Machine Learning (ML) and Deep Learning (DL) have shown significant promise in healthcare, particularly in medical image segmentation, which is crucial for accurate disease diagnosis and treatment planning. Despite their potential, challenges such as data privacy concerns, limited annotated data, and inadequate training data persist. Decentralized learning approaches such as federated learning (FL), split learning (SL), and split federated learning (SplitFed/SFL) address these issues effectively. This paper introduces "MedSegNet10," a publicly accessible repository designed for medical image segmentation using split-federated learning. MedSegNet10 provides a collection of pre-trained neural network architectures optimized for various medical image types, including microscopic images of human blastocysts, dermatoscopic images of skin lesions, and endoscopic images of lesions, polyps, and ulcers, with applications extending beyond these examples. By leveraging SplitFed's benefits, MedSegNet10 allows collaborative training on privately stored, horizontally split data, ensuring privacy and integrity. This repository supports researchers, practitioners, trainees, and data scientists, aiming to advance medical image segmentation while maintaining patient data privacy. The repository is available at: https://vault.sfu.ca/index.php/s/ryhf6t12O0sobuX (password upon request to the authors).
Cross-Domain Few-Shot Segmentation (CDFSS) is proposed to transfer the pixel-level segmentation capabilities learned from large-scale source-domain datasets to downstream target-domain datasets, with only a few annotated images per class. In this paper, we focus on a well-observed but unresolved phenomenon in CDFSS: for target domains, particularly those distant from the source domain, segmentation performance peaks at the very early epochs, and declines sharply as the source-domain training proceeds. We delve into this phenomenon for an interpretation: low-level features are vulnerable to domain shifts, leading to sharper loss landscapes during the source-domain training, which is the devil of CDFSS. Based on this phenomenon and interpretation, we further propose a method that includes two plug-and-play modules: one to flatten the loss landscapes for low-level features during source-domain training as a novel sharpness-aware minimization method, and the other to directly supplement target-domain information to the model during target-domain testing by low-level-based calibration. Extensive experiments on four target datasets validate our rationale and demonstrate that our method surpasses the state-of-the-art method in CDFSS signifcantly by 3.71% and 5.34% average MIoU in 1-shot and 5-shot scenarios, respectively.
Accurate segmentation of cell nuclei in histopathology images is essential for numerous biomedical research and clinical applications. However, existing cell nucleus segmentation methods only consider a single dataset (i.e., primary domain), while neglecting to leverage supplementary data from diverse sources (i.e., auxiliary domains) to reduce overfitting and enhance the performance. Although incorporating multiple datasets could alleviate overfitting, it often exacerbates performance drops caused by domain shifts. In this work, we introduce Adversarial Multi-domain Alignment of Segment Anything Model (AMA-SAM) that extends the Segment Anything Model (SAM) to overcome these obstacles through two key innovations. First, we propose a Conditional Gradient Reversal Layer (CGRL), a multi-domain alignment module that harmonizes features from diverse domains to promote domain-invariant representation learning while preserving crucial discriminative features for the primary dataset. Second, we address SAM's inherent low-resolution output by designing a High-Resolution Decoder (HR-Decoder), which directly produces fine-grained segmentation maps in order to capture intricate nuclei boundaries in high-resolution histology images. To the best of our knowledge, this is the first attempt to adapt SAM for multi-dataset learning with application to histology nuclei segmentation. We validate our method on several publicly available datasets, demonstrating consistent and significant improvements over state-of-the-art approaches.
