3D Medical Image Segmentation

Overview

This field develops methods that label anatomical structures and disease in 3D CT, MRI, PET, and other scans, supporting diagnosis, treatment planning, and quantitative analysis. U-Net and nnU-Net remain common baselines, alongside Transformer and state-space models; newer work also uses anatomical and topological constraints, foundation models with prompts, and efficient ways to process volumes. To reduce dependence on costly voxel-level labels, researchers use self-supervised pretraining, synthetic data, semi-supervised learning, and interactive correction, evaluating methods on tasks such as BraTS, BTCV, and ACDC. A central challenge is that strong scores on familiar datasets may not hold across hospitals, scanners, or modalities, while thin structures, uncertain boundaries, and limited compute make reliable clinical deployment difficult.

Latest papers

213 papers14 papers in the last four weeks, down 53% on the four weeks before. 0.1% of all new papers.

Mar 17, 2026

TCATSeg: A Tooth Center-Wise Attention Network for 3D Dental Model Semantic Segmentation

Accurate semantic segmentation of 3D dental models is essential for digital dentistry applications such as orthodontics and dental implants. However, due to complex tooth arrangements and similarities in shape among adjacent teeth, existing methods struggle with accurate segmentation, because they often focus on local geometry while neglecting global contextual information. To address this, we propose TCATSeg, a novel framework that combines local geometric features with global semantic context. We introduce a set of sparse yet physically meaningful superpoints to capture global semantic relationships and enhance segmentation accuracy. Additionally, we present a new dataset of 400 dental models, including pre-orthodontic samples, to evaluate the generalization of our method. Extensive experiments demonstrate that TCATSeg outperforms state-of-the-art approaches.
Mar 15, 2026

Refining 3D Medical Segmentation with Verbal Instruction

Accurate 3D anatomical segmentation is essential for clinical diagnosis and surgical planning. However, automated models frequently generate suboptimal shape predictions due to factors such as limited and imbalanced training data, inadequate labeling quality, and distribution shifts between training and deployment settings. A natural solution is to iteratively refine the predicted shape based on the radiologists' verbal instructions. However, this is hindered by the scarcity of paired data that explicitly links erroneous shapes to corresponding corrective instructions. As an initial step toward addressing this limitation, we introduce CoWTalk, a benchmark comprising 3D arterial anatomies with controllable synthesized anatomical errors and their corresponding repairing instructions. Building on this benchmark, we further propose an iterative refinement model that represents 3D shapes as vector sets and interacts with textual instructions to progressively update the target shape. Experimental results demonstrate that our method achieves significant improvements over corrupted inputs and competitive baselines, highlighting the feasibility of language-driven clinician-in-the-loop refinement for 3D medical shapes modeling.
Mar 15, 2026

ITKIT: Feasible CT Image Analysis based on SimpleITK and MMEngine

CT images are widely used in clinical diagnosis and treatment, and their data have formed a de facto standard - DICOM. It is clear and easy to use, and can be efficiently utilized by data-driven analysis methods such as deep learning. In the past decade, many program frameworks for medical image analysis have emerged in the open-source community. ITKIT analyzed the characteristics of these frameworks and hopes to provide a better choice in terms of ease of use and configurability. ITKIT offers a complete pipeline from DICOM to 3D segmentation inference. Its basic practice only includes some essential steps, enabling users with relatively weak computing capabilities to quickly get started using the CLI according to the documentation. For advanced users, the OneDL-MMEngine framework provides a flexible model configuration and deployment entry. This paper conducted 12 typical experiments to verify that ITKIT can meet the needs of most basic scenarios.
Mar 14, 2026

Leveraging a Statistical Shape Model for Efficient Generation of Annotated Training Data: A Case Study on Liver Landmarks Segmentation

Anatomical landmark segmentation serves as a critical initial step for robust multimodal registration during computer-assisted interventions. Current approaches predominantly rely on deep learning, which often necessitates the extensive manual generation of annotated datasets. In this paper, we present a novel strategy for creating large annotated datasets using a statistical shape model (SSM) based on a mean shape that is manually labeled only once. We demonstrate the method's efficacy through its application to deep-learning-based anatomical landmark segmentation, specifically targeting the detection of the anterior ridge and the falciform ligament in 3D liver shapes. A specialized deep learning network was trained with 8,800 annotated liver shapes generated by the SSM. The network's performance was evaluated on 500 unseen synthetic SSM shapes, yielding a mean Intersection over Union of 91.4% (87.4% for the anterior ridge and 87.6% for the falciform ligament). Subsequently, the network was applied to clinical patient liver shapes, with qualitative evaluation indicating promising results and highlighting the generalizability of the proposed approach. Our findings suggest that the SSM-based data generation approach alleviates the labor-intensive process of manual labeling while enabling the creation of large annotated training datasets for machine learning. Although our study focuses on liver anatomy, the proposed methodology holds potential for a broad range of applications where annotated training datasets play a pivotal role in developing accurate deep-learning models.
Mar 12, 2026

