Image Segmentation

Panoptic segmentation requires the simultaneous recognition of countable thing instances and amorphous stuff regions, placing joint demands on long-range context modelling, multi-scale feature representation, and efficient dense prediction. Existing convolutional and transformer-based methods struggle to satisfy all three requirements concurrently: convolutional architectures are limited in their capacity to model long-range dependencies, while transformer-based methods incur quadratic computational cost that is prohibitive at high resolutions. In this paper, we propose MambaPanoptic, a fully Mamba-based panoptic segmentation framework that addresses these limitations through two principal contributions. First, we introduce MambaFPN, a top-down feature pyramid that leverages Mamba blocks to generate globally coherent, multi-scale feature representations with linear computational complexity. Second, we adopt a PanopticFCN-style kernel generator that produces unified thing and stuff kernels for proposal-free panoptic prediction, enhanced by a QuadMamba-based feature refinement module applied at multiple network stages. Experiments on the Cityscapes and COCO panoptic segmentation benchmarks demonstrate that MambaPanoptic consistently outperforms PanopticDeepLab and PanopticFCN under comparable model sizes, and matches or surpasses Mask2Former on Cityscapes in PQ and AP while requiring fewer parameters.

Continual Panoptic Segmentation (CPS) requires methods that can quickly adapt to new categories over time. The nature of this dense prediction task means that training images may contain a mix of labeled and unlabeled objects. As nothing is known about these unlabeled objects a priori, existing methods often simply group any unlabeled pixel into a single "background" class during training. In effect, during training, they repeatedly tell the model that all the different background categories are the same (even when they aren't). This makes learning to identify different background categories as they are added challenging since these new categories may require using information the model was previously told was unimportant and ignored. Thus, we propose a Future-Targeted Contrastive and Repulsive (FuTCR) framework that addresses this limitation by restructuring representations before new classes are introduced. FuTCR first discovers confident future-like regions by grouping model-predicted masks whose pixels are consistently classified as background but exhibit non-background logits. Next, FuTCR applies pixel-to-region contrast to build coherent prototypes from these unlabeled regions, while simultaneously repelling background features away from known-class prototypes to explicitly reserve representational space for future categories. Experiments across six CPS settings and a range of dataset sizes show FuTCR improves relative new-class panoptic quality over the state-of-the-art by up to 28%, while preserving or improving base-class performance with gains up to 4%.

Segmenting small and sparse structures in large-scale images is fundamentally constrained by voxel-level, lattice-bound computation and extreme class imbalance -- dense, full-resolution inference scales poorly and forces most pipelines to rely on fixed regionization or downsampling, coupling computational cost to image resolution and attenuating boundary evidence precisely where minority structures are most informative. We introduce SEMIR (Semantic Minor-Induced Representation Learning), a representation framework that decouples inference from the native grid by learning a task-adapted, topology-preserving latent graph representation with exact decoding. SEMIR transforms the underlying grid graph into a compact, boundary-aligned graph minor through parameterized edge contraction, node deletion, and edge deletion, while preserving an exact lifting map from minor predictions to lattice labels. Minor construction is formalized as a few-shot structure learning problem that replaces hand-tuned preprocessing with a boundary-alignment objective: minor parameters are learned by maximizing agreement between predicted boundary elements and target-specific semantic edges under a boundary Dice criterion, and the induced minor is annotated with scale- and rotation-robust geometric and intensity descriptors and supports efficient region-level inference via message passing on a graph neural network (GNN) with relational edge features. We benchmark SEMIR on three tumor segmentation datasets -- BraTS 2021, KiTS23, and LiTS -- where targets exhibit high structural variability and distributional uncertainty. SEMIR yields consistent improvements in minority-structure Dice at practical runtime. More broadly, SEMIR establishes a framework for learning task-adapted, topology-preserving latent representations with exact decoding for high-resolution structured visual data.

