Zero-Shot Medical Image Segmentation

Pretrained models for cell and nuclear instance segmentation differ substantially in architecture, pretraining data and objectives, parameter count, inference strategy, adaptation requirements, postprocessing pipeline, and computational demand. Large pretrained and foundation models are increasingly adopted because of their strong zero-shot capabilities, but their use also imposes greater energy consumption, memory requirements, computational demands, adaptation costs, and operational carbon emissions. Whether these additional demands are justified by meaningful gains in segmentation performance remains unclear. We address this question by introducing the Sustainability-Aware Performance Index (SAPI), a configurable metric that combines segmentation performance, energy consumption, and model size. We benchmark 19 pretrained and foundation models across six CellBinDB datasets under zero-shot inference and evaluate 16 fine-tunable models using few-shot adaptation with both frozen encoder and full-model fine-tuning. We estimate energy consumption for GPU, CPU, and RAM using software-based monitoring tools. Our results show that larger and more computationally demanding models do not consistently achieve proportionate improvements in segmentation quality. While few-shot adaptation benefits several models, the gains and resource costs vary considerably across architectures, datasets, and adaptation strategies, causing SAPI-based rankings to differ from rankings based on performance alone. This study provides a practical framework for comparing segmentation models more comprehensively and supports more computationally accessible and environmentally responsible model selection in biomedical image analysis.

Medical image segmentation remains challenging in practical deployment, as models often struggle to generalize beyond the distributions covered by their training data and high-quality pixel-level annotations are typically unavailable for adaptation. Inspired by the cross-task transferability of large language models, we investigate whether unified multimodal models (UMMs) can transfer their pretrained visual understanding, reasoning, and generation capabilities to medical image segmentation without task-specific post-training. By recasting segmentation as structured visual generation, we find that frontier UMMs (e.g., Nano Banana) already exhibit basic segmentation capabilities across diverse clinical scenarios, but still struggle with challenging tasks requiring specialized anatomical or domain-specific knowledge. We further show that these limitations can be effectively mitigated by incorporating visual anatomical knowledge from in-context exemplars, expanding candidate solutions through repeated sampling, and refining suboptimal predictions via targeted editing.Motivated by these observations, we propose SegBanana, to our knowledge, the first agentic visual generation framework for training-free medical image segmentation. SegBanana builds on a frozen UMM as the core generative model, augmented with Anatomy-Aware Knowledge Retrieval and Comparative Quality Critique to unlock its potential segmentation capability. A State-Aware Multimodal Controller maintains structured state and iteratively orchestrates these tools, repeatedly refining intermediate predictions toward higher-quality masks. Across eight medical segmentation datasets, SegBanana achieves an average mDice of 77.45%, outperforming representative generalist (SAM3 and SegGPT) and medical-specific (BiomedParse and MedSAM3) baselines by at least 14.93 points, while remaining robust to out-of-domain visual supports.

Accurate segmentation of corneal layers in optical coherence tomography (OCT) is essential for quantitative assessment of corneal morphology, including layer thickness and structural changes associated with disease or surgery. However, automatic segmentation remains challenging because corneal interfaces are thin, affected by speckle noise, and variable across acquisition devices. In this work, we propose ARCOS, a patch-based zero-shot boundary localization framework for corneal layer segmentation in clinical anterior-segment OCT images. Rather than performing conventional region classification, the method predicts boundary heatmaps for the main corneal interfaces from overlapping native-resolution patches. Patch-level predictions are stitched across the full B-scan and converted into boundary locations to obtain continuous, anatomically ordered layer segmentations. The network combines multi-scale feature fusion with a self-conditioned refinement module that uses intermediate boundary information to improve local heatmap predictions while preserving spatial detail. The method was evaluated on clinical OCT images acquired from multiple devices and compared with representative segmentation baselines using boundary localization and derived thickness metrics. The proposed method achieved an off-by-one boundary localization accuracy of 95.1% and a mean absolute boundary error of 0.514 pixels on the matched-device test set. In zero-shot cross-device evaluation, it maintained an average off-by-one accuracy of 84.3% and a mean absolute boundary error of 0.855 pixels across unseen acquisition devices, outperforming the baseline models. Thickness estimates derived from the predicted boundaries showed low error across corneal regions, supporting the method's use for quantitative corneal OCT analysis.