Developing Foundation Models for Universal Segmentation from 3D Whole-Body Positron Emission Tomography

Positron emission tomography (PET) is a key nuclear medicine imaging modality that visualizes radiotracer distributions to quantify in vivo physiological and metabolic processes, playing an irreplaceable role in disease management. Despite its clinical importance, the development of deep learning models for quantitative PET image analysis remains severely limited, driven by both the inherent segmentation challenge from PET's paucity of anatomical contrast and the high costs of data acquisition and annotation. To bridge this gap, we develop generalist foundational models for universal segmentation from 3D whole-body PET imaging. We first build the largest and most comprehensive PET dataset to date, comprising 11041 3D whole-body PET scans with 59831 segmentation masks for model development. Based on this dataset, we present SegAnyPET, an innovative foundational model with general-purpose applicability to diverse segmentation tasks. Built on a 3D architecture with a prompt engineering strategy for mask generation, SegAnyPET enables universal and scalable organ and lesion segmentation, supports efficient human correction with minimal effort, and enables a clinical human-in-the-loop workflow. Extensive evaluations on multi-center, multi-tracer, multi-disease datasets demonstrate that SegAnyPET achieves strong zero-shot performance across a wide range of segmentation tasks, highlighting its potential to advance the clinical applications of molecular imaging.
Mar 11, 2026

Prompting with the human-touch: evaluating model-sensitivity of foundation models for musculoskeletal CT segmentation

Promptable Foundation Models (FMs), initially introduced for natural image segmentation, have also revolutionized medical image segmentation. The increasing number of models, along with evaluations varying in datasets, metrics, and compared models, makes direct performance comparison between models difficult and complicates the selection of the most suitable model for specific clinical tasks. In our study, 11 promptable FMs are tested using non-iterative 2D and 3D prompting strategies on a private and public dataset focusing on bone and implant segmentation in four anatomical regions (wrist, shoulder, hip and lower leg). The Pareto-optimal models are identified and further analyzed using human prompts collected through a dedicated observer study. Our findings are: 1) The segmentation performance varies a lot between FMs and prompting strategies; 2) The Pareto-optimal models in 2D are SAM and SAM2.1, in 3D nnInteractive and Med-SAM2; 3) Localization accuracy and rater consistency vary with anatomical structures, with higher consistency for simple structures (wrist bones) and lower consistency for complex structures (pelvis, tibia, implants); 4) The segmentation performance drops using human prompts, suggesting that performance reported on "ideal" prompts extracted from reference labels might overestimate the performance in a human-driven setting; 5) All models were sensitive to prompt variations. While two models demonstrated intra-rater robustness, it did not scale to inter-rater settings. We conclude that the selection of the most optimal FM for a human-driven setting remains challenging, with even high-performing FMs being sensitive to variations in human input prompts. Our code base for prompt extraction and model inference is available: https://github.com/CarolineMagg/segmentation-FM-benchmark/
Mar 10, 2026

A Guideline-Aware AI Agent for Zero-Shot Target Volume Auto-Delineation

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.
Mar 7, 2026

LightMedSeg: Lightweight 3D Medical Image Segmentation with Learned Spatial Anchors

Accurate and efficient 3D medical image segmentation is essential for clinical AI, where models must remain reliable under stringent memory, latency, and data availability constraints. Transformer-based methods achieve strong accuracy but suffer from excessive parameters, high FLOPs, and limited generalization. We propose LightMedSeg, a modular UNet-style segmentation architecture that integrates anatomical priors with adaptive context modeling. Anchor-conditioned FiLM modulation enables anatomy-aware feature calibration, while a local structural prior module and texture-aware routing dynamically allocate representational capacity to boundary-rich regions. Computational redundancy is minimized through ghost and depthwise convolutions, and multi-scale features are adaptively fused via a learned skip router with anchor-relative spatial position bias. Despite requiring only 0.48M parameters and 14.64~GFLOPs, LightMedSeg achieves segmentation accuracy within a few Dice points of heavy transformer baselines. Therefore, LightMedSeg is a deployable and data-efficient solution for 3D medical image segmentation. Code will be released publicly upon acceptance.
Mar 6, 2026

Self-Auditing Parameter-Efficient Fine-Tuning for Few-Shot 3D Medical Image Segmentation

Adapting foundation models to new clinical sites remains challenging in practice. Domain shift and scarce annotations must be handled by experts, yet many clinical groups do not have ready access to skilled AI engineers to tune adapter designs and training recipes. As a result, adaptation cycles can stretch from weeks to months, particularly in few-shot settings. Existing PEFT methods either require manual adapter configuration or automated searches that are computationally infeasible in few-shot 3D settings. We propose SEA-PEFT (SElf-Auditing Parameter-Efficient Fine-Tuning) to automate this process. SEA-PEFT treats adapter configuration as an online allocation problem solved during fine-tuning rather than through manual, fixed-topology choices. SEA-PEFT uses a search-audit-allocate loop that trains active adapters, estimates each adapter's Dice utility by momentarily toggling it off, and then reselects the active set under a parameter budget using a greedy knapsack allocator. Exponential Moving Average and Interquartile Range smoothing, together with a Finite-State Ranking controller, stabilize the loop and improve reliability in high-noise few-shot regimes. On TotalSegmentator and FLARE'22, SEA-PEFT improves mean Dice by 2.4--2.8 points over the strongest fixed-topology PEFT baselines across 1/5/10-shot settings while training <1% of parameters. For reproducibility purposes, we made our code publicly available at https://github.com/tsly123/SEA_PEFT
Mar 5, 2026

