Large-scale pre-trained models, such as Vision Foundation Models (VFMs), have demonstrated impressive performance across various downstream tasks by transferring generalized knowledge, especially when target data is limited. However, their high computational cost and the domain gap between natural and medical images limit their practical application in medical segmentation tasks. Motivated by this, we pose the following important question: "How can we effectively utilize the knowledge of large pre-trained VFMs to train a small, task-specific model for medical image segmentation when training data is limited?" To address this problem, we propose a novel and generalizable task-specific knowledge distillation framework. Our method fine-tunes the VFM on the target segmentation task to capture task-specific features before distilling the knowledge to smaller models, leveraging Low-Rank Adaptation (LoRA) to reduce the computational cost of fine-tuning. Additionally, we incorporate synthetic data generated by diffusion models to augment the transfer set, enhancing model performance in data-limited scenarios. Experimental results across five medical image datasets demonstrate that our method consistently outperforms task-agnostic knowledge distillation and self-supervised pretraining approaches like MoCo v3 and Masked Autoencoders (MAE). For example, on the KidneyUS dataset, our method achieved a 28% higher Dice score than task-agnostic KD using 80 labeled samples for fine-tuning. On the CHAOS dataset, it achieved an 11% improvement over MAE with 100 labeled samples. These results underscore the potential of task-specific knowledge distillation to train accurate, efficient models for medical image segmentation in data-constrained settings.
Accurate medical image segmentation is crucial for precise anatomical delineation. Deep learning models like U-Net have shown great success but depend heavily on large datasets and struggle with domain shifts, complex structures, and limited training samples. Recent studies have explored diffusion models for segmentation by iteratively refining masks. However, these methods still retain the conventional image-to-mask mapping, making them highly sensitive to input data, which hampers stability and generalization. In contrast, we introduce DiffAtlas, a novel generative framework that models both images and masks through diffusion during training, effectively ``GenAI-fying'' atlas-based segmentation. During testing, the model is guided to generate a specific target image-mask pair, from which the corresponding mask is obtained. DiffAtlas retains the robustness of the atlas paradigm while overcoming its scalability and domain-specific limitations. Extensive experiments on CT and MRI across same-domain, cross-modality, varying-domain, and different data-scale settings using the MMWHS and TotalSegmentator datasets demonstrate that our approach outperforms existing methods, particularly in limited-data and zero-shot modality segmentation. Code is available at https://github.com/M3DV/DiffAtlas.
Interactive segmentation models use real-time user interactions, such as mouse clicks, as extra inputs to dynamically refine the model predictions. After model deployment, user corrections of model predictions could be used to adapt the model to the post-deployment data distribution, countering distribution-shift and enhancing reliability. Motivated by this, we introduce an online adaptation framework that enables an interactive segmentation model to continuously learn from user interaction and improve its performance on new data distributions, as it processes a sequence of test images. We introduce the Gaussian Point Loss function to train the model how to leverage user clicks, along with a two-stage online optimization method that adapts the model using the corrected predictions generated via user interactions. We demonstrate that this simple and therefore practical approach is very effective. Experiments on 5 fundus and 4 brain MRI databases demonstrate that our method outperforms existing approaches under various data distribution shifts, including segmentation of image modalities and pathologies not seen during training.
Remote sensing image segmentation faces persistent challenges in distinguishing morphologically similar categories and adapting to diverse scene variations. While existing methods rely on implicit representation learning paradigms, they often fail to dynamically adjust semantic embeddings according to contextual cues, leading to suboptimal performance in fine-grained scenarios such as cloud thickness differentiation. This work introduces a dynamic dictionary learning framework that explicitly models class ID embeddings through iterative refinement. The core contribution lies in a novel dictionary construction mechanism, where class-aware semantic embeddings are progressively updated via multi-stage alternating cross-attention querying between image features and dictionary embeddings. This process enables adaptive representation learning tailored to input-specific characteristics, effectively resolving ambiguities in intra-class heterogeneity and inter-class homogeneity. To further enhance discriminability, a contrastive constraint is applied to the dictionary space, ensuring compact intra-class distributions while maximizing inter-class separability. Extensive experiments across both coarse- and fine-grained datasets demonstrate consistent improvements over state-of-the-art methods, particularly in two online test benchmarks (LoveDA and UAVid). Code is available at https://anonymous.4open.science/r/D2LS-8267/.