Pursuing training-free open-vocabulary semantic segmentation in an efficient and generalizable manner remains challenging due to the deep-seated spatial bias in CLIP. To overcome the limitations of existing solutions, this work moves beyond the CLIP-based paradigm and harnesses the recent spatially-aware dino$.$txt framework to facilitate more efficient and high-quality dense prediction. While dino$.$txt exhibits robust spatial awareness, we find that the semantic ambiguity of text queries gives rise to severe mismatch within its dense cross-modal interactions. To address this, we introduce Visual-guided Prompt evolution (VIP) to rectify the semantic expressiveness of text queries in dino$.$txt, unleashing its potential for fine-grained object perception. Towards this end, VIP integrates alias expansion with a visual-guided distillation mechanism to mine valuable semantic cues, which are robustly aggregated in a saliency-aware manner to yield a high-fidelity prediction. Extensive evaluations demonstrate that VIP: 1. surpasses the top-leading methods by 1.4%-8.4% average mIoU, 2. generalizes well to diverse challenging domains, and 3. requires marginal inference time and memory overhead.

Unsupervised segmentation of pulmonary pathologies in CT remains an open challenge due to the absence of annotated multi pathology cohorts and the failure of existing diffusion-based methods to exploit the quantitative Hounsfield Unit (HU) signal that physically distinguishes tissue classes. To address this, we propose DiffSegLung,a framework that introduces Diffusion Radiomic Distillation, in which handcrafted radiomic descriptors serve as a physics grounded teacher to shape the bottleneck of a 3D diffusion U-Net via a contrastive objective, transferring pathology discriminative structure into the learned representation without any annotations. At inference, the teacher is discarded and multitimestep bottleneck features are clustered by a Gaussian Mixture Model with HU-guided label assignment, followed by Sobel Diffusion Fusion for boundary refinement. Evaluated on 190 expert annotated axial slices drawn from four heterogeneous CT cohorts, Diff-SegLung improves segmentation across all four pathology classes over unsupervised baselines and improves generation fidelity over prior CT diffusion models.

Accurate medical image segmentation is an integral part of the medical image analysis pipeline that requires the ability to merge local and global information. While vision transformers are able to capture global interactions using vanilla self-attention, their quadratic computational complexity in the input size remains a struggle for medical image segmentation tasks. Motivated by the dispersion property of vanilla self-attention and recent development of Mamba form of attention, Scalable and Efficient Mamba like Attention (SEMA) utilizes token localization via local window attention to avoid dispersion and maintain focusing, complemented by theoretically consistent arithmetic averaging to capture global aspect of attention. In this work, we present USEMA, a hybrid UNet architecture that merges the local feature extraction ability of convolutional neural networks (CNNs) with SEMA attention. We conduct experiments with USEMA across a variety of modalities and image sizes, demonstrating improved computational efficiency compared to transformer based models using full self-attention, and superior segmentation performance relative to purely convolution and Mamba-based models.

Cross-domain few-shot medical image segmentation (CD-FSMIS) requires a model to generalise simultaneously to novel anatomical categories and unseen imaging domains from only a handful of annotated examples. Existing prototypical approaches inevitably entangle anatomical structure with domain-specific appearance variations, and thus lack a stable reference for reliable matching under domain shift. We observe that the geometric structure of human anatomy constitutes a reliable, domain-transferable prior that has been overlooked. Building on this insight, we propose GeoProto, a geometry-aware CD-FSMIS framework that enriches prototypical matching with explicit structural priors. The core component, Geometry-Aware Prototype Enrichment (GAPE), augments each local appearance prototype with a learned geometric offset encoding its ordinal position within the organ's interior topology. This offset is derived from an auxiliary Ordinal Shape Branch (OSB) trained under an ordinally consistent objective that enforces monotonic variation of geometric embeddings across interior strata, requiring no annotation beyond standard segmentation masks. Extensive experiments across seven datasets spanning three evaluation settings (cross-modality, cross-sequence, and cross-context) demonstrate that GeoProto achieves state-of-the-art performance.