Meta-D: Metadata-Aware Architectures for Brain Tumor Analysis and Missing-Modality Segmentation

We present Meta-D, an architecture that explicitly leverages categorical scanner metadata such as MRI sequence and plane orientation to guide feature extraction for brain tumor analysis. We aim to improve the performance of medical image deep learning pipelines by integrating explicit metadata to stabilize feature representations. We first evaluate this in 2D tumor detection, where injecting sequence (e.g., T1, T2) and plane (e.g., axial) metadata dynamically modulates convolutional features, yielding an absolute increase of up to 2.62% in F1-score over image-only baselines. Because metadata grounds feature extraction when data are available, we hypothesize it can serve as a robust anchor when data are missing. We apply this to 3D missing-modality tumor segmentation. Our Transformer Maximizer utilizes metadata-based cross-attention to isolate and route available modalities, ensuring the network focuses on valid slices. This targeted attention improves brain tumor segmentation Dice scores by up to 5.12% under extreme modality scarcity while reducing model parameters by 24.1%.
Mar 4, 2026

Volumetric Directional Diffusion: Anchoring Uncertainty Quantification in Anatomical Consensus for Ambiguous Medical Image Segmentation

Ambiguous 3D medical image segmentation often involves boundaries where different expert delineations are non-identical yet clinically plausible. Modeling such inter-observer variability requires a careful balance between diversity and anatomical fidelity: deterministic models preserve coherent volumetric structures but collapse expert disagreement into a single mask, while stochastic generative models can produce diverse samples but may introduce disconnected components or slice-to-slice inconsistency when generating full 3D masks from unstructured noise. We propose Volumetric Directional Diffusion (VDD), a prior-anchored diffusion framework that shifts stochastic generation from full-mask synthesis to residual boundary exploration. VDD uses a coarse consensus prediction as an anatomical anchor and learns a directional diffusion process to generate plausible boundary variations around ambiguous regions while preserving stable volumetric topology. Experiments on three multi-rater datasets, including LIDC-IDRI, KiTS21, and ISBI 2015, show that VDD improves uncertainty distribution alignment while maintaining competitive segmentation accuracy and 3D structural consistency. These results suggest that prior-anchored residual diffusion can model clinically plausible expert disagreement without sacrificing anatomical fidelity.
Mar 3, 2026

ProSMA-UNet: Decoder Conditioning for Proximal-Sparse Skip Feature Selection

Medical image segmentation commonly relies on U-shaped encoder-decoder architectures such as U-Net, where skip connections preserve fine spatial detail by injecting high-resolution encoder features into the decoder. However, these skip pathways also propagate low-level textures, background clutter, and acquisition noise, allowing irrelevant information to bypass deeper semantic filtering -- an issue that is particularly detrimental in low-contrast clinical imaging. Although attention gates have been introduced to address this limitation, they typically produce dense sigmoid masks that softly reweight features rather than explicitly removing irrelevant activations. We propose ProSMA-UNet (Proximal-Sparse Multi-Scale Attention U-Net), which reformulates skip gating as a decoder-conditioned sparse feature selection problem. ProSMA constructs a multi-scale compatibility field using lightweight depthwise dilated convolutions to capture relevance across local and contextual scales, then enforces explicit sparsity via an ℓ1\ell_1 proximal operator with learnable per-channel thresholds, yielding a closed-form soft-thresholding gate that can remove noisy responses. To further suppress semantically irrelevant channels, ProSMA incorporates decoder-conditioned channel gating driven by global decoder context. Extensive experiments on challenging 2D and 3D benchmarks demonstrate state-of-the-art performance, with particularly large gains (≈20\approx20%) on difficult 3D segmentation tasks. Project page: https://math-ml-x.github.io/ProSMA-UNet/
Mar 2, 2026

Aligning Fetal Anatomy with Kinematic Tree Log-Euclidean PolyRigid Transforms

Automated analysis of articulated bodies is crucial in medical imaging. Existing surface-based models often ignore internal volumetric structures and rely on deformation methods that lack anatomical consistency guarantees. To address this problem, we introduce a differentiable volumetric body model based on the Skinned Multi-Person Linear (SMPL) formulation, driven by a new Kinematic Tree-based Log-Euclidean PolyRigid (KTPolyRigid) transform. KTPolyRigid resolves Lie algebra ambiguities associated with large, non-local articulated motions, and encourages smooth, bijective volumetric mappings. Evaluated on 53 fetal MRI volumes, KTPolyRigid yields deformation fields with significantly fewer folding artifacts. Furthermore, our framework enables robust groupwise image registration and a label-efficient, template-based segmentation of fetal organs. It provides a robust foundation for standardized volumetric analysis of articulated bodies in medical imaging.
Mar 1, 2026