Medical image segmentation is essential for clinical diagnosis, surgical planning, and treatment monitoring. Traditional approaches typically strive to tackle all medical image segmentation scenarios via one-time learning. However, in practical applications, the diversity of scenarios and tasks in medical image segmentation continues to expand, necessitating models that can dynamically evolve to meet the demands of various segmentation tasks. Here, we introduce EvoSAM, a dynamically evolving medical image segmentation model that continuously accumulates new knowledge from an ever-expanding array of scenarios and tasks, enhancing its segmentation capabilities. Extensive evaluations on surgical image blood vessel segmentation and multi-site prostate MRI segmentation demonstrate that EvoSAM not only improves segmentation accuracy but also mitigates catastrophic forgetting. Further experiments conducted by surgical clinicians on blood vessel segmentation confirm that EvoSAM enhances segmentation efficiency based on user prompts, highlighting its potential as a promising tool for clinical applications.
Dichotomous Image Segmentation (DIS) is a high-precision object segmentation task for high-resolution natural images. The current mainstream methods focus on the optimization of local details but overlook the fundamental challenge of modeling the integrity of objects. We have found that the depth integrity-prior implicit in the the pseudo-depth maps generated by Depth Anything Model v2 and the local detail features of image patches can jointly address the above dilemmas. Based on the above findings, we have designed a novel Patch-Depth Fusion Network (PDFNet) for high-precision dichotomous image segmentation. The core of PDFNet consists of three aspects. Firstly, the object perception is enhanced through multi-modal input fusion. By utilizing the patch fine-grained strategy, coupled with patch selection and enhancement, the sensitivity to details is improved. Secondly, by leveraging the depth integrity-prior distributed in the depth maps, we propose an integrity-prior loss to enhance the uniformity of the segmentation results in the depth maps. Finally, we utilize the features of the shared encoder and, through a simple depth refinement decoder, improve the ability of the shared encoder to capture subtle depth-related information in the images. Experiments on the DIS-5K dataset show that PDFNet significantly outperforms state-of-the-art non-diffusion methods. Due to the incorporation of the depth integrity-prior, PDFNet achieves or even surpassing the performance of the latest diffusion-based methods while using less than 11% of the parameters of diffusion-based methods. The source code at https://github.com/Tennine2077/PDFNet
Residual moveout (RMO) provides critical information for travel time tomography. The current industry-standard method for fitting RMO involves scanning high-order polynomial equations. However, this analytical approach does not accurately capture local saltation, leading to low iteration efficiency in tomographic inversion. Supervised learning-based image segmentation methods for picking can effectively capture local variations; however, they encounter challenges such as a scarcity of reliable training samples and the high complexity of post-processing. To address these issues, this study proposes a deep learning-based cascade picking method. It distinguishes accurate and robust RMOs using a segmentation network and a post-processing technique based on trend regression. Additionally, a data synthesis method is introduced, enabling the segmentation network to be trained on synthetic datasets for effective picking in field data. Furthermore, a set of metrics is proposed to quantify the quality of automatically picked RMOs. Experimental results based on both model and real data demonstrate that, compared to semblance-based methods, our approach achieves greater picking density and accuracy.
Computed tomography (CT) is extensively used for accurate visualization and segmentation of organs and lesions. While deep learning models such as convolutional neural networks (CNNs) and vision transformers (ViTs) have significantly improved CT image analysis, their performance often declines when applied to diverse, real-world clinical data. Although foundation models offer a broader and more adaptable solution, their potential is limited due to the challenge of obtaining large-scale, voxel-level annotations for medical images. In response to these challenges, prompting-based models using visual or text prompts have emerged. Visual-prompting methods, such as the Segment Anything Model (SAM), still require significant manual input and can introduce ambiguity when applied to clinical scenarios. Instead, foundation models that use text prompts offer a more versatile and clinically relevant approach. Notably, current text-prompt models, such as the CLIP-Driven Universal Model, are limited to text prompts already encountered during training and struggle to process the complex and diverse scenarios of real-world clinical applications. Instead of fine-tuning models trained from natural imaging, we propose OpenVocabCT, a vision-language model pretrained on large-scale 3D CT images for universal text-driven segmentation. Using the large-scale CT-RATE dataset, we decompose the diagnostic reports into fine-grained, organ-level descriptions using large language models for multi-granular contrastive learning. We evaluate our OpenVocabCT on downstream segmentation tasks across nine public datasets for organ and tumor segmentation, demonstrating the superior performance of our model compared to existing methods. All code, datasets, and models will be publicly released at https://github.com/ricklisz/OpenVocabCT.
