Medical image segmentation models are often trained on curated datasets, leading to performance degradation when deployed in real-world clinical settings due to mismatches between training and test distributions. While data augmentation techniques are widely used to address these challenges, traditional visually consistent augmentation strategies lack the robustness needed for diverse real-world scenarios. In this work, we systematically evaluate alternative augmentation strategies, focusing on MixUp and Auxiliary Fourier Augmentation. These methods mitigate the effects of multiple variations without explicitly targeting specific sources of distribution shifts. We demonstrate how these techniques significantly improve out-of-distribution generalization and robustness to imaging variations across a wide range of transformations in cardiac cine MRI and prostate MRI segmentation. We quantitatively find that these augmentation methods enhance learned feature representations by promoting separability and compactness. Additionally, we highlight how their integration into nnU-Net training pipelines provides an easy-to-implement, effective solution for enhancing the reliability of medical segmentation models in real-world applications.
Obtaining large-scale medical data, annotated or unannotated, is challenging due to stringent privacy regulations and data protection policies. In addition, annotating medical images requires that domain experts manually delineate anatomical structures, making the process both time-consuming and costly. As a result, semi-supervised methods have gained popularity for reducing annotation costs. However, the performance of semi-supervised methods is heavily dependent on the availability of unannotated data, and their effectiveness declines when such data are scarce or absent. To overcome this limitation, we propose a simple, yet effective and computationally efficient approach for medical image segmentation that leverages only existing annotations. We propose BoundarySeg , a multi-task framework that incorporates organ boundary prediction as an auxiliary task to full organ segmentation, leveraging consistency between the two task predictions to provide additional supervision. This strategy improves segmentation accuracy, especially in low data regimes, allowing our method to achieve performance comparable to or exceeding state-of-the-art semi supervised approaches all without relying on unannotated data or increasing computational demands. Code will be released upon acceptance.
Cardiac image segmentation is an important step in many cardiac image analysis and modeling tasks such as motion tracking or simulations of cardiac mechanics. While deep learning has greatly advanced segmentation in clinical settings, there is limited work on pre-clinical imaging, notably in porcine models, which are often used due to their anatomical and physiological similarity to humans. However, differences between species create a domain shift that complicates direct model transfer from human to pig data. Recently, foundation models trained on large human datasets have shown promise for robust medical image segmentation; yet their applicability to porcine data remains largely unexplored. In this work, we investigate whether foundation models can generate sufficiently accurate pseudo-labels for pig cardiac CT and propose a simple self-training approach to iteratively refine these labels. Our method requires no manually annotated pig data, relying instead on iterative updates to improve segmentation quality. We demonstrate that this self-training process not only enhances segmentation accuracy but also smooths out temporal inconsistencies across consecutive frames. Although our results are encouraging, there remains room for improvement, for example by incorporating more sophisticated self-training strategies and by exploring additional foundation models and other cardiac imaging technologies.
Medical imaging is a cornerstone of modern healthcare, driving advancements in diagnosis, treatment planning, and patient care. Among its various tasks, segmentation remains one of the most challenging problem due to factors such as data accessibility, annotation complexity, structural variability, variation in medical imaging modalities, and privacy constraints. Despite recent progress, achieving robust generalization and domain adaptation remains a significant hurdle, particularly given the resource-intensive nature of some proposed models and their reliance on domain expertise. This survey explores cutting-edge advancements in medical image segmentation, focusing on methodologies such as Generative AI, Few-Shot Learning, Foundation Models, and Universal Models. These approaches offer promising solutions to longstanding challenges. We provide a comprehensive overview of the theoretical foundations, state-of-the-art techniques, and recent applications of these methods. Finally, we discuss inherent limitations, unresolved issues, and future research directions aimed at enhancing the practicality and accessibility of segmentation models in medical imaging. We are maintaining a \href{https://github.com/faresbougourzi/Awesome-DL-for-Medical-Imaging-Segmentation}{GitHub Repository} to continue tracking and updating innovations in this field.