The Texture-Shape Dilemma: Boundary-Safe Synthetic Generation for 3D Medical Transformers

Vision Transformers (ViTs) have revolutionized medical image analysis, yet their data-hungry nature clashes with the scarcity and privacy constraints of clinical archives. Formula-Driven Supervised Learning (FDSL) has emerged as a promising solution to this bottleneck, synthesizing infinite annotated samples from mathematical formulas without utilizing real patient data. However, existing FDSL paradigms rely on simple geometric shapes with homogeneous intensities, creating a substantial gap by neglecting tissue textures and noise patterns inherent in modalities like CT and MRI. In this paper, we identify a critical optimization conflict termed boundary aliasing: when high-frequency synthetic textures are naively added, they corrupt the image gradient signals necessary for learning structural boundaries, causing the model to fail in delineating real anatomical margins. To bridge this gap, we propose a novel Physics-inspired Spatially-Decoupled Synthesis framework. Our approach orthogonalizes the synthesis process: it first constructs a gradient-shielded buffer zone based on boundary distance to ensure stable shape learning, and subsequently injects physics-driven spectral textures into the object core. This design effectively reconciles robust shape representation learning with invariance to acquisition noise. Extensive experiments on the BTCV and MSD datasets demonstrate that our method significantly outperforms previous FDSL, as well as SSL methods trained on real-world medical datasets, by 1.43% on BTCV and up to 1.51% on MSD task, offering a scalable, annotation-free foundation for medical ViTs. The code will be made publicly available upon acceptance.
Mar 1, 2026

Fake It Right: Injecting Anatomical Logic into Synthetic Supervised Pre-training for Medical Segmentation

Vision Transformers (ViTs) excel in 3D medical segmentation but require massive annotated datasets. While Self-Supervised Learning (SSL) mitigates this using unlabeled data, it still faces strict privacy and logistical barriers. Formula-Driven Supervised Learning (FDSL) offers a privacy-preserving alternative by pre-training on synthetic mathematical primitives. However, a critical semantic gap limits its efficacy: generic shapes lack the morphological fidelity, fixed spatial layouts, and inter-organ relationships of real anatomy, preventing models from learning essential global structural priors. To bridge this gap, we propose an Anatomy-Informed Synthetic Supervised Pre-training framework unifying FDSL's infinite scalability with anatomical realism. We replace basic primitives with a lightweight shape bank with de-identified, label-only segmentation masks from 5 subjects. Furthermore, we introduce a structure-aware sequential placement strategy to govern the patch synthesis process. Instead of random placement, we enforce physiological plausibility using spatial anchors for correct localization and a topological graph to manage inter-organ interactions (e.g., preventing impossible overlaps). Extensive experiments on BTCV and MSD datasets demonstrate that our method significantly outperforms state-of-the-art FDSL baselines and SSL methods by 1.74% and up to 1.66%, while exhibiting a robust scaling effect where performance improves with increased synthetic data volume. This provides a data-efficient, privacy-compliant solution for medical segmentation. The code will be made publicly available upon acceptance.
Feb 27, 2026

Extending 2D foundational DINOv3 representations to 3D segmentation of neonatal brain MR images

Precise volumetric delineation of hippocampal structures is essential for quantifying neurodevelopmental trajectories in pre-term and term infants, where subtle morphological variations may carry prognostic significance. While foundation encoders trained on large-scale visual data offer discriminative representations, their 2D formulation is a limitation with respect to the 33D organization of brain anatomy. We propose a volumetric segmentation strategy that reconciles this tension through a structured window-based disassembly-reassembly mechanism: the global MRI volume is decomposed into non-overlapping 3D windows or sub-cubes, each processed via a separate decoding arm built upon frozen high-fidelity features, and subsequently reassembled prior to a ground-truth correspendence using a dense-prediction head. This architecture preserves constant a decoder memory footprint while forcing predictions to lie within an anatomically consistent geometry. Evaluated on the ALBERT dataset for hippocampal segmentation, the proposed approach achieves a Dice score of 0.65 for a single 3D window. The method demonstrates that volumetric anatomical structure could be recovered from frozen 2D foundation representations through structured compositional decoding, and offers a principled and generalizable extension for foundation models for 3D medical applications.
Feb 27, 2026

BiM-GeoAttn-Net: Linear-Time Depth Modeling with Geometry-Aware Attention for 3D Aortic Dissection CTA Segmentation