The multimodal fusion of images and scene captions has been extensively explored and applied in various fields. However, when dealing with complex remote sensing (RS) scenes, existing studies have predominantly concentrated on architectural optimizations for integrating textual semantic information with visual features, while largely neglecting the generation of high-quality RS captions and the investigation of their effectiveness in multimodal semantic fusion.In this context, we propose the Dynamic MLLM Mixture-of-Experts Perception-Guided Remote Sensing Scene Segmentation, referred to as MPerS.We design multiple prompts for MLLMs to generate high-quality RS captions, enabling MLLMs to perceive RS scenes from diverse expert perspectives. DINOv3 is employed to extract dense visual representations of land-covers.We design a Dynamic MixExperts module that adaptively integrates the most effective textual semantics. Linguistic Query Guided Attention is constructed to utilize textual semantic information to guide visual features for precise segmentation. The MLLMs include LLaVA, ChatGPT, and Qwen. Our method achieves superior performance on three public semantic segmentation RS datasets.

Despite strong zero-shot performance, SAM is unreliable under domain shift due to Mask-level Confidence Confusion (MCC), where a single IoU-based mask score fails to reflect pixel-wise reliability near boundaries. Motivated by the contrast between texture-biased shortcuts in neural networks and shape-centric processing in human vision, we model out-of-domain variation as appearance shifts and non-rigid deformations that jointly stress calibration. We propose Segment Anything with Robust Uncertainty-Accuracy Correlation (RUAC) for robust pixel-wise uncertainty estimation under appearance and deformation shifts. RUAC adds a lightweight uncertainty head, trains it with a collaborative style-deformation attack that jointly perturbs texture and geometry, and applies Uncertainty-Accuracy Alignment to ensure uncertainty consistently highlights erroneous pixels even under adversarial perturbations. Across 23 zero-shot domains, RUAC improves segmentation quality and yields more faithful uncertainty with stronger uncertainty-accuracy correlation. Project page: https://hongyouzhou.github.io/ruac/.

Rapid and accurate damage assessment following natural disasters is critical for effective emergency response. However, identifying fine-grained damage levels (e.g., distinguishing minor from major roof damage) in UAV imagery remains challenging due to the degradation of texture cues during resizing and extreme class imbalance. We propose DA-SegFormer, a damage-aware adaptation of the SegFormer architecture optimized for high-resolution disaster imagery. Our method introduces a Class-Aware Sampling strategy to guarantee exposure to rare damage features, and it integrates Online Hard Example Mining (OHEM) with Dice Loss to dynamically focus on underrepresented classes. In addition, we employ a resolution-preserving inference protocol that maintains native texture details. Evaluated on the RescueNet dataset, DA-SegFormer achieves 74.61% mIoU, outperforming the baseline by 2.55%. Notably, our improvements yield double-digit gains in critical damage classes: Minor Damage (+11.7%) and Major Damage (+21.3%).

Segmentation is a fundamental vision task underlying numerous downstream applications. Recent promptable segmentation models, such as Segment Anything Model 3 (SAM3), extend segmentation from category-agnostic mask prediction to concept-guided localization conditioned on high-level textual prompts. However, existing benchmarks primarily evaluate mask accuracy or object presence, leaving unclear whether these models faithfully ground the queried concept or instead rely on visually salient but semantically misleading cues. We introduce CAFE: \textbf{C}ounterfactual \textbf{A}ttribute \textbf{F}actuality \textbf{E}valuation, a novel benchmark for evaluating concept-faithful segmentation in promptable segmentation models. Our \textbf{CAFE} is built on attribute-level counterfactual manipulation: the target region and ground-truth mask are preserved, while attributes such as surface appearance, context, or material composition are modified to introduce misleading semantic cues. The benchmark contains 2,146 paired test samples, each consisting of a target image, a ground-truth mask, a positive prompt, and a misleading negative prompt. These samples cover three counterfactual categories: Superficial Mimicry (\textbf{SM}), Context Conflict (\textbf{CC}), and Ontological Conflict (\textbf{OC}). We evaluate various model types and sizes on our CAFE. Experiments reveal a systematic gap between localization quality and concept discrimination: models often generate accurate masks even for misleading prompts, suggesting that strong mask prediction does not necessarily imply faithful semantic grounding. Our CAFE provides a controlled benchmark for diagnosing whether promptable segmentation models perform concept-faithful grounding rather than shortcut-driven mask retrieval.