Vision-Language Pretrained Models (VLPMs) offer a scalable path to open-vocabulary chest radiology understanding, yet two aspects remain underexplored: how structured clinical semantics extracted from medical reports can reduce in-batch noise during contrastive learning, and how cross-modal fusion can be designed to produce more faithful spatial grounding without added complexity. We introduce AlphaRAD, addressing these opportunities through two contributions. First, we construct a large-scale structured medical concept space from medical reports parsed by a Large Language Model for training, thereby mitigating in-batch learning noise and removing heuristic pair matching in contrastive learning, and thus naturally positioning AlphaRAD as a medical concept discriminator trained via $α$-Corrected Binary Cross-Entropy. Second, we propose FLaS (Factorized Latent Supervision), an extremely simple yet effective cross-modal feature fusion module that factorizes VLPM representations into independent subspaces, using dedicated alignment supervision to enhance the expressiveness of spatial grounding without introducing additional model parameters. Through extensive empirical validation, AlphaRAD shows strong zero-shot generalization across diverse chest radiology tasks. Notably, it establishes state-of-the-art average performance across 16 classification benchmarks, while achieving individual state-of-the-art results via distinct gains on 7 grounding/phrase grounding and 3 segmentation datasets.

Medical image segmentation remains difficult to scale because high-performing methods typically rely on dense expert annotations and task-specific training. We introduce GazeRefine, a training-free framework that uses gaze as an inference-time prompt for zero-shot medical image segmentation. Sparse, duration-weighted fixations are converted into foreground and background priors that initialize semantic prototypes in frozen DINOv3 feature space. These prototypes are iteratively refined through foreground-background discrimination, feature-space affinity propagation, and anchoring to the initial gaze guidance, allowing segmentation to extend beyond directly fixated regions while limiting semantic drift. GazeRefine requires no segmentation masks, fine-tuning, adapters, prompt encoders, or gradient updates. We evaluate the method on gaze-annotated polyp segmentation and prostate MRI segmentation. The results show strong performance on colonoscopy images and competitive performance on prostate MRI, supporting gaze-guided prototype refinement as a promising approach for segmentation-label-efficient, human-in-the-loop medical image segmentation. Our tools and code can be found in the following repository: https://github.com/MohammedOussamaBEN/GazeRefine.git

Computed tomography (CT) vision-language pretraining from paired volumes and radiology reports is a scalable yet challenging task. Existing methods commonly adopt global scan-report contrast, which is scalable but obscures heterogeneous organ evidence. Meanwhile, direct organ-level alignment remains coarse, since the same anatomy can exhibit multiple distinct radiological appearances. Therefore, pretraining requires a finer alignment unit: the organ-conditioned radiological pattern. In this work, we propose OCP-CT, an organ-conditioned pattern-token alignment framework for CT vision-language pretraining. Specifically, OCP-CT preserves a stable global CT-report contrastive branch and introduces an organ pattern interface: sparse Mixture-of-Experts (MoE) routes image and text tokens according to latent radiological patterns, learnable slots query the routed tokens into continuous pattern tokens, and paired token contrast aligns image-text pattern tokens with structured soft targets built from report-derived clinical similarity. On the publicly available CT-RATE and RAD-ChestCT benchmarks, OCP-CT achieves average AUROCs of 84.5% and 69.9% for zero-shot abnormality diagnosis, respectively. Compared with the strongest prior reported results, these results yield absolute AUROC gains of 6.7 and 0.8 percentage points.

Vision-language pre-training (VLP) holds great promise for general-purpose medical AI by leveraging radiology reports as rich textual supervision, yet existing methods struggle with 3D CT imaging due to inefficient visual backbones and coarse semantic alignment. To address these issues, we propose a tailored VLP framework featuring three key components: (1) a CNN-ViT hybrid encoder that replaces ViT's patch embedding with a 3D CNN backbone to efficiently capture local anatomical details while preserving global attention and compatibility with pre-trained cross-modal priors; (2) a disease-level contrastive learning mechanism using learnable query tokens to dynamically extract disease-specific semantics from full reports and align them with corresponding visual features, thereby disentangling distinct diseases within the same anatomical region; and (3) a diagnosis-aware prompt strategy that employs real clinical phrases and aggregated disease prototypes to bridge the pre-training-inference gap and enhance zero-shot diagnostic reliability. Our model achieves state-of-the-art performance on CT-RATE (84.4% AUC, +5.1%) and Rad-ChestCT (75.4% AUC, +5.4%), with even larger gains (+9.8% AUC) on a challenging 60-disease benchmark, and demonstrates strong transferability to radiology report generation, underscoring the generality and clinical utility of our approach.

Foreground segmentation is the critical first step of every computational pathology pipeline, yet existing methods rely on hand-tuned heuristics or supervised models that overfit to narrow stain and scanner distributions, failing silently on specialised stains such as Jones silver or Elastica van Gieson. We propose a coarse-to-fine approach that recasts foreground segmentation as a visual perception task and leverages general-purpose vision-language models (VLMs) as zero-annotation oracles. Our key insight is that tissue-versus-background discrimination is a natural-image recognition problem, not a histopathological one, so VLMs trained on internet-scale corpora generalise where domain-specific models cannot. We introduce Leica-75, a benchmark of 75 renal transplant whole-slide images spanning three stain families. On Leica-75, our method achieves the highest segmentation quality on out-of-distribution stains (Dice 0.858 +/- 0.027 on Jones, 0.853 +/- 0.041 on EVG) with 7x lower cross-stain variance than the best supervised baseline, while remaining competitive on in-distribution H&E. Few-shot prompting with automatically curated exemplars (Auto-context) rescues hard cases on Stress-32 (n=32), a curated stress-test subset (Dice 0.470 to 0.819 for the 2B model). VLM-based annotation review matches human expert consensus (kappa=0.989 for blur detection; mean precision/recall grading accuracy 0.708 vs. human 0.646 for segmentation mask review). The resulting pseudo-labels are used to distil lightweight student models that are as performant as the teacher model while running for a fraction of the cost. Our framework provides a principled, scalable solution to a persistent infrastructure bottleneck in digital pathology.