Accurate segmentation of aortic dissection (AD) lumens in CT angiography (CTA) is essential for quantitative morphological assessment and clinical decision-making. However, reliable 3D delineation remains challenging due to limited long-range context modeling, which compromises inter-slice coherence, and insufficient structural discrimination under low-contrast conditions. To address these limitations, we propose BiM-GeoAttn-Net, a lightweight framework that integrates linear-time depth-wise state-space modeling with geometry-aware vessel refinement. Our approach is featured by Bidirectional Depth Mamba (BiM) to efficiently capture cross-slice dependencies and Geometry-Aware Vessel Attention (GeoAttn) module that employs orientation-sensitive anisotropic filtering to refine tubular structures and sharpen ambiguous boundaries. Extensive experiments on a multi-source AD CTA dataset demonstrate that BiM-GeoAttn-Net achieves a Dice score of 93.35% and an HD95 of 12.36 mm, outperforming representative CNN-, Transformer-, and SSM-based baselines in overlap metrics while maintaining competitive boundary accuracy. These results suggest that coupling linear-time depth modeling with geometry-aware refinement provides an effective, computationally efficient solution for robust 3D AD segmentation.
Feb 27, 2026

VesselBridge3D: A Foundation Model Adaptation Framework for Label-Efficient 3D Vessel Segmentation

State-of-the-art vessel segmentation methods typically require large-scale annotated datasets and suffer from severe performance degradation under domain shifts. In clinical practice, however, acquiring extensive annotations for every new scanner or protocol is unfeasible. To address this, we propose VesselBridge3D, a foundation model adaptation framework that bridges frozen vision foundation models and volumetric vessel segmentation through lightweight 3D adaptation modules. The framework combines a lightweight 3D Adapter, a multi-scale 3D Aggregator, and Z-channel embedding for efficient adaptation to volumetric medical images. We instantiate VesselBridge3D with three frozen foundation encoders (DINOv3, MedSAM, and MedGemma) and evaluate it on the TopCoW (ID) and Lausanne (OOD) datasets. In the extreme low-data regime with 5 training samples, our method achieved a Dice score of 43.42%, marking a 30% relative improvement over the state-of-the-art nnU-Net (33.41%) and outperforming other Transformer-based baselines by up to 45%. The proposed framework was effective across all evaluated frozen foundation encoders, with DINOv3 yielding the best performance in the most label-efficient settings. Furthermore, in the out-of-distribution setting, our model demonstrated superior robustness, achieving a 50% relative improvement over nnU-Net (21.37% vs. 14.22%), which suffered from severe domain overfitting. Ablation studies confirmed the effectiveness of the proposed 3D adaptation modules. Our results demonstrate that VesselBridge3D is an effective framework for label-efficient 3D vessel segmentation under data scarcity and domain shifts.
Feb 26, 2026

Interactive Medical-SAM2 GUI: A Napari-based semi-automatic annotation tool for medical images

Interactive Medical-SAM2 GUI is an open-source desktop application for semi-automatic annotation of 2D and 3D medical images. Built on the Napari multi-dimensional viewer, box/point prompting is integrated with SAM2-style propagation by treating a 3D volume as a slice sequence, enabling mask propagation from sparse prompts using Medical-SAM2 on top of SAM2. Voxel-level annotation remains essential for developing and validating medical imaging algorithms, yet manual labeling is slow and expensive for 3D scans, and existing integrations frequently emphasize per-slice interaction without providing a unified, cohort-oriented workflow for navigation, propagation, interactive correction, and quantitative export in a single local pipeline. To address this practical limitation, a local-first Napari workflow is provided for efficient 3D annotation across multiple studies using standard DICOM series and/or NIfTI volumes. Users can annotate cases sequentially under a single root folder with explicit proceed/skip actions, initialize objects via box-first prompting (including first/last-slice initialization for single-object propagation), refine predictions with point prompts, and finalize labels through prompt-first correction prior to saving. During export, per-object volumetry and 3D volume rendering are supported, and image geometry is preserved via SimpleITK. The GUI is implemented in Python using Napari and PyTorch, with optional N4 bias-field correction, and is intended exclusively for research annotation workflows. The code is released on the project page: https://github.com/SKKU-IBE/Medical-SAM2GUI/.
Feb 25, 2026

VasGuideNet: Vascular Topology-Guided Couinaud Liver Segmentation with Structural Contrastive Loss

Accurate Couinaud liver segmentation is critical for preoperative surgical planning and tumor localization.However, existing methods primarily rely on image intensity and spatial location cues, without explicitly modeling vascular topology. As a result, they often produce indistinct boundaries near vessels and show limited generalization under anatomical variability.We propose VasGuideNet, the first Couinaud segmentation framework explicitly guided by vascular topology. Specifically, skeletonized vessels, Euclidean distance transform (EDT)--derived geometry, and k-nearest neighbor (kNN) connectivity are encoded into topology features using Graph Convolutional Networks (GCNs). These features are then injected into a 3D encoder--decoder backbone via a cross-attention fusion module. To further improve inter-class separability and anatomical consistency, we introduce a Structural Contrastive Loss (SCL) with a global memory bank.On Task08_HepaticVessel and our private LASSD dataset, VasGuideNet achieves Dice scores of 83.68% and 76.65% with RVDs of 1.68 and 7.08, respectively. It consistently outperforms representative baselines including UNETR, Swin UNETR, and G-UNETR++, delivering higher Dice/mIoU and lower RVD across datasets, demonstrating its effectiveness for anatomically consistent segmentation. Code is available at https://github.com/Qacket/VasGuideNet.git.
Feb 24, 2026