Large Vision-Language Models (VLMs) are increasingly being regarded as foundation models that can be instructed to solve diverse tasks by prompting, without task-specific training. We examine the seemingly obvious question: how to effectively prompt VLMs for semantic segmentation. To that end, we systematically evaluate the segmentation performance of several recent models guided by either text or visual prompts on the out-of-distribution MESS dataset collection. We introduce a scalable prompting scheme, few-shot prompted semantic segmentation, inspired by open-vocabulary segmentation and few-shot learning. It turns out that VLMs lag far behind specialist models trained for a specific segmentation task, by about 30% on average on the Intersection-over-Union metric. Moreover, we find that text prompts and visual prompts are complementary: each one of the two modes fails on many examples that the other one can solve. Our analysis suggests that being able to anticipate the most effective prompt modality can lead to a 11% improvement in performance. Motivated by our findings, we propose PromptMatcher, a remarkably simple training-free baseline that combines both text and visual prompts, achieving state-of-the-art results outperforming the best text-prompted VLM by 2.5%, and the top visual-prompted VLM by 3.5% on few-shot prompted semantic segmentation.
Segmentation is a fundamental task in computer vision, with prompt-driven methods gaining prominence due to their flexibility. The recent Segment Anything Model (SAM) has demonstrated powerful point-prompt segmentation capabilities, while text-based segmentation models offer rich semantic understanding. However, existing approaches rarely explore how to effectively combine these complementary modalities for optimal segmentation performance. This paper presents BiPrompt-SAM, a novel dual-modal prompt segmentation framework that fuses the advantages of point and text prompts through an explicit selection mechanism. Specifically, we leverage SAM's inherent ability to generate multiple mask candidates, combined with a semantic guidance mask from text prompts, and explicitly select the most suitable candidate based on similarity metrics. This approach can be viewed as a simplified Mixture of Experts (MoE) system, where the point and text modules act as distinct "experts," and the similarity scoring serves as a rudimentary "gating network." We conducted extensive evaluations on both the Endovis17 medical dataset and RefCOCO series natural image datasets. On Endovis17, BiPrompt-SAM achieved 89.55\% mDice and 81.46\% mIoU, comparable to state-of-the-art specialized medical segmentation models. On the RefCOCO series datasets, our method attained 87.1\%, 86.5\%, and 85.8\% IoU, significantly outperforming existing approaches. Experiments demonstrate that our explicit dual-selection method effectively combines the spatial precision of point prompts with the semantic richness of text prompts, particularly excelling in scenarios involving semantically complex objects, multiple similar objects, and partial occlusions. BiPrompt-SAM not only provides a simple yet effective implementation but also offers a new perspective on multi-modal prompt fusion.
Accurate object segmentation is crucial for high-quality scene understanding in the 3D vision domain. However, 3D segmentation based on 3D Gaussian Splatting (3DGS) struggles with accurately delineating object boundaries, as Gaussian primitives often span across object edges due to their inherent volume and the lack of semantic guidance during training. In order to tackle these challenges, we introduce Clear Object Boundaries for 3DGS Segmentation (COB-GS), which aims to improve segmentation accuracy by clearly delineating blurry boundaries of interwoven Gaussian primitives within the scene. Unlike existing approaches that remove ambiguous Gaussians and sacrifice visual quality, COB-GS, as a 3DGS refinement method, jointly optimizes semantic and visual information, allowing the two different levels to cooperate with each other effectively. Specifically, for the semantic guidance, we introduce a boundary-adaptive Gaussian splitting technique that leverages semantic gradient statistics to identify and split ambiguous Gaussians, aligning them closely with object boundaries. For the visual optimization, we rectify the degraded suboptimal texture of the 3DGS scene, particularly along the refined boundary structures. Experimental results show that COB-GS substantially improves segmentation accuracy and robustness against inaccurate masks from pre-trained model, yielding clear boundaries while preserving high visual quality. Code is available at https://github.com/ZestfulJX/COB-GS.