Federated semantic segmentation enables pixel-level classification in images through collaborative learning while maintaining data privacy. However, existing research commonly overlooks the fine-grained class relationships within the semantic space when addressing heterogeneous problems, particularly domain shift. This oversight results in ambiguities between class representation. To overcome this challenge, we propose a novel federated segmentation framework that strikes class consistency, termed FedSaaS. Specifically, we introduce class exemplars as a criterion for both local- and global-level class representations. On the server side, the uploaded class exemplars are leveraged to model class prototypes, which supervise global branch of clients, ensuring alignment with global-level representation. On the client side, we incorporate an adversarial mechanism to harmonize contributions of global and local branches, leading to consistent output. Moreover, multilevel contrastive losses are employed on both sides to enforce consistency between two-level representations in the same semantic space. Extensive experiments on several driving scene segmentation datasets demonstrate that our framework outperforms state-of-the-art methods, significantly improving average segmentation accuracy and effectively addressing the class-consistency representation problem.
Zero- and few-shot visual anomaly segmentation relies on powerful vision-language models that detect unseen anomalies using manually designed textual prompts. However, visual representations are inherently independent of language. In this paper, we explore the potential of a pure visual foundation model as an alternative to widely used vision-language models for universal visual anomaly segmentation. We present a novel paradigm that unifies anomaly segmentation into change segmentation. This paradigm enables us to leverage large-scale synthetic image pairs, featuring object-level and local region changes, derived from existing image datasets, which are independent of target anomaly datasets. We propose a one-prompt Meta-learning framework for Universal Anomaly Segmentation (MetaUAS) that is trained on this synthetic dataset and then generalizes well to segment any novel or unseen visual anomalies in the real world. To handle geometrical variations between prompt and query images, we propose a soft feature alignment module that bridges paired-image change perception and single-image semantic segmentation. This is the first work to achieve universal anomaly segmentation using a pure vision model without relying on special anomaly detection datasets and pre-trained visual-language models. Our method effectively and efficiently segments any anomalies with only one normal image prompt and enjoys training-free without guidance from language. Our MetaUAS significantly outperforms previous zero-shot, few-shot, and even full-shot anomaly segmentation methods. The code and pre-trained models are available at https://github.com/gaobb/MetaUAS.
Crack segmentation can play a critical role in Structural Health Monitoring (SHM) by enabling accurate identification of crack size and location, which allows to monitor structural damages over time. However, deploying deep learning models for crack segmentation on resource-constrained microcontrollers presents significant challenges due to limited memory, computational power, and energy resources. To address these challenges, this study explores lightweight U-Net architectures tailored for TinyML applications, focusing on three optimization strategies: filter number reduction, network depth reduction, and the use of Depthwise Separable Convolutions (DWConv2D). Our results demonstrate that reducing convolution kernels and network depth significantly reduces RAM and Flash requirement, and inference times, albeit with some accuracy trade-offs. Specifically, by reducing the filer number to 25%, the network depth to four blocks, and utilizing depthwise convolutions, a good compromise between segmentation performance and resource consumption is achieved. This makes the network particularly suitable for low-power TinyML applications. This study not only advances TinyML-based crack segmentation but also provides the possibility for energy-autonomous edge SHM systems.
Tertiary lymphoid structures (TLS) are organized clusters of immune cells, whose maturity and area can be quantified in whole slide image (WSI) for various prognostic tasks. Existing methods for assessing these characteristics typically rely on cell proxy tasks and require additional post-processing steps. In this work, We focus on a novel task-TLS Semantic Segmentation (TLS-SS)-which segments both the regions and maturation stages of TLS in WSI in an end-to-end manner. Due to the extensive scale of WSI and patch-based segmentation strategies, TLS-SS necessitates integrating from neighboring patches to guide target patch (target) segmentation. Previous techniques often employ on multi-resolution approaches, constraining the capacity to leverage the broader neighboring context while tend to preserve coarse-grained information. To address this, we propose a GNN-based Neighboring Context Aggregation Framework (GNCAF), which progressively aggregates multi-hop neighboring context from the target and employs a self-attention mechanism to guide the segmentation of the target. GNCAF can be integrated with various segmentation models to enhance their ability to perceive contextual information outside of the patch. We build two TLS-SS datasets, called TCGA-COAD and INHOUSE-PAAD, and make the former (comprising 225 WSIs and 5041 TLSs) publicly available. Experiments on these datasets demonstrate the superiority of GNCAF, achieving a maximum of 22.08% and 26.57% improvement in mF1 and mIoU, respectively. Additionally, we also validate the task scalability of GNCAF on segmentation of lymph node metastases.
