Few-Shot Medical Image Segmentation

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.

Few-shot medical image segmentation (FSMIS) has achieved notable progress, yet most existing methods mainly rely on semantic correspondences from scarce annotations while under-utilizing a key property of medical imagery: anatomical targets exhibit repeatable high-frequency morphology (e.g., boundary geometry and spatial layout) across patients and acquisitions. We propose RAP, a training-free framework that retrieves, adapts, and prompts Segment Anything Model 2 (SAM2) for FSMIS. First, RAP retrieves morphologically compatible supports from an archive using DINOv3 features to reduce brittleness in single-support choice. Second, it adapts the retrieved support mask to the query by fitting boundary-aware structural cues, yielding an anatomy-consistent pre-mask under domain shifts. Third, RAP converts the pre-mask into prompts by sampling positive points via Voronoi partitioning and negative points via sector-based sampling, and feeds them into SAM2 for final refinement without any fine-tuning. Extensive experiments on multiple medical segmentation benchmarks show that RAP consistently surpasses prior FSMIS baselines and achieves state-of-the-art performance. Overall, RAP demonstrates that explicit structural fitting combined with retrieval-augmented prompting offers a simple and effective route to robust training-free few-shot medical segmentation.

Segmenting the left atrial (LA) wall from late gadolinium enhancement magnetic resonance imaging (LGE-MRI) is challenging because of its thin geometry, low contrast, and limited expert annotations. We propose a model-agnostic meta-learning (MAML) framework with a 3D residual U-Net backbone for K-shot (K = 5, 10, 20) LA wall segmentation. The framework is meta-trained on LA wall tasks together with auxiliary LA and right atrial (RA) cavity tasks and uses a boundary-aware composite loss to improve thin-structure delineation. We evaluated MAML on a held-out clean test set and assessed its robustness under an unseen synthetic domain shift and on a local cohort. On the held-out clean test set, MAML outperformed the K-shot fine-tuning baseline at 5-shot, achieving Dice coefficient (DSC) = 0.54 versus 0.48 and Hausdorff distance (HD95) = 4.60 versus 6.40 mm. At 20-shot, MAML approached the fully supervised model trained from scratch, with DSC = 0.59 versus 0.61. Under unseen shifts, performance decreased relative to clean testing but improved consistently as K increased. At 5-shot, MAML achieved DSC = 0.52 and HD95 = 5.02 mm under the unseen synthetic shift, and DSC = 0.50 and HD95 = 5.43 mm on the local cohort. These results suggest that meta-learning can improve thin-wall delineation in low-shot adaptation and may reduce the annotation burden for atrial remodeling assessment.

Conventional few-shot medical image segmentation (FSMIS) approaches face performance bottlenecks that hinder broader clinical applicability. Although the Segment Anything Model (SAM) exhibits strong category-agnostic segmentation capabilities, its direct application to medical images often leads to over-segmentation due to ambiguous anatomical boundaries. In this paper, we reformulate SAM-based FSMIS as a prompt localization task and propose FoB (Focus on Background), a background-centric prompt generator that provides accurate background prompts to constrain SAM's over-segmentation. Specifically, FoB bridges the gap between segmentation and prompt localization by category-agnostic generation of support background prompts and localizing them directly in the query image. To address the challenge of prompt localization for novel categories, FoB models rich contextual information to capture foreground-background spatial dependencies. Moreover, inspired by the inherent structural patterns of background prompts in medical images, FoB models this structure as a constraint to progressively refine background prompt predictions. Experiments on three diverse medical image datasets demonstrate that FoB outperforms other baselines by large margins, achieving state-of-the-art performance on FSMIS, and exhibiting strong cross-domain generalization. Our code is available at https://github.com/primebo1/FoB_SAM.