Uncertainty quantification complements model predictions by characterizing their reliability, which is essential for high-stakes decision making such as medical image segmentation. However, most existing methods reduce uncertainty to a scalar confidence estimate, leaving its spatial distribution semantically underconstrained. In this work, we focus on uncertainty interpretability, namely, whether estimated uncertainty behaves in a human-understandable manner with respect to sources of ambiguity. We identify three perception-aligned principles requiring the spatial distribution of uncertainty to reflect: (1) image contrast between structures, (2) severity of image corruption, and (3) geometric complexity in anatomical structures. Accordingly, we develop a principle-guided uncertainty supervision framework (PriUS) based on evidential learning, in which the corresponding supervision objectives are explicitly enforced during training. We further introduce quantitative metrics to measure the consistency between predicted uncertainty and image attributes that induce ambiguity. Experiments on ACDC, ISIC, and WHS datasets showed that, compared with state-of-the-art methods, PriUS produced more consistent uncertainty estimates while maintaining competitive segmentation performance.

Tree ring marking remains a key step in dendrometry and dendrochronology, but it is often performed manually, making the process time-consuming, subjective, and difficult to scale to large image datasets. We present the Tree Ring Analyzer Suite (TRAS), an open-source graphical software for automatic delineation, manual correction, and measurement of tree rings in wood cross-sectional images. TRAS integrates three complementary detection algorithms: the classical image-processing method CS-TRD and two deep-learning approaches, DeepCS-TRD and INBD. The interface allows users to refine automatic detections, remove false positives, and manually add missing rings. It also computes dendrochronological metrics such as earlywood and latewood areas, ring perimeter, equivalent ring width, and custom path-based ring-width measurements. TRAS was evaluated on 18 expertly annotated Pinus taeda L. cross-section images. DeepCS-TRD achieved the best automatic detection performance, with an F-score of 81.0% and precision of 86.4%. Automatic detection reduced the required manual correction effort to approximately 20% of ring boundaries. For one-dimensional ring-width measurements, TRAS showed excellent agreement with CooRecorder ($r > 0.99$). Common detection errors, such as jump propagation or false positives near knots, were easily corrected through the postprocessing interface. TRAS provides a flexible and reproducible solution for tree-ring analysis on Windows, macOS, and Linux. Code is available at the https://hmarichal93.github.io/tras.

Adapting foundation models to medical segmentation typically requires either backbone fine-tuning or high-capacity task-specific decoders, both of which are difficult to fit reliably when annotations are scarce. We show that frozen DINOv3 features already contain useful structural and boundary cues for medical segmentation, and that the main bottleneck lies in how these features are read out. We propose DINO-MVR, a Multi-View Readout framework for annotation-efficient medical segmentation. DINO-MVR trains only lightweight MLP probes on features from the final three transformer blocks of a frozen DINOv3 backbone, without updating the backbone itself. At inference, each input is interpreted through complementary resolutions and test-time augmentations, whose probability maps are combined by entropy-weighted fusion and refined with simple spatial regularization. For volumetric inputs, Gaussian z-axis smoothing further improves inter-slice consistency. Under fixed evaluation protocols on endoscopy, dermoscopy, and MRI benchmarks, DINO-MVR achieves strong readout-only performance, including 0.895 Dice on Kvasir-SEG, 0.897 Dice on ISIC 2018, and 0.908 Dice on BraTS FLAIR whole-tumor segmentation. With only five annotated BraTS patients, it recovers 98.4% of the performance obtained by the 40-patient BraTS reference run. These results suggest that frozen self-supervised vision backbones can support accurate medical segmentation when paired with an effective multi-view readout.