Accurate segmentation of nodules in both 2D breast ultrasound (BUS) and 3D automated breast ultrasound (ABUS) is crucial for clinical diagnosis and treatment planning. Therefore, developing an automated system for nodule segmentation can enhance user independence and expedite clinical analysis. Unlike fully-supervised learning, weakly-supervised segmentation (WSS) can streamline the laborious and intricate annotation process. However, current WSS methods face challenges in achieving precise nodule segmentation, as many of them depend on inaccurate activation maps or inefficient pseudo-mask generation algorithms. In this study, we introduce a novel multi-agent reinforcement learning-based WSS framework called Flip Learning, which relies solely on 2D/3D boxes for accurate segmentation. Specifically, multiple agents are employed to erase the target from the box to facilitate classification tag flipping, with the erased region serving as the predicted segmentation mask. The key contributions of this research are as follows: (1) Adoption of a superpixel/supervoxel-based approach to encode the standardized environment, capturing boundary priors and expediting the learning process. (2) Introduction of three meticulously designed rewards, comprising a classification score reward and two intensity distribution rewards, to steer the agents' erasing process precisely, thereby avoiding both under- and over-segmentation. (3) Implementation of a progressive curriculum learning strategy to enable agents to interact with the environment in a progressively challenging manner, thereby enhancing learning efficiency. Extensively validated on the large in-house BUS and ABUS datasets, our Flip Learning method outperforms state-of-the-art WSS methods and foundation models, and achieves comparable performance as fully-supervised learning algorithms.
Coral reefs are declining worldwide due to climate change and local stressors. To inform effective conservation or restoration, monitoring at the highest possible spatial and temporal resolution is necessary. Conventional coral reef surveying methods are limited in scalability due to their reliance on expert labor time, motivating the use of computer vision tools to automate the identification and abundance estimation of live corals from images. However, the design and evaluation of such tools has been impeded by the lack of large high quality datasets. We release the Coralscapes dataset, the first general-purpose dense semantic segmentation dataset for coral reefs, covering 2075 images, 39 benthic classes, and 174k segmentation masks annotated by experts. Coralscapes has a similar scope and the same structure as the widely used Cityscapes dataset for urban scene segmentation, allowing benchmarking of semantic segmentation models in a new challenging domain which requires expert knowledge to annotate. We benchmark a wide range of semantic segmentation models, and find that transfer learning from Coralscapes to existing smaller datasets consistently leads to state-of-the-art performance. Coralscapes will catalyze research on efficient, scalable, and standardized coral reef surveying methods based on computer vision, and holds the potential to streamline the development of underwater ecological robotics.
Whole-heart segmentation from CT and MRI scans is crucial for cardiovascular disease analysis, yet existing methods struggle with modality-specific biases and the need for extensive labeled datasets. To address these challenges, we propose a foundation model for whole-heart segmentation using a self-supervised learning (SSL) framework based on a student-teacher architecture. Our model is pretrained on a large, unlabeled dataset of CT and MRI scans, leveraging the xLSTM backbone to capture long-range spatial dependencies and complex anatomical structures in 3D medical images. By incorporating multi-modal pretraining, our approach ensures strong generalization across both CT and MRI modalities, mitigating modality-specific variations and improving segmentation accuracy in diverse clinical settings. The use of large-scale unlabeled data significantly reduces the dependency on manual annotations, enabling robust performance even with limited labeled data. We further introduce an xLSTM-UNet-based architecture for downstream whole-heart segmentation tasks, demonstrating its effectiveness on few-label CT and MRI datasets. Our results validate the robustness and adaptability of the proposed model, highlighting its potential for advancing automated whole-heart segmentation in medical imaging.
Cortical thickness measurements from magnetic resonance imaging, an important biomarker in many neurodegenerative and neurological disorders, are derived by many tools from an initial voxel-wise tissue segmentation. White matter (WM) hypointensities in T1-weighted imaging, such as those arising from multiple sclerosis or small vessel disease, are known to affect the output of brain segmentation methods and therefore bias cortical thickness measurements. These effects are well-documented among traditional brain segmentation tools but have not been studied extensively in tools based on deep-learning segmentations, which promise to be more robust. In this paper, we explore the potential of deep learning to enhance the accuracy and efficiency of cortical thickness measurement in the presence of WM lesions, using a high-quality lesion filling algorithm leveraging denoising diffusion networks. A pseudo-3D U-Net architecture trained on the OASIS dataset to generate synthetic healthy tissue, conditioned on binary lesion masks derived from the MSSEG dataset, allows realistic removal of white matter lesions in multiple sclerosis patients. By applying morphometry methods to patient images before and after lesion filling, we analysed robustness of global and regional cortical thickness measurements in the presence of white matter lesions. Methods based on a deep learning-based segmentation of the brain (Fastsurfer, DL+DiReCT, ANTsPyNet) exhibited greater robustness than those using classical segmentation methods (Freesurfer, ANTs).
