Retinal vessel segmentation is a vital early detection method for several severe ocular diseases. Despite significant progress in retinal vessel segmentation with the advancement of Neural Networks, there are still challenges to overcome. Specifically, retinal vessel segmentation aims to predict the class label for every pixel within a fundus image, with a primary focus on intra-image discrimination, making it vital for models to extract more discriminative features. Nevertheless, existing methods primarily focus on minimizing the difference between the output from the decoder and the label, but ignore fully using feature-level fine-grained representations from the encoder. To address these issues, we propose a novel Attention U-shaped Kolmogorov-Arnold Network named AttUKAN along with a novel Label-guided Pixel-wise Contrastive Loss for retinal vessel segmentation. Specifically, we implement Attention Gates into Kolmogorov-Arnold Networks to enhance model sensitivity by suppressing irrelevant feature activations and model interpretability by non-linear modeling of KAN blocks. Additionally, we also design a novel Label-guided Pixel-wise Contrastive Loss to supervise our proposed AttUKAN to extract more discriminative features by distinguishing between foreground vessel-pixel pairs and background pairs. Experiments are conducted across four public datasets including DRIVE, STARE, CHASE_DB1, HRF and our private dataset. AttUKAN achieves F1 scores of 82.50%, 81.14%, 81.34%, 80.21% and 80.09%, along with MIoU scores of 70.24%, 68.64%, 68.59%, 67.21% and 66.94% in the above datasets, which are the highest compared to 11 networks for retinal vessel segmentation. Quantitative and qualitative results show that our AttUKAN achieves state-of-the-art performance and outperforms existing retinal vessel segmentation methods. Our code will be available at https://github.com/stevezs315/AttUKAN.
The recent Segment Anything Model 2 (SAM2) has demonstrated exceptional capabilities in interactive object segmentation for both images and videos. However, as a foundational model on interactive segmentation, SAM2 performs segmentation directly based on mask memory from the past six frames, leading to two significant challenges. Firstly, during inference in videos, objects may disappear since SAM2 relies solely on memory without accounting for object motion information, which limits its long-range object tracking capabilities. Secondly, its memory is constructed from fixed past frames, making it susceptible to challenges associated with object disappearance or occlusion, due to potentially inaccurate segmentation results in memory. To address these problems, we present MoSAM, incorporating two key strategies to integrate object motion cues into the model and establish more reliable feature memory. Firstly, we propose Motion-Guided Prompting (MGP), which represents the object motion in both sparse and dense manners, then injects them into SAM2 through a set of motion-guided prompts. MGP enables the model to adjust its focus towards the direction of motion, thereby enhancing the object tracking capabilities. Furthermore, acknowledging that past segmentation results may be inaccurate, we devise a Spatial-Temporal Memory Selection (ST-MS) mechanism that dynamically identifies frames likely to contain accurate segmentation in both pixel- and frame-level. By eliminating potentially inaccurate mask predictions from memory, we can leverage more reliable memory features to exploit similar regions for improving segmentation results. Extensive experiments on various benchmarks of video object segmentation and video instance segmentation demonstrate that our MoSAM achieves state-of-the-art results compared to other competitors.
One-shot medical image segmentation (MIS) is crucial for medical analysis due to the burden of medical experts on manual annotation. The recent emergence of the segment anything model (SAM) has demonstrated remarkable adaptation in MIS but cannot be directly applied to one-shot medical image segmentation (MIS) due to its reliance on labor-intensive user interactions and the high computational cost. To cope with these limitations, we propose a novel SAM-guided robust representation learning framework, named RRL-MedSAM, to adapt SAM to one-shot 3D MIS, which exploits the strong generalization capabilities of the SAM encoder to learn better feature representation. We devise a dual-stage knowledge distillation (DSKD) strategy to distill general knowledge between natural and medical images from the foundation model to train a lightweight encoder, and then adopt a mutual exponential moving average (mutual-EMA) to update the weights of the general lightweight encoder and medical-specific encoder. Specifically, pseudo labels from the registration network are used to perform mutual supervision for such two encoders. Moreover, we introduce an auto-prompting (AP) segmentation decoder which adopts the mask generated from the general lightweight model as a prompt to assist the medical-specific model in boosting the final segmentation performance. Extensive experiments conducted on three public datasets, i.e., OASIS, CT-lung demonstrate that the proposed RRL-MedSAM outperforms state-of-the-art one-shot MIS methods for both segmentation and registration tasks. Especially, our lightweight encoder uses only 3\% of the parameters compared to the encoder of SAM-Base.
