irreversible information loss even before the data enters the network. Standard volumetric metrics such as the Dice score do not capture this loss because thick vessel pixels dominate the evaluation. We investigated this effect by training a baseline UNet at multiple downsampling ratios across five fundus datasets (DRIVE, STARE, CHASE_DB1, HRF, and FIVES) with native widths ranging from 565 to 3504 pixels, keeping all other settings fixed. We introduce a width-stratified sensitivity metric that evaluates thin (half-width <3 pixels), medium (3 to 7 pixels), and thick (>7 pixels) vessel detection separately, using native resolution width estimates derived from a Euclidean distance transform. Results show that for high-resolution datasets (HRF, FIVES), thin vessel sensitivity improves monotonically as images are downsampled toward the encoder's effective operating range, peaking at processed widths between 256 and 876 pixels. For low-to-mid resolution datasets (DRIVE, STARE, CHASE_DB1), thin vessel sensitivity is highest at or near native resolution and degrades with any downsampling. Across all five datasets, aggressive downsampling reduced thin vessel sensitivity by up to 15.8 percentage points (DRIVE) while Dice remained relatively stable, confirming that Dice alone is insufficient for evaluating microvascular segmentation.

To continuously enhance model adaptability in surgical video scene parsing, recent studies incrementally update it to progressively learn to segment an increasing number of surgical instruments over time. However, prior works constantly overlooked the potential of positive forward knowledge transfer, i.e., how past knowledge could help learn new classes, and positive backward knowledge transfer, i.e., how learning new classes could help refine past knowledge. In this paper, we propose a self-reflection hierarchical prompt framework that unlocks the power of positive forward and backward knowledge transfer in class incremental segmentation, aiming to proficiently learn new instruments, improve existing skills of regular instruments, and avoid catastrophic forgetting of old instruments. Our framework is built on a frozen, pre-trained model that adaptively appends instrument-aware prompts for new classes throughout training episodes. To enable positive forward knowledge transfer, we organize instrument prompts into a hierarchical prompt parsing tree with the instrument-shared prompt partition as the root node, n-part-shared prompt partitions as intermediate nodes and instrument-distinct prompt partitions as leaf nodes, to expose the reusable historical knowledge for new classes to simplify their learning. Conversely, to encourage positive backward knowledge transfer, we conduct self-reflection refining on existing knowledge by directed-weighted graph propagation, examining the knowledge associations recorded in the tree to improve its representativeness without causing catastrophic forgetting. Our framework is applicable to both CNN-based models and advanced transformer-based foundation models, yielding more than 5% and 11% improvements over the competing methods on two public benchmarks respectively.

Data heterogeneity hinders clinical deployment of medical image analysis models, and generative data augmentation helps mitigate this issue. However, recent diffusion-based methods that synthesize image-mask pairs often ignore distribution shifts between generated and real images across scenarios, and such mismatches can markedly degrade downstream performance. To address this issue, we propose AlignFlow, a flow matching model that aligns with the target reference image distribution via differentiable reward fine-tuning, and remains effective even when only a small number of reference images are provided. Specifically, we divide the training of the flow matching model into two stages: in the first stage, the model fits the training data to generate plausible images; Then, we introduce a distribution alignment mechanism and employ differentiable reward to steer the generated images toward the distribution of the given samples from the target domain. In addition, to enhance the diversity of generated masks, we also design a flow matching based mask generation to complement the diversity in regions of interest. Extensive experiments demonstrate the effectiveness of our approach, i.e., performance improvement by 3.5-4.0% in mDice and 3.5-5.6% in mIoU across a variety of datasets and scenarios.

LLMs have demonstrated remarkable capabilities in linguistic reasoning and are increasingly adept at vision-language tasks. The integration of image tokens into transformers has enabled direct visual input and output, advancing research from image-to-text descriptions to text-to-image generation. However, simple text-to-image generation holds limited clinical utility. In medical imaging, tasks such as image segmentation for localizing pathologies or image translation for reconstructing missing sequences have much greater clinical importance. Despite this, integrating these diverse, clinically relevant tasks within a single, versatile language model remains unexplored. Our method, LLaBIT (Large Language Model for Brain Image Translation), extends the visual reasoning of LLMs to these clinically meaningful tasks in the brain MRI domain. To mitigate the spatial information loss inherent in image tokenization, we incorporate a mechanism to reuse feature maps from the image encoder, minimizing data degradation. We also generate text data using LLMs with strict predefined instructions to augment limited image-text paired data in brain MRI. We comprehensively evaluated our method on five brain MRI datasets across four distinct tasks: report generation, visual question answering, image segmentation, and image translation. Our model not only demonstrated superior performance across all tasks but also outperformed specialized, task-specific models in direct comparisons, highlighting its efficacy and versatility