Federated Learning for Cross-Modality Medical Image Segmentation via Augmentation-Driven Generalization

Purpose: Developing generalizable medical image segmentation models is challenging because imaging data are distributed across institutions and differ in modality and acquisition protocol. Federated learning (FL) enables collaborative training without centralizing raw medical images, but cross-modality domain shifts between computed tomography (CT) and magnetic resonance imaging (MRI) can substantially reduce model performance. This study investigates augmentation-driven cross-modality FL for abdominal organ and whole-heart segmentation. Methods: We evaluate convolution-based spatial augmentation, frequency-domain argumentation, domain-specific normalization, and global intensity nonlinear (GIN) augmentation for multimodal segmentation. Abdominal organ segmentation and whole-heart segmentation are first evaluated using a 2D U-Net framework. For whole-heart segmentation, we additionally perform native 3D experiments using a self-configuring nnU-Net architecture on the CARE-WHS 2026 dataset, enabling evaluation of whether the observed cross-modality FL behavior persists when moving from slice-based 2D segmentation to volumetric 3D segmentation. Results: GIN provides the most consistent cross-modality performance among the evaluated approaches in the original 2D experiments. For pancreas segmentation, the Dice similarity coefficient (DSC) improved from 0.073 to 0.437 when CT data were incorporated through federated cross-modality training. In 3D whole-heart segmentation, FedGIN improved mean DSC over FedAvg from 0.8696 to 0.8901 on the unseen CT center and from 0.7160 to 0.7956 on the unseen MRI center. Relative to centralized GIN training, FedGIN retained 92.4% of performance on unseen CT data and achieved comparable performance on unseen MRI data (0.7956 versus 0.7937).
Feb 23, 2026

Token-UNet: A New Case for Transformers Integration in Efficient and Interpretable 3D UNets for Brain Imaging Segmentation

We present Token-UNet, adopting the TokenLearner and TokenFuser modules to encase Transformers into UNets. While Transformers have enabled global interactions among input elements in medical imaging, current computational challenges hinder their deployment on common hardware. Models like (Swin)UNETR adapt the UNet architecture by incorporating (Swin)Transformer encoders, which process tokens that each represent small subvolumes (838^3 voxels) of the input. The Transformer attention mechanism scales quadratically with the number of tokens, which is tied to the cubic scaling of 3D input resolution. This work reconsiders the role of convolution and attention, introducing Token-UNets, a family of 3D segmentation models that can operate in constrained computational environments and time frames. To mitigate computational demands, our approach maintains the convolutional encoder of UNet-like models, and applies TokenLearner to 3D feature maps. This module pools a preset number of tokens from local and global structures. Our results show this tokenization effectively encodes task-relevant information, yielding naturally interpretable attention maps. The memory footprint, computation times at inference, and parameter counts of our heaviest model are reduced to 33%, 10%, and 35% of the SwinUNETR values, with better average performance (86.75% ±0.19%\pm 0.19\% Dice score for SwinUNETR vs our 87.21% ±0.35%\pm 0.35\%). This work opens the way to more efficient trainings in contexts with limited computational resources, such as 3D medical imaging. Easing model optimization, fine-tuning, and transfer-learning in limited hardware settings can accelerate and diversify the development of approaches, for the benefit of the research community.
Feb 23, 2026

OrthoAI: A Neurosymbolic Framework for Evidence-Grounded Biomechanical Reasoning in Clear Aligner Orthodontics

Automated clinical decision support for clear aligner orthodontics faces a key challenge: bridging geometric perception (3D tooth segmentation) with clinical reasoning (biomechanical feasibility). We address this with OrthOAI, introducing three methodological contributions. First, sparse-supervision segmentation: a landmark-to-point-cloud synthesis protocol enables training from sparse anatomical annotations (6-8 points per tooth) instead of dense labels, combined with a clinically stratified loss mixing label-smoothed cross-entropy and a batch-adaptive Dice term for class imbalance. Second, knowledge-grounded constraint inference: biomechanical feasibility is modeled as a Constraint Satisfaction Problem over a domain ontology of tooth movements, encoding evidence-based per-stage limits as soft and hard constraints. Third, multi-criteria treatment evaluation: treatment quality is scored through a formal Multi-Criteria Decision Analysis framework using a weighted Additive Value Function grounded in clinical priority theory. On landmark-reconstructed point clouds from 3DTeethLand (MICCAI 2024), segmentation reaches 81.4% Tooth Identification Rate with 60,705 parameters. Ablations quantify the impact of each design choice. End-to-end inference runs in under 4 seconds on CPU. We also outline the gap between the current prototype-trained on synthetic ellipsoidal approximations-and clinical deployment, with a roadmap for validation. Code and weights are released.
Feb 23, 2026