This study integrates PET metabolic information with CT anatomical structures to establish a 3D multimodal segmentation dataset for lymphoma based on whole-body FDG PET/CT examinations, which bridges the gap of the lack of standardised multimodal segmentation datasets in the field of haematological malignancies. We retrospectively collected 483 examination datasets acquired between March 2011 and May 2024, involving 220 patients (106 non-Hodgkin lymphoma, 42 Hodgkin lymphoma); all data underwent ethical review and were rigorously de-identified. Complete 3D structural information was preserved during data acquisition, preprocessing and annotation, and a high-quality dataset was constructed based on the nnUNet format. By systematic technical validation and evaluation of the preprocessing process, annotation quality and automatic segmentation algorithm, the deep learning model trained based on this dataset is verified to achieve accurate segmentation of lymphoma lesions in PET/CT images with high accuracy, good robustness and reproducibility, which proves the applicability and stability of this dataset in accurate segmentation and quantitative analysis. The deep fusion of PET/CT images achieved with this dataset not only significantly improves the accurate portrayal of the morphology, location and metabolic features of tumour lesions, but also provides solid data support for early diagnosis, clinical staging and personalized treatment, and promotes the development of automated image segmentation and precision medicine based on deep learning. The dataset and related resources are available at https://github.com/SuperD0122/LymphAtlas-.
Event cameras provide rich signals that are suitable for motion estimation since they respond to changes in the scene. As any visual changes in the scene produce event data, it is paramount to classify the data into different motions (i.e., motion segmentation), which is useful for various tasks such as object detection and visual servoing. We propose an iterative motion segmentation method, by classifying events into background (e.g., dominant motion hypothesis) and foreground (independent motion residuals), thus extending the Contrast Maximization framework. Experimental results demonstrate that the proposed method successfully classifies event clusters both for public and self-recorded datasets, producing sharp, motion-compensated edge-like images. The proposed method achieves state-of-the-art accuracy on moving object detection benchmarks with an improvement of over 30%, and demonstrates its possibility of applying to more complex and noisy real-world scenes. We hope this work broadens the sensitivity of Contrast Maximization with respect to both motion parameters and input events, thus contributing to theoretical advancements in event-based motion segmentation estimation. https://github.com/aoki-media-lab/event_based_segmentation_vcmax
Morphometry of medial temporal lobe (MTL) subregions in brain MRI is sensitive biomarker to Alzheimers Disease and other related conditions. While T2-weighted (T2w) MRI with high in-plane resolution is widely used to segment hippocampal subfields due to its higher contrast in hippocampus, its lower out-of-plane resolution reduces the accuracy of subregion thickness measurements. To address this issue, we developed a nearly isotropic segmentation pipeline that incorporates image and label upsampling and high-resolution segmentation in T2w MRI. First, a high-resolution atlas was created based on an existing anisotropic atlas derived from 29 individuals. Both T1-weighted and T2w images in the atlas were upsampled from their original resolution to a nearly isotropic resolution 0.4x0.4x0.52mm3 using a non-local means approach. Manual segmentations within the atlas were also upsampled to match this resolution using a UNet-based neural network, which was trained on a cohort consisting of both high-resolution ex vivo and low-resolution anisotropic in vivo MRI with manual segmentations. Second, a multi-modality deep learning-based segmentation model was trained within this nearly isotropic atlas. Finally, experiments showed the nearly isotropic subregion segmentation improved the accuracy of cortical thickness as an imaging biomarker for neurodegeneration in T2w MRI.
Medical image segmentation is often considered as the task of labelling each pixel or voxel as being inside or outside a given anatomy. Processing the images at their original size and resolution often result in insuperable memory requirements, but downsampling the images leads to a loss of important details. Instead of aiming to represent a smooth and continuous surface in a binary voxel-grid, we propose to learn a Neural Unsigned Distance Field (NUDF) directly from the image. The small memory requirements of NUDF allow for high resolution processing, while the continuous nature of the distance field allows us to create high resolution 3D mesh models of shapes of any topology (i.e. open surfaces). We evaluate our method on the task of left atrial appendage (LAA) segmentation from Computed Tomography (CT) images. The LAA is a complex and highly variable shape, being thus difficult to represent with traditional segmentation methods using discrete labelmaps. With our proposed method, we are able to predict 3D mesh models that capture the details of the LAA and achieve accuracy in the order of the voxel spacing in the CT images.
Diabetic foot ulcers (DFUs) pose a significant challenge in healthcare, requiring precise and efficient wound assessment to enhance patient outcomes. This study introduces the Attention Diffusion Zero-shot Unsupervised System (ADZUS), a novel text-guided diffusion model that performs wound segmentation without relying on labeled training data. Unlike conventional deep learning models, which require extensive annotation, ADZUS leverages zero-shot learning to dynamically adapt segmentation based on descriptive prompts, offering enhanced flexibility and adaptability in clinical applications. Experimental evaluations demonstrate that ADZUS surpasses traditional and state-of-the-art segmentation models, achieving an IoU of 86.68\% and the highest precision of 94.69\% on the chronic wound dataset, outperforming supervised approaches such as FUSegNet. Further validation on a custom-curated DFU dataset reinforces its robustness, with ADZUS achieving a median DSC of 75\%, significantly surpassing FUSegNet's 45\%. The model's text-guided segmentation capability enables real-time customization of segmentation outputs, allowing targeted analysis of wound characteristics based on clinical descriptions. Despite its competitive performance, the computational cost of diffusion-based inference and the need for potential fine-tuning remain areas for future improvement. ADZUS represents a transformative step in wound segmentation, providing a scalable, efficient, and adaptable AI-driven solution for medical imaging.