We present MaskGen, a theoretically grounded and deliberately simple approach for domain generalization in 3D biomedical image segmentation. Modern segmentation models degrade sharply under shifts in modality, disease severity, clinical sites, and more, limiting their reliable adoption. Existing generalization methods address this using extreme augmentations, hand-engineered domain statistics mixing, or architectural redesigns that add significant implementation overhead while yielding inconsistent performance across biomedical settings. MaskGen instead presents a principled learning strategy with marginal overhead that utilizes both source-domain image intensities and domain-stable foundation model representations to train robust segmentation models. As a result, MaskGen achieves strong gains in both fully supervised and few-shot segmentation across broad clinical shifts in biomedical studies. Unlike prior approaches, MaskGen is architecture- and loss-agnostic, compatible with standard augmentation pipelines, easy to implement, and tackles arbitrary anatomical regions. Its implementation is freely available at https://github.com/sebodiaz/MaskGen.

Lumbar Spinal Stenosis (LSS) diagnosis remains a critical clinical challenge, with diagnosis heavily dependent on labor-intensive manual interpretation of multi-view Magnetic Resonance Imaging (MRI), leading to substantial inter-observer variability and diagnostic delays. Existing vision-language models simultaneously fail to address the extreme class imbalance prevalent in clinical segmentation datasets while preserving spatial accuracy, primarily due to global pooling mechanisms that discard crucial anatomical hierarchies. We present an end-to-end Explainable Vision-Language Model framework designed to overcome these limitations, achieved through two principal objectives. We propose a Spatial Patch Cross-Attention module that enables precise, text-directed localization of spinal anomalies with spatial precision. A novel Adaptive PID-Tversky Loss function by integrating control theory principles dynamically further modifies training penalties to specifically address difficult, under-segmented minority instances. By incorporating foundational VLMs alongside an Automated Radiology Report Generation module, our framework demonstrates considerable performance: a diagnostic classification accuracy of 90.69%, a macro-averaged Dice score of 0.9512 for segmentation, and a CIDEr score of 92.80%. Furthermore, the framework shows explainability by converting complex segmentation predictions into radiologist-style clinical reports, thereby establishing a new benchmark for transparent, interpretable AI in clinical medical imaging that keeps essential human supervision while enhancing diagnostic capabilities.

Accurate segmentation of the prostate gland in multiparametric MRI (mpMRI) is a fundamental step for a wide range of clinical and research applications, including image registration, volume estimation, and radiomic analysis. However, manual delineation is time-consuming and subject to inter-observer variability, while general-purpose segmentation tools often fail to provide sufficient accuracy for prostate-specific tasks. In this work, we propose a dedicated deep learning-based approach for automatic prostate gland segmentation using the nnU-Net v2 framework. The model leverages multimodal mpMRI data, including T2-weighted imaging, diffusion-weighted imaging (DWI), and apparent diffusion coefficient (ADC) maps, to exploit complementary tissue information. Training was performed on 981 cases from the PI-CAI dataset using whole-gland annotations, and model performance was assessed through 5-fold cross-validation and external validation on an independent cohort of 54 patients from Hospital La Fe. The proposed model achieved a mean Dice score of 0.96 +/- 0.00 in cross-validation and 0.82 on the external test set, demonstrating strong generalization despite domain shift. In comparison, a general-purpose approach (TotalSegmentator) showed substantially lower performance, with a Dice score of 0.15, primarily due to under-segmentation of the gland. These results highlight the importance of task-specific, multimodal segmentation strategies and demonstrate the potential of the proposed approach for reliable integration into clinical research workflows. To facilitate reproducibility and deployment, the model has been fully containerized and is available as a ready-to-use inference tool.