Traditional brain lesion segmentation models for multi-modal MRI are typically tailored to specific pathologies, relying on datasets with predefined modalities. Adapting to new MRI modalities or pathologies often requires training separate models, which contrasts with how medical professionals incrementally expand their expertise by learning from diverse datasets over time. Inspired by this human learning process, we propose a unified segmentation model capable of sequentially learning from multiple datasets with varying modalities and pathologies. Our approach leverages a privacy-aware continual learning framework that integrates a mixture-of-experts mechanism and dual knowledge distillation to mitigate catastrophic forgetting while not compromising performance on newly encountered datasets. Extensive experiments across five diverse brain MRI datasets and four dataset sequences demonstrate the effectiveness of our framework in maintaining a single adaptable model, capable of handling varying hospital protocols, imaging modalities, and disease types. Compared to widely used privacy-aware continual learning methods such as LwF, SI, EWC, and MiB, our method achieves an average Dice score improvement of approximately 11%. Our framework represents a significant step toward more versatile and practical brain lesion segmentation models, with implementation available at \href{https://github.com/xmindflow/BrainCL}{GitHub}.
3D ultrasound delivers high-resolution, real-time images of soft tissues, which is essential for pain research. However, manually distinguishing various tissues for quantitative analysis is labor-intensive. To streamline this process, we developed and validated GRN+, a novel multi-model framework that automates layer segmentation with minimal annotated data. GRN+ combines a ResNet-based generator and a U-Net segmentation model. Through a method called Segmentation-guided Enhancement (SGE), the generator produces new images and matching masks under the guidance of the segmentation model, with its weights adjusted according to the segmentation loss gradient. To prevent gradient explosion and secure stable training, a two-stage backpropagation strategy was implemented: the first stage propagates the segmentation loss through both the generator and segmentation model, while the second stage concentrates on optimizing the segmentation model alone, thereby refining mask prediction using the generated images. Tested on 69 fully annotated 3D ultrasound scans from 29 subjects with six manually labeled tissue layers, GRN+ outperformed all other semi-supervised methods in terms of the Dice coefficient using only 5% labeled data, despite not using unlabeled data for unsupervised training. Additionally, when applied to fully annotated datasets, GRN+ with SGE achieved a 2.16% higher Dice coefficient while incurring lower computational costs compared to other models. Overall, GRN+ provides accurate tissue segmentation while reducing both computational expenses and the dependency on extensive annotations, making it an effective tool for 3D ultrasound analysis in cLBP patients.
Available studies on chronic lower back pain (cLBP) typically focus on one or a few specific tissues rather than conducting a comprehensive layer-by-layer analysis. Since three-dimensional (3-D) images often contain hundreds of slices, manual annotation of these anatomical structures is both time-consuming and error-prone. We aim to develop and validate a novel approach called InterSliceBoost to enable the training of a segmentation model on a partially annotated dataset without compromising segmentation performance. The architecture of InterSliceBoost includes two components: an inter-slice generator and a segmentation model. The generator utilizes residual block-based encoders to extract features from adjacent image-mask pairs (IMPs). Differential features are calculated and input into a decoder to generate inter-slice IMPs. The segmentation model is trained on partially annotated datasets (e.g., skipping 1, 2, 3, or 7 images) and the generated inter-slice IMPs. To validate the performance of InterSliceBoost, we utilized a dataset of 76 B-mode ultrasound scans acquired on 29 subjects enrolled in an ongoing cLBP study. InterSliceBoost, trained on only 33% of the image slices, achieved a mean Dice coefficient of 80.84% across all six layers on the independent test set, with Dice coefficients of 73.48%, 61.11%, 81.87%, 95.74%, 83.52% and 88.74% for segmenting dermis, superficial fat, superficial fascial membrane, deep fat, deep fascial membrane, and muscle. This performance is significantly higher than the conventional model trained on fully annotated images (p<0.05). InterSliceBoost can effectively segment the six tissue layers depicted on 3-D B-model ultrasound images in settings with partial annotations.