Deep learning (DL) has become the dominant approach for medical image segmentation, yet ensuring the reliability and clinical applicability of these models requires addressing key challenges such as annotation variability, calibration, and uncertainty estimation. This is why we created the Calibration and Uncertainty for multiRater Volume Assessment in multiorgan Segmentation (CURVAS), which highlights the critical role of multiple annotators in establishing a more comprehensive ground truth, emphasizing that segmentation is inherently subjective and that leveraging inter-annotator variability is essential for robust model evaluation. Seven teams participated in the challenge, submitting a variety of DL models evaluated using metrics such as Dice Similarity Coefficient (DSC), Expected Calibration Error (ECE), and Continuous Ranked Probability Score (CRPS). By incorporating consensus and dissensus ground truth, we assess how DL models handle uncertainty and whether their confidence estimates align with true segmentation performance. Our findings reinforce the importance of well-calibrated models, as better calibration is strongly correlated with the quality of the results. Furthermore, we demonstrate that segmentation models trained on diverse datasets and enriched with pre-trained knowledge exhibit greater robustness, particularly in cases deviating from standard anatomical structures. Notably, the best-performing models achieved high DSC and well-calibrated uncertainty estimates. This work underscores the need for multi-annotator ground truth, thorough calibration assessments, and uncertainty-aware evaluations to develop trustworthy and clinically reliable DL-based medical image segmentation models.
Surgical scene segmentation is critical in computer-assisted surgery and is vital for enhancing surgical quality and patient outcomes. Recently, referring surgical segmentation is emerging, given its advantage of providing surgeons with an interactive experience to segment the target object. However, existing methods are limited by low efficiency and short-term tracking, hindering their applicability in complex real-world surgical scenarios. In this paper, we introduce ReSurgSAM2, a two-stage surgical referring segmentation framework that leverages Segment Anything Model 2 to perform text-referred target detection, followed by tracking with reliable initial frame identification and diversity-driven long-term memory. For the detection stage, we propose a cross-modal spatial-temporal Mamba to generate precise detection and segmentation results. Based on these results, our credible initial frame selection strategy identifies the reliable frame for the subsequent tracking. Upon selecting the initial frame, our method transitions to the tracking stage, where it incorporates a diversity-driven memory mechanism that maintains a credible and diverse memory bank, ensuring consistent long-term tracking. Extensive experiments demonstrate that ReSurgSAM2 achieves substantial improvements in accuracy and efficiency compared to existing methods, operating in real-time at 61.2 FPS. Our code and datasets will be available at https://github.com/jinlab-imvr/ReSurgSAM2.
Accurate segmentation of tubular topological structures (e.g., fissures and vasculature) is critical in various fields to guarantee dependable downstream quantitative analysis and modeling. However, in dense prediction tasks such as semantic segmentation and super-resolution, conventional upsampling operators cannot accommodate the slenderness of tubular structures and the curvature of morphology. This paper introduces a dynamic snake upsampling operators and a boundary-skeleton weighted loss tailored for topological tubular structures. Specifically, we design a snake upsampling operators based on an adaptive sampling domain, which dynamically adjusts the sampling stride according to the feature map and selects a set of subpixel sampling points along the serpentine path, enabling more accurate subpixel-level feature recovery for tubular structures. Meanwhile, we propose a skeleton-to-boundary increasing weighted loss that trades off main body and boundary weight allocation based on mask class ratio and distance field, preserving main body overlap while enhancing focus on target topological continuity and boundary alignment precision. Experiments across various domain datasets and backbone networks show that this plug-and-play dynamic snake upsampling operator and boundary-skeleton weighted loss boost both pixel-wise segmentation accuracy and topological consistency of results.