Chest X-ray (CXR) segmentation is an important step in computer-aided diagnosis, yet deploying large foundation models in clinical settings remains challenging due to computational constraints. We propose AdaLoRA-QAT, a two-stage fine-tuning framework that combines adaptive low-rank encoder adaptation with full quantization-aware training. Adaptive rank allocation improves parameter efficiency, while selective mixed-precision INT8 quantization preserves structural fidelity crucial for clinical reliability. Evaluated across large-scale CXR datasets, AdaLoRA-QAT achieves 95.6% Dice, matching full-precision SAM decoder fine-tuning while reducing trainable parameters by 16.6\times and yielding 2.24\times model compression. A Wilcoxon signed-rank test confirms that quantization does not significantly degrade segmentation accuracy. These results demonstrate that AdaLoRA-QAT effectively balances accuracy, efficiency, and structural trust-worthiness, enabling compact and deployable foundation models for medical image segmentation. Code and pretrained models are available at: https://prantik-pdeb.github.io/adaloraqat.github.io/

Automated medical image segmentation has achieved remarkable progress with fully labeled data. However, site-specific clinical priorities and the high cost of manual annotation often yield scans with only a subset of organs labeled, leading to the partially labeled problem that degrades performance. To address this issue, we propose IPnP, an Iteratively Prompting and Pseudo-labeling framework, for partially labeled medical image segmentation. IPnP iteratively generates and refines pseudo-labels for unlabeled organs through collaboration between a trainable segmentation network (specialist) and a frozen foundation model (generalist), progressively recovering full-organ supervision. On the public dataset AMOS with the simulated partial-label setting, IPnP consistently improves segmentation performance over prior methods and approaches the performance of the fully labeled reference. We further evaluate on a private, partially labeled dataset of 210 head-and-neck cancer patients and demonstrate our effectiveness in real-world clinical settings.

Detecting and delineating tiny targets in 3D brain scans is a central yet under-addressed challenge in medical imaging.In ischemic stroke, for instance, the culprit thrombus is small, low-contrast, and variably expressed across modalities(e.g., susceptibility-weighted T2 blooming, diffusion restriction on DWI/ADC), while real-world multi-center dataintroduce domain shifts, anisotropy, and frequent missing sequences. We introduce a methodology that couples an attention-based recurrent segmentation network (UpAttLLSTM), a training schedule that progressively increases the difficulty of hetero-modal learning, with gradual modality dropout, UpAttLLSTM aggregates context across slices via recurrent units (2.5D) and uses attention gates to fuse complementary cues across available sequences, making it robust to anisotropy and class imbalance. Gradual modality dropout systematically simulates site heterogeneity,noise, and missing modalities during training, acting as both augmentation and regularization to improve multi-center generalization. On a monocentric cohort, our approach detects thrombi in >90% of cases with a Dice score of 0.65. In a multi-center setting with missing modalities, it achieves-80% detection with a Dice score around 0.35. Beyond stroke, the proposed methodology directly transfers to other small-lesion tasks in 3D medical imaging where targets are scarce, subtle, and modality-dependent

Building a unified model with a single set of parameters to efficiently handle diverse types of medical lesion segmentation has become a crucial objective for AI-assisted diagnosis. Existing unified segmentation approaches typically rely on shared encoders across heterogeneous tasks and modalities, which often leads to feature entanglement, gradient interference, and suboptimal lesion discrimination. In this work, we propose TP-Seg, a task-prototype framework for unified medical lesion segmentation. On one hand, the task-conditioned adapter effectively balances shared and task-specific representations through a dual-path expert structure, enabling adaptive feature extraction across diverse medical imaging modalities and lesion types. On the other hand, the prototype-guided task decoder introduces learnable task prototypes as semantic anchors and employs a cross-attention mechanism to achieve fine-grained modeling of task-specific foreground and background semantics. Without bells and whistles, TP-Seg consistently outperforms specialized, general and unified segmentation methods across 8 different medical lesion segmentation tasks covering multiple imaging modalities, demonstrating strong generalization, scalability and clinical applicability.

Dental diagnosis from Orthopantomograms (OPGs) requires coordination of tooth detection, caries segmentation (CarSeg), anomaly detection (AD), and dental developmental staging (DDS). We propose Mamba-based Architectural Tooth Hierarchical Estimator and Holistic Evaluation Network for Anatomy (MATHENA), a unified framework leveraging Mamba's linear-complexity State Space Models (SSM) to address all four tasks. MATHENA integrates MATHE, a multi-resolution SSM-driven detector with four-directional Vision State Space (VSS) blocks for O(N) global context modeling, generating per-tooth crops. These crops are processed by HENA, a lightweight Mamba-UNet with a triple-head architecture and Global Context State Token (GCST). In the triple-head architecture, CarSeg is first trained as an upstream task to establish shared representations, which are then frozen and reused for downstream AD fine-tuning and DDS classification via linear probing, enabling stable, efficient learning. We also curate PARTHENON, a benchmark comprising 15,062 annotated instances from ten datasets. MATHENA achieves 93.78% mAP@50 in tooth detection, 90.11% Dice for CarSeg, 88.35% for AD, and 72.40% ACC for DDS.