Open-world referring segmentation requires grounding unconstrained language expressions to precise pixel-level regions. Existing multimodal large language models (MLLMs) exhibit strong open-world visual grounding, but their outputs remain limited to sparse bounding-box coordinates and are insufficient for dense visual prediction. Recent MLLM-based segmentation methods either directly predict sparse contour coordinates, struggling to reconstruct continuous object boundaries, or rely on external segmentation foundation models such as the Segment Anything Model (SAM), introducing substantial architectural and deployment overhead. We present Qwen3-VL-Seg, a parameter-efficient framework that treats the MLLM-predicted box as a semantically grounded structural prior and decodes it into pixel-level referring segmentation. At its core, a lightweight box-guided mask decoder combines multi-scale spatial feature injection, spatial-semantic query construction, box-guided high-resolution pixel fusion, and iterative mask-aware query refinement, introducing only 17M parameters (about 0.4% of the base model). For scalable open-world training, we construct SA1B-ORS, an SA-1B-derived dataset with two subsets: SA1B-CoRS (category-oriented samples) and SA1B-DeRS (descriptive, instance-specific samples). For evaluation, we curate ORS-Bench, a manually screened benchmark with in-distribution and out-of-distribution subsets covering diverse referring expression types. Extensive experiments on referring expression segmentation, visual grounding, and ORS-Bench show that Qwen3-VL-Seg performs strongly across closed-set and open-world settings, with clear advantages on language-intensive instructions and strong out-of-distribution generalization. Evaluations on general multimodal benchmarks further show that the model broadly preserves general-purpose multimodal competence after segmentation-oriented adaptation.

Labeled datasets reflect the biases of their annotation pipelines, which sometimes introduce label bias: group-conditional label errors that cause systematic performance disparities across demographic subgroups. Label bias in image segmentation remains underexplored, as even detecting it typically requires clean, unbiased annotations, which are not readily available. We present a data-centric adaptation of Confident Learning to segmentation, allowing detection of label bias directly in the training data without a clean, unbiased ground truth. By comparing the provided training labels to the model's confident predictions, we isolate directional errors that quantify the presence and nature of bias, where standard overlap metrics like Dice fail. We further show that label bias influences subgroup separability in the encoder's feature space, an artifact we leverage for bias mitigation rather than suppressing it. We evaluate three datasets, spanning from synthetic to real-life bias, showing how our framework reliably detects and mitigates bias without access to clean labels, achieving equitable performance across experimental conditions.

Curating fully annotated datasets for medical image segmentation is labour-intensive and expertise-demanding. To alleviate this problem, prior studies have explored scribble annotations for weakly supervised segmentation. Existing solutions mainly compute losses on annotated areas and generate pseudo labels by propagating annotations to adjacent regions. However, these methods often suffer from inaccurate and unrealistic segmentations due to insufficient supervision and incomplete shape information. In contrast, we first investigate the principle of good scribble annotations, which leads to efficient scribble forms via supervision maximization and randomness simulation. We further introduce regularization terms to encode the spatial relationship and the shape constraints, where the EM algorithm is utilized to estimate the mixture ratios of label classes. These ratios are critical in identifying the unlabeled pixels for each class and correcting erroneous predictions, thus the accurate estimation lays the foundation for the incorporation of spatial prior. Finally, we integrate the efficient scribble supervision with the prior into a framework, referred to as ZScribbleSeg, and apply it to multiple scenarios. Leveraging only scribble annotations, ZScribbleSeg achieves competitive performance on six segmentation tasks including ACDC, MSCMRseg, BTCV, MyoPS, Decathlon-BrainTumor and Decathlon-Prostate. Our code will be released via https://github.com/DLwbm123/ZScribbleSeg.

Although self-supervised pretraining is expected to learn broadly transferable representations, its effectiveness across imaging modalities substantially different from the pretraining domain, and on complex tumor-segmentation tasks, remains understudied. Evaluating CT-pretrained transformers on MRI rectal cancer segmentation, we identified two interacting failure modes in CT-to-MRI transfer: (a) inefficient token usage caused by zero-padding to match pretrained input dimensions, and (b) ineffective feature adaptation. We investigated these vulnerabilities using two primary CT-pretrained hierarchical shifted-window transformer backbones, SMIT and Swin UNETR, together with VoCo as a large-scale-pretrained supporting benchmark; these models differ in pretraining objectives and datasets. Mechanistic analysis leveraged an attention dilution index (ADI), an entropy-based metric quantifying attention diverted toward uninformative padding tokens, and centered kernel alignment (CKA) to measure feature reuse during MRI adaptation. ADI increased with zero-padding, while high feature reuse did not necessarily translate to improved downstream accuracy. To mitigate these issues, we introduced two interventions: a tumor-aware augmentation strategy to expand tumor appearance heterogeneity coverage, and an anisotropic cropping strategy to restore token efficiency. Fine-tuning with these strategies on identical rectal MRI datasets yielded detection rates of 91.1% (225/247) and 88.7% (219/247) for the primary SMIT and Swin UNETR backbones, with the supporting VoCo benchmark reaching 90.3% (223/247), demonstrating significantly improved robustness under CT-to-MRI transfer. This study is among the first to examine when pretrained transformers fail to transfer across imaging modalities and demonstrates how targeted mitigation strategies can systematically overcome cross-modality transfer limitations.