Skin lesion segmentation is a critical challenge in computer vision, and it is essential to separate pathological features from healthy skin for diagnostics accurately. Traditional Convolutional Neural Networks (CNNs) are limited by narrow receptive fields, and Transformers face significant computational burdens. This paper presents a novel skin lesion segmentation framework, the Atrous Shifted Parallel Vision Mamba UNet (ASP-VMUNet), which integrates the efficient and scalable Mamba architecture to overcome limitations in traditional CNNs and computationally demanding Transformers. The framework introduces an atrous scan technique that minimizes background interference and expands the receptive field, enhancing Mamba's scanning capabilities. Additionally, the inclusion of a Parallel Vision Mamba (PVM) layer and a shift round operation optimizes feature segmentation and fosters rich inter-segment information exchange. A supplementary CNN branch with a Selective-Kernel (SK) Block further refines the segmentation by blending local and global contextual information. Tested on four benchmark datasets (ISIC16/17/18 and PH2), ASP-VMUNet demonstrates superior performance in skin lesion segmentation, validated by comprehensive ablation studies. This approach not only advances medical image segmentation but also highlights the benefits of hybrid architectures in medical imaging technology. Our code is available at https://github.com/BaoBao0926/ASP-VMUNet/tree/main.
The MedSAM model, built upon the SAM framework, enhances medical image segmentation through generalizable training but still exhibits notable limitations. First, constraints in the perturbation window settings during training can cause MedSAM to incorrectly segment small tissues or organs together with adjacent structures, leading to segmentation errors. Second, when dealing with medical image targets characterized by irregular shapes and complex structures, segmentation often relies on narrowing the bounding box to refine segmentation intent. However, MedSAM's performance under reduced bounding box prompts remains suboptimal. To address these challenges, this study proposes a bounding box adaptive perturbation algorithm to optimize the training process. The proposed approach aims to reduce segmentation errors for small targets and enhance the model's accuracy when processing reduced bounding box prompts, ultimately improving the robustness and reliability of the MedSAM model for complex medical imaging tasks.
Achieving meticulous segmentation of tooth point clouds from intra-oral scans stands as an indispensable prerequisite for various orthodontic applications. Given the labor-intensive nature of dental annotation, a significant amount of data remains unlabeled, driving increasing interest in semi-supervised approaches. One primary challenge of existing semi-supervised medical segmentation methods lies in noisy pseudo labels generated for unlabeled data. To address this challenge, we propose GeoT, the first framework that employs instance-dependent transition matrix (IDTM) to explicitly model noise in pseudo labels for semi-supervised dental segmentation. Specifically, to handle the extensive solution space of IDTM arising from tens of thousands of dental points, we introduce tooth geometric priors through two key components: point-level geometric regularization (PLGR) to enhance consistency between point adjacency relationships in 3D and IDTM spaces, and class-level geometric smoothing (CLGS) to leverage the fixed spatial distribution of tooth categories for optimal IDTM estimation. Extensive experiments performed on the public Teeth3DS dataset and private dataset demonstrate that our method can make full utilization of unlabeled data to facilitate segmentation, achieving performance comparable to fully supervised methods with only $20\%$ of the labeled data.