Redefining the Down-Sampling Scheme of U-Net for Precision Biomedical Image Segmentation

U-Net architectures have been instrumental in advancing biomedical image segmentation (BIS) but often struggle with capturing long-range information. One reason is the conventional down-sampling techniques that prioritize computational efficiency at the expense of information retention. This paper introduces a simple but effective strategy, we call it Stair Pooling, which moderates the pace of down-sampling and reduces information loss by leveraging a sequence of concatenated small and narrow pooling operations in varied orientations. Specifically, our method modifies the reduction in dimensionality within each 2D pooling step from 14\frac{1}{4} to 12\frac{1}{2}. This approach can also be adapted for 3D pooling to preserve even more information. Such preservation aids the U-Net in more effectively reconstructing spatial details during the up-sampling phase, thereby enhancing its ability to capture long-range information and improving segmentation accuracy. Extensive experiments on three BIS benchmarks demonstrate that the proposed Stair Pooling can increase both 2D and 3D U-Net performance by an average of 3.8% in Dice scores. Moreover, we leverage the transfer entropy to select the optimal down-sampling paths and quantitatively show how the proposed Stair Pooling reduces the information loss.
Feb 18, 2026

RefineFormer3D: Efficient 3D Medical Image Segmentation via Adaptive Multi-Scale Transformer with Cross Attention Fusion

Accurate and computationally efficient 3D medical image segmentation remains a critical challenge in clinical workflows. Transformer-based architectures often demonstrate superior global contextual modeling but at the expense of excessive parameter counts and memory demands, restricting their clinical deployment. We propose RefineFormer3D, a lightweight hierarchical transformer architecture that balances segmentation accuracy and computational efficiency for volumetric medical imaging. The architecture integrates three key components: (i) GhostConv3D-based patch embedding for efficient feature extraction with minimal redundancy, (ii) MixFFN3D module with low-rank projections and depthwise convolutions for parameter-efficient feature extraction, and (iii) a cross-attention fusion decoder enabling adaptive multi-scale skip connection integration. RefineFormer3D contains only 2.94M parameters, substantially fewer than contemporary transformer-based methods. Extensive experiments on ACDC and BraTS benchmarks demonstrate that RefineFormer3D achieves 93.44% and 85.9% average Dice scores respectively, outperforming or matching state-of-the-art methods while requiring significantly fewer parameters. Furthermore, the model achieves fast inference (8.35 ms per volume on GPU) with low memory requirements, supporting deployment in resource-constrained clinical environments. These results establish RefineFormer3D as an effective and scalable solution for practical 3D medical image segmentation.
Feb 17, 2026

Bayesian Optimization for Design Parameters of 3D Image Data Analysis

Deep learning-based segmentation and classification are crucial to large-scale biomedical imaging, particularly for 3D data, where manual analysis is impractical. Although many methods exist, selecting suitable models and tuning parameters remains a major bottleneck in practice. Hence, we introduce the 3D data Analysis Optimization Pipeline, a method designed to facilitate the design and parameterization of segmentation and classification using two Bayesian Optimization stages. First, the pipeline selects a segmentation model and optimizes postprocessing parameters using a domain-adapted syntactic benchmark dataset. To ensure a concise evaluation of segmentation performance, we introduce a segmentation quality metric that serves as the objective function. Second, the pipeline optimizes design choices of a classifier, such as encoder and classifier head architectures, incorporation of prior knowledge, and pretraining strategies. To reduce manual annotation effort, this stage includes an assisted class-annotation workflow that extracts predicted instances from the segmentation results and sequentially presents them to the operator, eliminating the need for manual tracking. In four case studies, the 3D data Analysis Optimization Pipeline efficiently identifies effective model and parameter configurations for individual datasets.
Jan 14, 2026

MedVL-SAM2: A unified 3D medical vision-language model for multimodal reasoning and prompt-driven segmentation

Recent progress in medical vision-language models (VLMs) has achieved strong performance on image-level text-centric tasks such as report generation and visual question answering (VQA). However, achieving fine-grained visual grounding and volumetric spatial reasoning in 3D medical VLMs remains challenging, particularly when aiming to unify these capabilities within a single, generalizable framework. To address this challenge, we proposed MedVL-SAM2, a unified 3D medical multimodal model that concurrently supports report generation, VQA, and multi-paradigm segmentation, including semantic, referring, and interactive segmentation. MedVL-SAM2 integrates image-level reasoning and pixel-level perception through a cohesive architecture tailored for 3D medical imaging, and incorporates a SAM2-based volumetric segmentation module to enable precise multi-granular spatial reasoning. The model is trained in a multi-stage pipeline: it is first pre-trained on a large-scale corpus of 3D CT image-text pairs to align volumetric visual features with radiology-language embeddings. It is then jointly optimized with both language-understanding and segmentation objectives using a comprehensive 3D CT segmentation dataset. This joint training enables flexible interaction via language, point, or box prompts, thereby unifying high-level visual reasoning with spatially precise localization. Our unified architecture delivers state-of-the-art performance across report generation, VQA, and multiple 3D segmentation tasks. Extensive analyses further show that the model provides reliable 3D visual grounding, controllable interactive segmentation, and robust cross-modal reasoning, demonstrating that high-level semantic reasoning and precise 3D localization can be jointly achieved within a unified 3D medical VLM.
Dec 27, 2025