Accurate image segmentation is essential for modern computer vision applications such as image editing, autonomous driving, and medical image analysis. In recent years, Dichotomous Image Segmentation (DIS) has become a standard task for training and evaluating highly accurate segmentation models. Existing DIS approaches often fail to preserve fine-grained details or fully capture the semantic structure of the foreground. To address these challenges, we present FlowDIS, a novel dichotomous image segmentation method built on the flow matching framework, which learns a time-dependent vector field to transport the image distribution to the corresponding mask distribution, optionally conditioned on a text prompt. Moreover, with our Position-Aware Instance Pairing (PAIP) training strategy, FlowDIS offers strong controllability through text prompts, enabling precise, pixel-level object segmentation. Extensive experiments demonstrate that our method significantly outperforms state-of-the-art approaches both with and without language guidance. Compared with the best prior DIS method, FlowDIS achieves a 5.5% higher $F_β^ω$ measure and 43% lower MAE ($\mathcal{M}$) on the DIS-TE test set. The code is available at: https://github.com/Picsart-AI-Research/FlowDIS

Text-based image segmentation aims to delineate object boundaries within an image from text prompts, offering higher flexibility and broader application scope compared to traditional fixed-category segmentation tasks. Recent studies have shown that diffusion models (e.g., Stable Diffusion) can provide rich multimodal semantic features, leading to studies of using diffusion models as feature extractors for segmentation tasks. Such methods, however, inherit the generative natures of diffusion models that are harmful to discriminative segmentation tasks. In response, we propose RLFSeg, a novel framework that leverages Rectified Flow to learn direct mapping from the image to the segmentation mask within the latent space. The model is thus freed from the noise-denoise process and the need to optimize the time step of diffusion models, resulting in substantially better performance than previous diffusion-based methods, especially on zero-shot scenarios. By introducing label refinement and an Adaptive One-Step Sampling strategy, the model achieves higher accuracy even on a single inference step. The framework redirects a pretrained generative model to the discriminative segmentation task with zero modification to model structure, thus reveals promising application potential and significant research value.

Automatic brain tumor segmentation from multi-modal MRI remains challenging because volumetric models often incur substantial computational cost. This paper presents DALight-3D, a compact 3D U-Net variant that combines depthwise separable 3D convolutions, identifier-conditioned normalization, cross-slice attention, and adaptive skip fusion. The method is evaluated on the Medical Segmentation Decathlon Task01 BrainTumour benchmark under matched optimization settings against standard 3D U-Net, Attention U-Net, Residual 3D U-Net, and V-Net baselines. In the reported 50-epoch comparison, DALight-3D achieves a mean Dice of 0.727 with 2.22M parameters, compared with 0.710 Dice and 3.20M parameters for Residual 3D U-Net. Component-wise ablations show consistent performance degradation when SepConv, identifier-conditioned normalization, CSA, or SSFB is removed. These results indicate that DALight-3D offers a favorable accuracy-efficiency trade-off within the present benchmark setting.

The remote sensing (RS) domain suffers from a lack of densely labeled datasets, which are costly to obtain. Thus, models that can segment RS imagery well without supervised fine-tuning are valuable, but existing solutions fall behind supervised methods. Recently, DINOv3 surpassed SOTA RS foundation models on the GEO-bench segmentation benchmark without pre-training on RS data. Additionally, DINO.txt has enabled open vocabulary semantic segmentation (OVSS) with the DINOv3 backbone. We leverage these developments to form an OVSS model for RS imagery, free of RS-domain fine-tuning. Our model, CAFe-DINO (Cost Aggregation + Feature Upsampling with DINO) exploits the strong OVSS performance of DINOv3 for RS imagery via cost aggregation and training-free upsampling of text-image similarity scores. The robust latent of the DINOv3 backbone eliminates the need for fine-tuning on RS imagery; we instead fine-tune our model on a RS-targeted subset of COCO-Stuff. CAFe-DINO achieves state-of-the-art performance on key RS segmentation datasets, outperforming OVSS methods fine-tuned on RS data. Our code and data are publicly available at https://github.com/rfaulk/DINO_Soars.