Compared with natural images, remote sensing images (RSIs) have the unique characteristic. i.e., larger intraclass variance, which makes semantic segmentation for remote sensing images more challenging. Moreover, existing semantic segmentation models for remote sensing images usually employ a vanilla softmax classifier, which has three drawbacks: (1) non-direct supervision for the pixel representations during training; (2) inadequate modeling ability of parametric softmax classifiers under large intraclass variance; and (3) opaque process of classification decision. In this paper, we propose a novel classifier (called CenterSeg) customized for RSI semantic segmentation, which solves the abovementioned problems with multiple prototypes, direct supervision under Grassmann manifold, and interpretability strategy. Specifically, for each class, our CenterSeg obtains local class centers by aggregating corresponding pixel features based on ground-truth masks, and generates multiple prototypes through hard attention assignment and momentum updating. In addition, we introduce the Grassmann manifold and constrain the joint embedding space of pixel features and prototypes based on two additional regularization terms. Especially, during the inference, CenterSeg can further provide interpretability to the model by restricting the prototype as a sample of the training set. Experimental results on three remote sensing segmentation datasets validate the effectiveness of the model. Besides the superior performance, CenterSeg has the advantages of simplicity, lightweight, compatibility, and interpretability. Code is available at https://github.com/xwmaxwma/rssegmentation.
Amodal segmentation aims to predict segmentation masks for both the visible and occluded regions of an object. Most existing works formulate this as a supervised learning problem, requiring manually annotated amodal masks or synthetic training data. Consequently, their performance depends on the quality of the datasets, which often lack diversity and scale. This work introduces a tuning-free approach that repurposes pretrained diffusion-based inpainting models for amodal segmentation. Our approach is motivated by the "occlusion-free bias" of inpainting models, i.e., the inpainted objects tend to be complete objects without occlusions. Specifically, we reconstruct the occluded regions of an object via inpainting and then apply segmentation, all without additional training or fine-tuning. Experiments on five datasets demonstrate the generalizability and robustness of our approach. On average, our approach achieves 5.3% more accurate masks over the state-of-the-art.
Vision foundation models (VFMs) trained on large-scale image datasets provide high-quality features that have significantly advanced 2D visual recognition. However, their potential in 3D vision remains largely untapped, despite the common availability of 2D images alongside 3D point cloud datasets. While significant research has been dedicated to 2D-3D fusion, recent state-of-the-art 3D methods predominantly focus on 3D data, leaving the integration of VFMs into 3D models underexplored. In this work, we challenge this trend by introducing DITR, a simple yet effective approach that extracts 2D foundation model features, projects them to 3D, and finally injects them into a 3D point cloud segmentation model. DITR achieves state-of-the-art results on both indoor and outdoor 3D semantic segmentation benchmarks. To enable the use of VFMs even when images are unavailable during inference, we further propose to distill 2D foundation models into a 3D backbone as a pretraining task. By initializing the 3D backbone with knowledge distilled from 2D VFMs, we create a strong basis for downstream 3D segmentation tasks, ultimately boosting performance across various datasets.
Egocentric open-surgery videos capture rich, fine-grained details essential for accurately modeling surgical procedures and human behavior in the operating room. A detailed, pixel-level understanding of hands and surgical tools is crucial for interpreting a surgeon's actions and intentions. We introduce EgoSurgery-HTS, a new dataset with pixel-wise annotations and a benchmark suite for segmenting surgical tools, hands, and interacting tools in egocentric open-surgery videos. Specifically, we provide a labeled dataset for (1) tool instance segmentation of 14 distinct surgical tools, (2) hand instance segmentation, and (3) hand-tool segmentation to label hands and the tools they manipulate. Using EgoSurgery-HTS, we conduct extensive evaluations of state-of-the-art segmentation methods and demonstrate significant improvements in the accuracy of hand and hand-tool segmentation in egocentric open-surgery videos compared to existing datasets. The dataset will be released at https://github.com/Fujiry0/EgoSurgery.