Foundation models have transformed vision and language by learning general-purpose representations from large-scale unlabeled data, yet 3D medical imaging lacks analogous approaches. Existing self-supervised methods rely on low-level reconstruction or contrastive objectives that fail to capture the anatomical semantics critical for medical image analysis, limiting transfer to downstream tasks. We present MASS (MAsk-guided Self-Supervised learning), which treats in-context segmentation as the pretext task for learning general-purpose medical imaging representations. MASS's key insight is that automatically generated class-agnostic masks provide sufficient structural supervision for learning semantically rich representations. By training on thousands of diverse mask proposals spanning anatomical structures and pathological findings, MASS learns what semantically defines medical structures: the holistic combination of appearance, shape, spatial context, and anatomical relationships. We demonstrate effectiveness across data regimes: from small-scale pretraining on individual datasets (20-200 scans) to large-scale multi-modal pretraining on 5K CT, MRI, and PET volumes, all without annotations. MASS demonstrates: (i) few-shot segmentation on novel structures, (ii) matching full supervision with only 20-40% labeled data while outperforming self-supervised baselines by over 20 in Dice score in low-data regimes, and (iii) frozen-encoder classification on unseen pathologies that matches full supervised training with thousands of samples. Mask-guided self-supervised pretraining captures broadly generalizable knowledge, opening a path toward 3D medical imaging foundation models without expert annotations. Code is available: https://github.com/Stanford-AIMI/MASS.

Directly inspired by findings in biological vision, high-dimensional hypercolumns are feature vectors built by concatenating multi-scale activations of convolutional neural networks for a single image pixel location. Together with powerful classifiers, they can be used for image segmentation i.e. pixel classification. However, in practice, there are only very few works dedicated to the use of hypercolumns. One reason is the computational complexity of processing concatenated dense hypercolumns that grows linearly with the size $N$ of the training set. In this work, we address this challenge by applying stratified subsampling to the VGG16 based hypercolumns. Furthermore, we investigate the performance of ensemble learning on sparse hypercolumns. Our experiments on a brain tumor dataset show that stacking and voting ensembles deliver competitive performance, but in the extreme low-shot case of $N \leq 20$, a simple Logistic Regression classifier is the most effective method. For 10% stratified subsampling rate, our best average Dice score is 0.66 for $N=20$. This is a statistically significant improvement of 24.53% over the standard multi-scale UNet baseline ($p$-value = $[3.07e-11]$, Wilcoxon signed-rank test), which is less effective due to overfitting.

Medical image segmentation is fundamental to clinical workflows, yet models trained on a single dataset often fail to generalize across institutions, scanners, or patient populations. While vision foundation models have shown great promise in addressing this challenge, their deployment typically requires task-specific fine-tuning, which introduces substantial communication overhead in federated learning and prevents continuous knowledge evolution during deployment. In this work, we propose a memory-augmented segmentation agent (MemSeg-Agent) that shifts adaptation from weight space to memory space, enabling few-shot learning, federated supervised learning, and test-time adaptation within a unified architecture. MemSeg-Agent conditions a fixed backbone with lightweight static, few-shot, and test-time working memories, which are dynamically composed by an agentic controller. In federated settings, we update compact memory units instead of model parameters, substantially reducing communication overhead. Experiments on four public datasets demonstrate strong performance and robustness to domain shift: Static memory alone matches or surpasses strong supervised baselines with high parameter efficiency, and test-time working memory further improves in-domain and cross-domain performance without fine-tuning. Overall, MemSeg-Agent introduces a new paradigm for scalable and adaptive medical image segmentation in the era of agentic AI.

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

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.

Medical image segmentation is a cornerstone of computer-assisted diagnosis and treatment planning. While recent multimodal vision-language models have shown promise in enhancing semantic understanding through textual descriptions, their resilience in "in-the-wild" clinical settings-characterized by scarce annotations and hardware-induced image degradations-remains under-explored. We introduce BiCLIP (Bidirectional and Consistent Language-Image Processing), a framework engineered to bolster robustness in medical segmentation. BiCLIP features a bidirectional multimodal fusion mechanism that enables visual features to iteratively refine textual representations, ensuring superior semantic alignment. To further stabilize learning, we implement an augmentation consistency objective that regularizes intermediate representations against perturbed input views. Evaluation on the QaTa-COV19 and MosMedData+ benchmarks demonstrates that BiCLIP consistently surpasses state-of-the-art image-only and multimodal baselines. Notably, BiCLIP maintains high performance when trained on as little as 1% of labeled data and exhibits significant resistance to clinical artifacts, including motion blur and low-dose CT noise.