Medical experts often manually segment images to obtain diagnostic statistics and discard the resulting annotations. We aim to train segmentation models to alleviate this burden, but constrained to the retained summary statistics (e.g., the area of the annotated region). Empirical results suggest that statistics alone are insufficient for this task, but adding weak information in the form of a few pixels within the area of interest significantly improves performance. We use a novel loss function that combines terms for image reconstruction quality, matching to summary statistics, and overlap between the predicted foreground and the weak supervisory signal. Experiments on standard image, ultrasound (breast cancer), and Computed Tomography (CT) scan (kidney tumors) data demonstrate the utility and potential of the approach.

Organoids are complex, three dimensional, self-organizing cell cultures which manifest organ-like features and represent a powerful platform for studying human disease and developing treatment options. Organoid development is characterized by dynamic morphological and cellular organization, which mimic some aspects of organ development. To study these rapid changes over the course of organoid development, advanced imaging and analytical tools are critical to accurately monitor the trajectory of organoid growth and investigate disease processes. In this work, we focus on computer vision and machine learning techniques to automatically measure the size and shape of developing spheroids derived from pluripotent stem cells (iPSCs), which are typically the starting material for generating organoid cultures. To facilitate this task, we introduce a composite method that combines the Segment Anything Model (SAM), a general-purpose foundation model, with an existing domain-specific tool. This composite method is evaluated together with several existing tools by testing them on organoid image data and comparing with the results of manual image segmentation. We find that no single existing tool is able to segment the test images with sufficient accuracy across all test conditions, but the newly introduced composite method produces consistent and accurate results for all but a very small fraction of the most challenging images. Finally, we compare the accuracy of this method to the variability between manual segmentations by independent annotators (inter-observer variability) and find that by one measure it performs at the level of inter-observer variability and by others it performs very close to it.

Recognizing unknown objects is crucial for safety-critical applications such as autonomous driving and robotics. Open-Set Panoptic Segmentation (OPS) aims to segment known thing and stuff classes while identifying valid unknown objects as separate instances. Prior OPS approaches largely treat known categories as a flat label set, ignoring the semantic hierarchy that provides valuable structural priors for distinguishing unknown objects from in-distribution classes. In this work, we propose Hyp2Former, an end-to-end framework for OPS that does not require explicit modeling of unknowns during training, and instead learns hierarchical semantic similarities continuously in hyperbolic space. By explicitly encoding hierarchical relationships among known categories, the model learns a structured embedding space that captures multiple levels of semantic abstraction. As a result, unknown objects that cannot be confidently classified as known categories still remain in close proximity to higher-level concepts (e.g., an unknown animal remains closer to "animal" or "object" than to unrelated concepts such as "electronics" or "stuff") and can therefore be reliably detected, even if their fine-grained category was not represented during training. Empirical evaluations across multiple public datasets such as MS COCO, Cityscapes, and Lost&Found demonstrate that Hyp2Former outperforms existing methods on OPS, achieving the best balance between unknown object discovery and in-distribution robustness.

Encoder-decoder imbalance and the reliance on large input volumes make many 3D brain tumor segmentation models both compute-heavy and brittle. We present M\textsuperscript{4}Fuse, a lightweight network that prioritizes discriminative brain tumor cues over exhaustive appearance reconstruction. Our method balances encoder and decoder capacity and replaces depth expansion with a synergistic design: it propagates long-range context with linear complexity via a grouped state space mixer, denoises and aligns skip features using a cross-scale dual-stage gating bridge, and absorbs cross-site acquisition shifts with a sample-level mixture-of-experts. On the BraTS2019 and BraTS2021 benchmarks, M\textsuperscript{4}Fuse outperforms other lightweight excellent methods in both parameter count and performance. Even at a challenging input resolution of $64\times128\times128$ (half that of existing excellent models), M\textsuperscript{4}Fuse reduces parameters by 62.63% and improves average performance by 0.09%. Ablations of key components validate the method's exceptional parameter-to-accuracy efficiency and robustness across diverse data centers.