Large-scale vision models like SAM have extensive visual knowledge, yet their general nature and computational demands limit their use in specialized tasks like medical image segmentation. In contrast, task-specific models such as U-Net++ often underperform due to sparse labeled data. This study introduces a strategic knowledge mining method that leverages SAM's broad understanding to boost the performance of small, locally hosted deep learning models. In our approach, we trained a U-Net++ model on a limited labeled dataset and extend its capabilities by converting SAM's output infered on unlabeled images into prompts. This process not only harnesses SAM's generalized visual knowledge but also iteratively improves SAM's prediction to cater specialized medical segmentation tasks via U-Net++. The mined knowledge, serving as "pseudo labels", enriches the training dataset, enabling the fine-tuning of the local network. Applied to the Kvasir SEG and COVID-QU-Ex datasets which consist of gastrointestinal polyp and lung X-ray images respectively, our proposed method consistently enhanced the segmentation performance on Dice by 3% and 1% respectively over the baseline U-Net++ model, when the same amount of labelled data were used during training (75% and 50% of labelled data). Remarkably, our proposed method surpassed the baseline U-Net++ model even when the latter was trained exclusively on labeled data (100% of labelled data). These results underscore the potential of knowledge mining to overcome data limitations in specialized models by leveraging the broad, albeit general, knowledge of large-scale models like SAM, all while maintaining operational efficiency essential for clinical applications.
The growing rate of chronic wound occurrence, especially in patients with diabetes, has become a concerning trend in recent years. Chronic wounds are difficult and costly to treat, and have become a serious burden on health care systems worldwide. Chronic wounds can have devastating consequences for the patient, with infection often leading to reduced quality of life and increased mortality risk. Innovative deep learning methods for the detection and monitoring of such wounds have the potential to reduce the impact to both patient and clinician. We present a novel multimodal segmentation method which allows for the introduction of patient metadata into the training workflow whereby the patient data are expressed as Gaussian random fields. Our results indicate that the proposed method improved performance when utilising multiple models, each trained on different metadata categories. Using the Diabetic Foot Ulcer Challenge 2022 test set, when compared to the baseline results (intersection over union = 0.4670, Dice similarity coefficient = 0.5908) we demonstrate improvements of +0.0220 and +0.0229 for intersection over union and Dice similarity coefficient respectively. This paper presents the first study to focus on integrating patient data into a chronic wound segmentation workflow. Our results show significant performance gains when training individual models using specific metadata categories, followed by average merging of prediction masks using distance transforms. All source code for this study is available at: https://github.com/mmu-dermatology-research/multimodal-grf
Medical image segmentation is fundamental for computer-aided diagnostics, providing accurate delineation of anatomical structures and pathological regions. While common metrics such as Accuracy, DSC, IoU, and HD primarily quantify spatial agreement between predictions and ground-truth labels, they do not assess the calibration quality of segmentation models, which is crucial for clinical reliability. To address this limitation, we propose pixel-wise Expected Calibration Error (pECE), a novel metric that explicitly measures miscalibration at the pixel level, thereby ensuring both spatial precision and confidence reliability. We further introduce a morphological adaptation strategy that applies morphological operations to ground-truth masks before computing calibration losses, particularly benefiting margin-based losses such as Margin SVLS and NACL. Additionally, we present the Signed Distance Calibration Loss (SDC), which aligns boundary geometry with calibration objectives by penalizing discrepancies between predicted and ground-truth signed distance functions (SDFs). Extensive experiments demonstrate that our method not only enhances segmentation performance but also improves calibration quality, yielding more trustworthy confidence estimates. Code is available at: https://github.com/EagleAdelaide/SDC-Loss.
The reliance on large labeled datasets presents a significant challenge in medical image segmentation. Few-shot learning offers a potential solution, but existing methods often still require substantial training data. This paper proposes a novel approach that leverages the Segment Anything Model 2 (SAM2), a vision foundation model with strong video segmentation capabilities. We conceptualize 3D medical image volumes as video sequences, departing from the traditional slice-by-slice paradigm. Our core innovation is a support-query matching strategy: we perform extensive data augmentation on a single labeled support image and, for each frame in the query volume, algorithmically select the most analogous augmented support image. This selected image, along with its corresponding mask, is used as a mask prompt, driving SAM2's video segmentation. This approach entirely avoids model retraining or parameter updates. We demonstrate state-of-the-art performance on benchmark few-shot medical image segmentation datasets, achieving significant improvements in accuracy and annotation efficiency. This plug-and-play method offers a powerful and generalizable solution for 3D medical image segmentation.