This paper presents a Multi-Elevation Semantic Segmentation Image (MESSI) dataset comprising 2525 images taken by a drone flying over dense urban environments. MESSI is unique in two main features. First, it contains images from various altitudes, allowing us to investigate the effect of depth on semantic segmentation. Second, it includes images taken from several different urban regions (at different altitudes). This is important since the variety covers the visual richness captured by a drone's 3D flight, performing horizontal and vertical maneuvers. MESSI contains images annotated with location, orientation, and the camera's intrinsic parameters and can be used to train a deep neural network for semantic segmentation or other applications of interest (e.g., localization, navigation, and tracking). This paper describes the dataset and provides annotation details. It also explains how semantic segmentation was performed using several neural network models and shows several relevant statistics. MESSI will be published in the public domain to serve as an evaluation benchmark for semantic segmentation using images captured by a drone or similar vehicle flying over a dense urban environment.
Prompt engineering has shown remarkable success with large language models, yet its systematic exploration in computer vision remains limited. In semantic segmentation, both textual and visual prompts offer distinct advantages: textual prompts through open-vocabulary methods allow segmentation of arbitrary categories, while visual reference prompts provide intuitive reference examples. However, existing benchmarks evaluate these modalities in isolation, without direct comparison under identical conditions. We present Show or Tell (SoT), a novel benchmark specifically designed to evaluate both visual and textual prompts for semantic segmentation across 14 datasets spanning 7 diverse domains (common scenes, urban, food, waste, parts, tools, and land-cover). We evaluate 5 open-vocabulary methods and 4 visual reference prompt approaches, adapting the latter to handle multi-class segmentation through a confidence-based mask merging strategy. Our extensive experiments reveal that open-vocabulary methods excel with common concepts easily described by text but struggle with complex domains like tools, while visual reference prompt methods achieve good average results but exhibit high variability depending on the input prompt. Through comprehensive quantitative and qualitative analysis, we identify the strengths and weaknesses of both prompting modalities, providing valuable insights to guide future research in vision foundation models for segmentation tasks.
Efficient crop-weed segmentation is critical for site-specific weed control in precision agriculture. Conventional CNN-based methods struggle to generalize and rely on RGB imagery, limiting performance under complex field conditions. To address these challenges, we propose a lightweight transformer-CNN hybrid. It processes RGB, Near-Infrared (NIR), and Red-Edge (RE) bands using specialized encoders and dynamic modality integration. Evaluated on the WeedsGalore dataset, the model achieves a segmentation accuracy (mean IoU) of 78.88%, outperforming RGB-only models by 15.8 percentage points. With only 8.7 million parameters, the model offers high accuracy, computational efficiency, and potential for real-time deployment on Unmanned Aerial Vehicles (UAVs) and edge devices, advancing precision weed management.
This report presents our semantic segmentation framework developed by team ACVLAB for the ICRA 2025 GOOSE 2D Semantic Segmentation Challenge, which focuses on parsing outdoor scenes into nine semantic categories under real-world conditions. Our method integrates a Swin Transformer backbone enhanced with Rotary Position Embedding (RoPE) for improved spatial generalization, alongside a Color Shift Estimation-and-Correction module designed to compensate for illumination inconsistencies in natural environments. To further improve training stability, we adopt a quantile-based denoising strategy that downweights the top 2.5\% of highest-error pixels, treating them as noise and suppressing their influence during optimization. Evaluated on the official GOOSE test set, our approach achieved a mean Intersection over Union (mIoU) of 0.848, demonstrating the effectiveness of combining color correction, positional encoding, and error-aware denoising in robust semantic segmentation.
In autonomous driving, thermal image semantic segmentation has emerged as a critical research area, owing to its ability to provide robust scene understanding under adverse visual conditions. In particular, unsupervised domain adaptation (UDA) for thermal image segmentation can be an efficient solution to address the lack of labeled thermal datasets. Nevertheless, since these methods do not effectively utilize the complementary information between RGB and thermal images, they significantly decrease performance during domain adaptation. In this paper, we present a comprehensive study on cross-spectral UDA for thermal image semantic segmentation. We first propose a novel masked mutual learning strategy that promotes complementary information exchange by selectively transferring results between each spectral model while masking out uncertain regions. Additionally, we introduce a novel prototypical self-supervised loss designed to enhance the performance of the thermal segmentation model in nighttime scenarios. This approach addresses the limitations of RGB pre-trained networks, which cannot effectively transfer knowledge under low illumination due to the inherent constraints of RGB sensors. In experiments, our method achieves higher performance over previous UDA methods and comparable performance to state-of-the-art supervised methods.