Objective: Accurate probability estimates are essential for the safe deployment of medical image segmentation models in clinical decision-making. However, modern deep segmentation networks are often poorly calibrated, a problem exacerbated when multiple expert annotations exhibit substantial disagreement. While inter-rater variability is typically treated as noise, it provides valuable information about intrinsic annotation ambiguity that must be reflected in model confidence. Methods: We improve the probabilistic calibration of medical image segmentation models by reformulating multi-rater supervision as an ordinal learning problem. Voxel-wise annotator agreement is treated as an ordered target, linking predictive confidence to the empirical variability in training data. This formulation allows the use of ordinal-aware scoring rules, such as the Ranked Probability Score ordinal loss, combined with a standard binary objective to preserve discriminative performance. Results: We evaluated the proposed approach across four public segmentation benchmarks spanning ophthalmology, histopathology, and thoracic imaging. Calibration was assessed using a multi-rater extension of expected calibration error. Results consistently show that ordinal-aware training yields substantially improved calibration with respect to inter-rater agreement without degrading segmentation accuracy. Conclusions: Treating multi-rater annotations as ordered information provides a principled and architecture-agnostic route to more reliable probabilistic segmentation models.

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.

Blood vessel segmentation and -tracing are essential tasks in many medical imaging applications. Although numerous methods exist, the prevailing segment-then-fix paradigm is fundamentally limited regarding its suitability for modeling the task of complete and topologically accurate vascular network reconstruction. Here, we propose an approach to extract topologically more accurate vascular graphs from 3D image data, building upon highly successful ideas from the related biomedical tasks of cell segmentation and -tracking. Our approach first predicts voxel-wise vessel direction vectors joint with standard vessel segmentation masks. Second, to extract the vascular graph from these predictions, we introduce a direction-vector-guided extension of the TEASAR algorithm. Our approach achieves state-of-the-art performance on three benchmark datasets, spanning both synthetic and real imagery. We further demonstrate the applicability of our approach to challenging 3D micro-CT scans of rat heart vasculature. Finally, we propose meaningful and interpretable measures of topological error, namely false splits and false merges for graphs. Overall, our approach substantially improves the topological accuracy of reconstructed vascular graphs, being able to separate closely apposed vessel segments and handle multiple vascular trees within a single volume.

SAM2 produces high-quality zero-shot segmentation on natural images, but applying it to large remote sensing scenes exposes two problems: (1) its mask generator faces an inherent quality-coverage trade-off: strict thresholds yield precise masks but leave most of the image unsegmented, while relaxed thresholds increase coverage at the cost of mask quality; and (2) large images must be tiled, fragmenting objects across tile boundaries. We propose Remote SAMsing, an open-source pipeline that solves both problems without modifying SAM2 or requiring training data. For coverage, a multi-pass algorithm runs SAM2 repeatedly on each tile, painting accepted masks black between passes to simplify the scene for the next iteration, and relaxing quality thresholds only when coverage gains stagnate, ensuring that the most precise masks are always captured first. For spatial consistency, contextual padding and a parameter-free best-match merge reconstruct objects fragmented across tile boundaries. Evaluated on seven scenes (5cm to 4.78m GSD), the pipeline raises coverage from 30--68% (single-pass SAM2) to 91--98%. Ablation experiments quantify the contribution of each component to coverage and detection quality. Per-class evaluation shows that SAM2 transfers well to discrete RS objects (buildings 95%, cars 82--93% [email protected]) with segment boundaries 3--8$\times$ more precise than SLIC and Felzenszwalb baselines. Tile size functions as an implicit scale parameter: reducing it from $1{,}000$ to 250 raises [email protected] from 56% to 85%, outperforming SAM2's built-in multi-scale mechanism. The pipeline generalizes to MNF false-color imagery without retraining (99.5% ASA) and scales to production-sized images: a 1.94 billion pixel Potsdam mosaic achieved 97% coverage without quality degradation.