Gliomas are aggressive brain tumors that require accurate imaging-based diagnosis, with segmentation playing a critical role in evaluating morphology and treatment decisions. Manual delineation of gliomas is time-consuming and prone to variability, motivating the use of deep learning to improve consistency and alleviate clinical workload. However, existing methods often fail to fully exploit the information available in multi-parametric MRI (mp-MRI), particularly inter-slice contextual features, and typically require considerable computational resources while lacking robustness across tumor type variations. We present GBT-SAM, a parameter-efficient deep learning framework that adapts the Segment Anything Model (SAM), a large-scale vision model, to volumetric mp-MRI data. GBT-SAM reduces input complexity by selecting fewer than 2.6\% of slices per scan while incorporating all four MRI modalities, preserving essential tumor-related information with minimal cost. Furthermore, our model is trained by a two-step fine-tuning strategy that incorporates a depth-aware module to capture inter-slice correlations and lightweight adaptation layers, resulting in just 6.5M trainable parameters, which is the lowest among SAM-based approaches. GBT-SAM achieves a Dice Score of 93.54 on the BraTS Adult Glioma dataset and demonstrates robust performance on Meningioma, Pediatric Glioma, and Sub-Saharan Glioma datasets. These results highlight GBT-SAM's potential as a computationally efficient and domain-robust framework for brain tumor segmentation using mp-MRI. Our code and models are available at https://github.com/vpulab/med-sam-brain .
Effective monitoring of underwater ecosystems is crucial for tracking environmental changes, guiding conservation efforts, and ensuring long-term ecosystem health. However, automating underwater ecosystem management with robotic platforms remains challenging due to the complexities of underwater imagery, which pose significant difficulties for traditional visual localization methods. We propose an integrated pipeline that combines Visual Place Recognition (VPR), feature matching, and image segmentation on video-derived images. This method enables robust identification of revisited areas, estimation of rigid transformations, and downstream analysis of ecosystem changes. Furthermore, we introduce the SQUIDLE+ VPR Benchmark-the first large-scale underwater VPR benchmark designed to leverage an extensive collection of unstructured data from multiple robotic platforms, spanning time intervals from days to years. The dataset encompasses diverse trajectories, arbitrary overlap and diverse seafloor types captured under varying environmental conditions, including differences in depth, lighting, and turbidity. Our code is available at: https://github.com/bev-gorry/underloc
The nnU-Net framework has played a crucial role in medical image segmentation and has become the gold standard in multitudes of applications targeting different diseases, organs, and modalities. However, so far it has been used primarily in a centralized approach where the data collected from hospitals are stored in one center and used to train the nnU-Net. This centralized approach has various limitations, such as leakage of sensitive patient information and violation of patient privacy. Federated learning is one of the approaches to train a segmentation model in a decentralized manner that helps preserve patient privacy. In this paper, we propose FednnU-Net, a federated learning extension of nnU-Net. We introduce two novel federated learning methods to the nnU-Net framework - Federated Fingerprint Extraction (FFE) and Asymmetric Federated Averaging (AsymFedAvg) - and experimentally show their consistent performance for breast, cardiac and fetal segmentation using 6 datasets representing samples from 18 institutions. Additionally, to further promote research and deployment of decentralized training in privacy constrained institutions, we make our plug-n-play framework public. The source-code is available at https://github.com/faildeny/FednnUNet .