ReFRM3D: A Radiomics-enhanced Fused Residual Multiparametric 3D Network with Multi-Scale Feature Fusion for Glioma Characterization

Gliomas are among the most aggressive cancers, with complex diagnostic processes. Existing glioma segmentation methods often struggle with high variability in imaging data and inadequate optimization. Furthermore, radiomic analysis is typically applied only after segmentation is finished, limiting its ability to inform the segmentation process itself. To address these challenges, we propose a novel radiomics-enhanced fused residual multiparametric 3D network (ReFRM3D) for brain tumor characterization. The framework is based on a 3D U-Net architecture and features multi-scale feature fusion, hybrid upsampling, and an extended residual skip mechanism. Additionally, we introduce a radiomic conditioning mechanism that extracts texture and intensity descriptors from an intermediate coarse segmentation and re-injects them into the decoder to refine the final output. Experimental results on BraTS2019, BraTS2020, and BraTS2021 show strong performance, with mean DSC values of 93.45%, 93.61%, and 92.06%, respectively, across whole tumor, enhancing tumor, and tumor core regions. Compared with recent models, ReFRM3D improves average DSC by 5.79%, 7.25%, and 0.96% on these datasets. Our model also generalized well on the BraTS-Africa dataset with an average DSC of 87.8%, despite differences in scanner field strength and patient demographics.
Sep 27, 2025

Confidence-Calibrating Regularization for Robust Brain MRI Segmentation Under Domain Shift

The Segment Anything Model (SAM) exhibits strong zero-shot performance on natural images but suffers from domain shift and overconfidence when applied to medical volumes. We propose CalSAM, a lightweight adaptation framework that (i) reduces encoder sensitivity to domain shift via a Feature Fisher Information Penalty (FIP) computed on 3D feature maps and (ii) penalizes overconfident voxel-wise errors through a Confidence Misalignment Penalty (CMP). The combined loss, LCalSAM\mathcal{L}_{\mathrm{CalSAM}} fine-tunes only the mask decoder while keeping SAM's encoders frozen. On cross-center and scanner-shift evaluations, CalSAM substantially improves accuracy and calibration: e.g., on the BraTS scanner split (Siemens→\toGE) CalSAM shows a +7.4%+7.4\% relative improvement in DSC\mathrm{DSC} (80.1% vs.\ 74.6%), a −26.9%-26.9\% reduction in HD95\mathrm{HD95} (4.6 mm vs.\ 6.3 mm), and a −39.5%-39.5\% reduction in ECE\mathrm{ECE} (5.2% vs.\ 8.6%). On ATLAS-C (motion corruptions), CalSAM achieves a +5.3%+5.3\% relative improvement in DSC\mathrm{DSC} (75.9%) and a −32.6%-32.6\% reduction in ECE\mathrm{ECE} (5.8%). Ablations show FIP and CMP contribute complementary gains (p<0.01p<0.01), and the Fisher penalty incurs a modest ∼\sim15% training-time overhead. CalSAM therefore delivers improved domain generalization and better-calibrated uncertainty estimates for brain MRI segmentation, while retaining the computational benefits of freezing SAM's encoder.
Sep 26, 2025

Johnson-Lindenstrauss Lemma Guided Network for Efficient 3D Medical Segmentation

Lightweight 3D medical image segmentation remains constrained by a fundamental *efficiency / robustness conflict''*, particularly when processing complex anatomical structures and heterogeneous modalities. In this paper, we study how to redesign the framework based on the characteristics of high-dimensional 3D images, and explore data synergy to overcome the fragile representation of lightweight methods. Our approach, VeloxSeg, begins with a deployable and extensible dual-stream CNN-Transformer architecture composed of Paired Window Attention (PWA) and Johnson-Lindenstrauss lemma-guided convolution (JLC). For each 3D image, we invoke a glance-and-focus'' principle, where PWA rapidly retrieves multi-scale information, and JLC ensures robust local feature extraction with minimal parameters, significantly enhancing the model's ability to operate with low computational budget. Followed by an extension of the dual-stream architecture that incorporates modal interaction into the multi-scale image-retrieval process, VeloxSeg efficiently models heterogeneous modalities. Finally, Spatially Decoupled Knowledge Transfer (SDKT) via Gram matrices injects the texture prior extracted by a self-supervised network into the segmentation network, yielding stronger representations than baselines at no extra inference cost. Experimental results on multimodal benchmarks show that VeloxSeg achieves a 26% Dice improvement, alongside increasing GPU throughput by 11×\times, CPU by 48×\times, and reducing training peak GPU memory usage by 1/201/20, inference by 1/241/24. Code is available at https://github.com/JinPLu/VeloxSeg.