Visible and infrared image fusion (VIF) has attracted significant attention in recent years. Traditional VIF methods primarily focus on generating fused images with high visual quality, while recent advancements increasingly emphasize incorporating semantic information into the fusion model during training. However, most existing segmentation-oriented VIF methods adopt a cascade structure comprising separate fusion and segmentation models, leading to increased network complexity and redundancy. This raises a critical question: can we design a more concise and efficient structure to integrate semantic information directly into the fusion model during training-Inspired by multi-task learning, we propose a concise and universal training framework, MultiTaskVIF, for segmentation-oriented VIF models. In this framework, we introduce a multi-task head decoder (MTH) to simultaneously output both the fused image and the segmentation result during training. Unlike previous cascade training frameworks that necessitate joint training with a complete segmentation model, MultiTaskVIF enables the fusion model to learn semantic features by simply replacing its decoder with MTH. Extensive experimental evaluations validate the effectiveness of the proposed method. Our code will be released upon acceptance.
Fusing and balancing multi-modal inputs from novel sensors for dense prediction tasks, particularly semantic segmentation, is critically important yet remains a significant challenge. One major limitation is the tendency of multi-modal frameworks to over-rely on easily learnable modalities, a phenomenon referred to as unimodal dominance or bias. This issue becomes especially problematic in real-world scenarios where the dominant modality may be unavailable, resulting in severe performance degradation. To this end, we apply a simple but effective plug-and-play regularization term based on functional entropy, which introduces no additional parameters or modules. This term is designed to intuitively balance the contribution of each visual modality to the segmentation results. Specifically, we leverage the log-Sobolev inequality to bound functional entropy using functional-Fisher-information. By maximizing the information contributed by each visual modality, our approach mitigates unimodal dominance and establishes a more balanced and robust segmentation framework. A multi-scale regularization module is proposed to apply our proposed plug-and-play term on high-level features and also segmentation predictions for more balanced multi-modal learning. Extensive experiments on three datasets demonstrate that our proposed method achieves superior performance, i.e., +13.94%, +3.25%, and +3.64%, without introducing any additional parameters.
Continual Anomaly Detection (CAD) enables anomaly detection models in learning new classes while preserving knowledge of historical classes. CAD faces two key challenges: catastrophic forgetting and segmentation of small anomalous regions. Existing CAD methods store image distributions or patch features to mitigate catastrophic forgetting, but they fail to preserve pixel-level detailed features for accurate segmentation. To overcome this limitation, we propose ReplayCAD, a novel diffusion-driven generative replay framework that replay high-quality historical data, thus effectively preserving pixel-level detailed features. Specifically, we compress historical data by searching for a class semantic embedding in the conditional space of the pre-trained diffusion model, which can guide the model to replay data with fine-grained pixel details, thus improving the segmentation performance. However, relying solely on semantic features results in limited spatial diversity. Hence, we further use spatial features to guide data compression, achieving precise control of sample space, thereby generating more diverse data. Our method achieves state-of-the-art performance in both classification and segmentation, with notable improvements in segmentation: 11.5% on VisA and 8.1% on MVTec. Our source code is available at https://github.com/HULEI7/ReplayCAD.
Interactive medical segmentation reduces annotation effort by refining predictions through user feedback. Vision Transformer (ViT)-based models, such as the Segment Anything Model (SAM), achieve state-of-the-art performance using user clicks and prior masks as prompts. However, existing methods treat interactions as independent events, leading to redundant corrections and limited refinement gains. We address this by introducing MAIS, a Memory-Attention mechanism for Interactive Segmentation that stores past user inputs and segmentation states, enabling temporal context integration. Our approach enhances ViT-based segmentation across diverse imaging modalities, achieving more efficient and accurate refinements.