Ultra-high field 7-tesla (7T) MRI improves visualization of multiple sclerosis (MS) white matter lesions (WML) but differs sufficiently in contrast and artifacts from 1.5-3T imaging - suggesting that widely used automated segmentation tools may not translate directly. We analyzed 7T FLAIR scans and generated reference WML masks from Lesion Segmentation Tool (LST) outputs followed by expert manual revision. As external comparators, we applied LST-LPA and the more recent LST-AI ensemble, both originally developed on lower-field data. We then trained 3D UNETR and SegFormer transformer-based models on 7T FLAIR at multiple resolutions (0.5x0.5x0.5^3, 1.0x1.0x1.0^3, and 1.5x1.5x2.0^3) and evaluated all methods using voxel-wise and lesion-wise metrics from the BraTS 2023 framework. On the held-out test set at native 0.5x0.5x0.5^3 resolution, 7T-trained transformers achieved competitive overlap with LST-AI while recovering additional small lesions that were missed by classical methods, at the cost of some boundary variability and occasional artifact-related false positives. On a held-out 7 T test set, our best transformer model (SegFormer) achieved a voxel-wise Dice of 0.61 and lesion-wise Dice of 0.20, improving on the classical LST-LPA tool (Dice 0.39, lesion-wise Dice 0.02). Performance decreased for models trained on downsampled images, underscoring the value of native 7T resolution for small-lesion detection. By releasing our 7T-trained models, we aim to provide a reproducible, ready-to-use resource for automated lesion quantification in ultra-high field MS research (https://github.com/maynord/7T-MS-lesion-segmentation).

Background: Deep learning has demonstrated significant potential for automated brain metastases (BM) segmentation; however, models trained at a singular institution often exhibit suboptimal performance at various sites due to disparities in scanner hardware, imaging protocols, and patient demographics. The goal of this work is to create a domain adaptation framework that will allow for BM segmentation to be used across multiple institutions. Methods: We propose a VAE-MMD preprocessing pipeline that combines variational autoencoders (VAE) with maximum mean discrepancy (MMD) loss, incorporating skip connections and self-attention mechanisms alongside nnU-Net segmentation. The method was tested on 740 patients from four public databases: Stanford, UCSF, UCLM, and PKG, evaluated by domain classifier's accuracy, sensitivity, precision, F1/F2 scores, surface Dice (sDice), and 95th percentile Hausdorff distance (HD95). Results: VAE-MMD reduced domain classifier accuracy from 0.91 to 0.50, indicating successful feature alignment across institutions. Reconstructed volumes attained a PSNR greater than 36 dB, maintaining anatomical accuracy. The combined method raised the mean F1 by 11.1% (0.700 to 0.778), the mean sDice by 7.93% (0.7121 to 0.7686), and reduced the mean HD95 by 65.5% (11.33 to 3.91 mm) across all four centers compared to the baseline nnU-Net. Conclusions: VAE-MMD effectively diminishes cross-institutional data heterogeneity and enhances BM segmentation generalization across volumetric, detection, and boundary-level metrics without necessitating target-domain labels, thereby overcoming a significant obstacle to the clinical implementation of AI-assisted segmentation.

Accurate segmentation of cardiac structures in cardiovascular magnetic resonance (CMR) images is essential for reliable diagnosis and treatment of cardiovascular diseases. However, manual segmentation remains time-consuming and suffers from significant inter-observer variability. Recent advances in deep learning, particularly foundation models such as the Segment Anything Model (SAM), demonstrate strong generalization but often lack the boundary precision required for clinical applications. To address this limitation, we propose CardioSAM, a hybrid architecture that combines the generalized feature extraction capability of a frozen SAM encoder with a lightweight, trainable cardiac-specific decoder. The proposed decoder introduces two key innovations: a Cardiac-Specific Attention module that incorporates anatomical topological priors, and a Boundary Refinement Module designed to improve tissue interface delineation. Experimental evaluation on the ACDC benchmark demonstrates that CardioSAM achieves a Dice coefficient of 93.39%, IoU of 87.61%, pixel accuracy of 99.20%, and HD95 of 4.2 mm. The proposed method surpasses strong baselines such as nnU-Net by +3.89% Dice and exceeds reported inter-expert agreement levels (91.2%), indicating its potential for reliable and clinically applicable cardiac segmentation.