Vision-language models (VLMs) for radiology have emerged as a scalable paradigm by leveraging image-report pairs naturally produced in clinical workflows. However, this pairing reveals a mismatch in scale: each finding occupies only a small region of the image, yet supervision is provided only at the global image-report level. This poses a central challenge: prior approaches spread weight densely across all patches rather than concentrating on the sparse subset relevant to a given query. To address this, we present GLINT (Gated Language-Image alignmeNT), a framework that explicitly models this sparse correspondence. On the alignment side, we introduce Sparsely Gated Alignment, a novel architecture in which a sigmoid gate over a separate gate embedding space activates only the patches relevant to each textual query, enforcing explicit sparsity. On the representation side, we add Dense Feature Regularization, which anchors the trainable encoder's intermediate features to a frozen self-supervised learning (SSL) teacher, preserving the fine-grained patch features that the gate relies on. The same recipe applies to both 2D chest X-ray (CXR) and 3D chest computed tomography (CT), built with DINOv3 and V-JEPA 2.1, respectively. GLINT enables zero-shot classification, grounding, and segmentation from free-text queries, and to our knowledge is the first to demonstrate zero-shot segmentation on 3D CT volumes without mask supervision. Notably, the most pronounced gains arise on zero-shot grounding and segmentation, where sparse, query-specific localization is required, consistent with our design intent. In downstream evaluation, GLINT outperforms both SSL encoders and medical VLMs on classification, report generation, and segmentation.

Zero-shot vision-language models (VLMs) offer a promptable alternative to task-specific training for gross tumor volume (GTV) delineation in non-small-cell lung cancer (NSCLC), but the prompt dimensions that govern their spatial behavior remain poorly understood. We study this question by probing alignment directions in VoxTell on a held-out internal NSCLC tumor dataset through sub-prompt decomposition into diagnosis, demographic, staging, anatomical, generic, and irrelevant controls; attribute-wise perturbation robustness; specificity ladders; and cross-case prompt swaps, while benchmarking against fine-tuned and zero-shot baselines using the Dice Similarity Coefficient (DSC) with Wilcoxon signed-rank tests and Benjamini-Hochberg correction. Alignment analyses revealed that anatomical location is the dominant driver of VoxTell's spatial attention: 63.4 percent of location perturbations caused catastrophic drops, prompt specificity improved from generic to full descriptions except for diagnosis-only prompts, irrelevant prompts correctly yielded zero segmentation, and cross-case prompt swaps confirmed patient-specific conditioning (matched DSC 0.906 vs. mismatched 0.406). Histology and stage substitutions had minimal effect, indicating that the model prioritizes "where to look" over "what to look for." In this context, VoxTell, operating fully zero-shot, achieved a mean DSC of 0.613, statistically indistinguishable from nnUNet (0.690, adjusted p = 0.156) and Ahmed et al. (0.675, adjusted p = 0.679), while significantly outperforming all other zero-shot models. Together, these findings argue that segmentation VLMs should be evaluated not only by Dice, but also by the prompt dimensions to which they align.

Increasingly advanced data augmentation techniques have greatly aided clinical medical research, increasing data diversity and improving model generalization capabilities. Although most current basic models exhibit strong generalization abilities, image quality varies due to differences in equipment and operators. To address these challenges, we present SegTTA, a framework that improves medical image segmentation without model retraining by combining four augmentations (Gamma correction, Contrast enhancement, Gaussian blur, Gaussian noise) with weighted voting across multiple MedSAM2 checkpoints. Experiments demonstrate consistent improvements across three diverse datasets: healthy uterus segmentation, uterine myoma detection, and multi class hepatic structure segmentation. Ablation studies reveal that large organs benefit from intensity augmentations while small lesions require noise augmentations. The voting threshold controls the coverage precision trade off, enabling task specific optimization for different clinical requirements. Ultimately, on a multiclass hepatic vessel dataset, compared to MedSAM2 baselines, our method achieves an increase of 1.6 in mIoU and 1.9 in aIoU, along with a reduction of approximately 2.0 in HD95. Code will be available at https://github.com/AIGeeksGroup/SegTTA.