We present TopoMortar, a brick wall dataset that is the first dataset specifically designed to evaluate topology-focused image segmentation methods, such as topology loss functions. TopoMortar enables to investigate in two ways whether methods incorporate prior topological knowledge. First, by eliminating challenges seen in real-world data, such as small training set, noisy labels, and out-of-distribution test-set images, that, as we show, impact the effectiveness of topology losses. Second, by allowing to assess in the same dataset topology accuracy across dataset challenges, isolating dataset-related effects from the effect of incorporating prior topological knowledge. In these two experiments, it is deliberately difficult to improve topology accuracy without actually using topology information, thus, permitting to attribute an improvement in topology accuracy to the incorporation of prior topological knowledge. To this end, TopoMortar includes three types of labels (accurate, noisy, pseudo-labels), two fixed training sets (large and small), and in-distribution and out-of-distribution test-set images. We compared eight loss functions on TopoMortar, and we found that clDice achieved the most topologically accurate segmentations, Skeleton Recall loss performed best particularly with noisy labels, and the relative advantageousness of the other loss functions depended on the experimental setting. Additionally, we show that simple methods, such as data augmentation and self-distillation, can elevate Cross entropy Dice loss to surpass most topology loss functions, and that those simple methods can enhance topology loss functions as well. clDice and Skeleton Recall loss, both skeletonization-based loss functions, were also the fastest to train, making this type of loss function a promising research direction. TopoMortar and our code can be found at https://github.com/jmlipman/TopoMortar
Image segmentation is a fundamental task in both image analysis and medical applications. State-of-the-art methods predominantly rely on encoder-decoder architectures with a U-shaped design, commonly referred to as U-Net. Recent advancements integrating transformers and MLPs improve performance but still face key limitations, such as poor interpretability, difficulty handling intrinsic noise, and constrained expressiveness due to discrete layer structures, often lacking a solid theoretical foundation.In this work, we introduce Implicit U-KAN 2.0, a novel U-Net variant that adopts a two-phase encoder-decoder structure. In the SONO phase, we use a second-order neural ordinary differential equation (NODEs), called the SONO block, for a more efficient, expressive, and theoretically grounded modeling approach. In the SONO-MultiKAN phase, we integrate the second-order NODEs and MultiKAN layer as the core computational block to enhance interpretability and representation power. Our contributions are threefold. First, U-KAN 2.0 is an implicit deep neural network incorporating MultiKAN and second order NODEs, improving interpretability and performance while reducing computational costs. Second, we provide a theoretical analysis demonstrating that the approximation ability of the MultiKAN block is independent of the input dimension. Third, we conduct extensive experiments on a variety of 2D and a single 3D dataset, demonstrating that our model consistently outperforms existing segmentation networks.
This paper introduces conformal Lyapunov optimization (CLO), a novel resource allocation framework for networked systems that optimizes average long-term objectives, while satisfying deterministic long-term reliability constraints. Unlike traditional Lyapunov optimization (LO), which addresses resource allocation tasks under average long-term constraints, CLO provides formal worst-case deterministic reliability guarantees. This is achieved by integrating the standard LO optimization framework with online conformal risk control (O-CRC), an adaptive update mechanism controlling long-term risks. The effectiveness of CLO is verified via experiments for hierarchal edge inference targeting image segmentation tasks in a networked computing architecture. Specifically, simulation results confirm that CLO can control reliability constraints, measured via the false negative rate of all the segmentation decisions made in the network, while at the same time minimizing the weighted sum of energy consumption and imprecision, with the latter accounting for the rate of false positives.
Existing approaches for color-concept association typically rely on query-based image referencing, and color extraction from image references. However, these approaches are effective only for common concepts, and are vulnerable to unstable image referencing and varying image conditions. Our formative study with designers underscores the need for primary-accent color compositions and context-dependent colors (e.g., 'clear' vs. 'polluted' sky) in design. In response, we introduce a generative approach for mining semantically resonant colors leveraging images generated by text-to-image models. Our insight is that contemporary text-to-image models can resemble visual patterns from large-scale real-world data. The framework comprises three stages: concept instancing produces generative samples using diffusion models, text-guided image segmentation identifies concept-relevant regions within the image, and color association extracts primarily accompanied by accent colors. Quantitative comparisons with expert designs validate our approach's effectiveness, and we demonstrate the applicability through cases in various design scenarios and a gallery.
Transformers have achieved remarkable success across multiple fields, yet their impact on 3D medical image segmentation remains limited with convolutional networks still dominating major benchmarks. In this work, we a) analyze current Transformer-based segmentation models and identify critical shortcomings, particularly their over-reliance on convolutional blocks. Further, we demonstrate that in some architectures, performance is unaffected by the absence of the Transformer, thereby demonstrating their limited effectiveness. To address these challenges, we move away from hybrid architectures and b) introduce a fully Transformer-based segmentation architecture, termed Primus. Primus leverages high-resolution tokens, combined with advances in positional embeddings and block design, to maximally leverage its Transformer blocks. Through these adaptations Primus surpasses current Transformer-based methods and competes with state-of-the-art convolutional models on multiple public datasets. By doing so, we create the first pure Transformer architecture and take a significant step towards making Transformers state-of-the-art for 3D medical image segmentation.