The performance of medical image segmentation models is usually evaluated using metrics like the Dice score and Hausdorff distance, which compare predicted masks to ground truth annotations. However, when applying the model to unseen data, such as in clinical settings, it is often impractical to annotate all the data, making the model's performance uncertain. To address this challenge, we propose the Segmentation Performance Evaluator (SPE), a framework for estimating segmentation models' performance on unlabeled data. This framework is adaptable to various evaluation metrics and model architectures. Experiments on six publicly available datasets across six evaluation metrics including pixel-based metrics such as Dice score and distance-based metrics like HD95, demonstrated the versatility and effectiveness of our approach, achieving a high correlation (0.956$\pm$0.046) and low MAE (0.025$\pm$0.019) compare with real Dice score on the independent test set. These results highlight its ability to reliably estimate model performance without requiring annotations. The SPE framework integrates seamlessly into any model training process without adding training overhead, enabling performance estimation and facilitating the real-world application of medical image segmentation algorithms. The source code is publicly available
Studying the growth and metabolism of microbes provides critical insights into their evolutionary adaptations to harsh environments, which are essential for microbial research and biotechnology applications. In this study, we developed an AI-driven image analysis system to efficiently segment individual cells and quantitatively analyze key cellular features. This system is comprised of four main modules. First, a denoising algorithm enhances contrast and suppresses noise while preserving fine cellular details. Second, the Segment Anything Model (SAM) enables accurate, zero-shot segmentation of cells without additional training. Third, post-processing is applied to refine segmentation results by removing over-segmented masks. Finally, quantitative analysis algorithms extract essential cellular features, including average intensity, length, width, and volume. The results show that denoising and post-processing significantly improved the segmentation accuracy of SAM in this new domain. Without human annotations, the AI-driven pipeline automatically and efficiently outlines cellular boundaries, indexes them, and calculates key cellular parameters with high accuracy. This framework will enable efficient and automated quantitative analysis of high-resolution fluorescence microscopy images to advance research into microbial adaptations to grow and metabolism that allow extremophiles to thrive in their harsh habitats.
In situ synchrotron X-ray computed tomography enables dynamic material studies, but automated segmentation remains challenging due to complex imaging artefacts and limited training data. We present a methodology for deep learning-based segmentation by transforming high-quality ex situ laboratory data to train models for binary segmentation of in situ synchrotron data, demonstrated through copper oxide dissolution studies. Using a modified SegFormer architecture, our approach achieves high segmentation performance on unseen data while reducing processing time from hours to seconds per 3D dataset. The method maintains consistent performance over significant morphological changes during experiments, despite training only on static specimens. This methodology can be readily applied to diverse materials systems, accelerating the analysis of time-resolved tomographic data across scientific disciplines.
In recent studies, numerous previous works emphasize the importance of semantic segmentation of LiDAR data as a critical component to the development of driver-assistance systems and autonomous vehicles. However, many state-of-the-art methods are tested on outdated, lower-resolution LiDAR sensors and struggle with real-time constraints. This study introduces a novel semantic segmentation framework tailored for modern high-resolution LiDAR sensors that addresses both accuracy and real-time processing demands. We propose a novel LiDAR dataset collected by a cutting-edge automotive 128 layer LiDAR in urban traffic scenes. Furthermore, we propose a semantic segmentation method utilizing surface normals as strong input features. Our approach is bridging the gap between cutting-edge research and practical automotive applications. Additionaly, we provide a Robot Operating System (ROS2) implementation that we operate on our research vehicle. Our dataset and code are publicly available: https://github.com/kav-institute/SemanticLiDAR.
We propose a result-level category-specific fusion architecture called ClassWise-CRF. This architecture employs a two-stage process: first, it selects expert networks that perform well in specific categories from a pool of candidate networks using a greedy algorithm; second, it integrates the segmentation predictions of these selected networks by adaptively weighting their contributions based on their segmentation performance in each category. Inspired by Conditional Random Field (CRF), the ClassWise-CRF architecture treats the segmentation predictions from multiple networks as confidence vector fields. It leverages segmentation metrics (such as Intersection over Union) from the validation set as priors and employs an exponential weighting strategy to fuse the category-specific confidence scores predicted by each network. This fusion method dynamically adjusts the weights of each network for different categories, achieving category-specific optimization. Building on this, the architecture further optimizes the fused results using unary and pairwise potentials in CRF to ensure spatial consistency and boundary accuracy. To validate the effectiveness of ClassWise-CRF, we conducted experiments on two remote sensing datasets, LoveDA and Vaihingen, using eight classic and advanced semantic segmentation networks. The results show that the ClassWise-CRF architecture significantly improves segmentation performance: on the LoveDA dataset, the mean Intersection over Union (mIoU) metric increased by 1.00% on the validation set and by 0.68% on the test set; on the Vaihingen dataset, the mIoU improved by 0.87% on the validation set and by 0.91% on the test set. These results fully demonstrate the effectiveness and generality of the ClassWise-CRF architecture in semantic segmentation of remote sensing images. The full code is available at https://github.com/zhuqinfeng1999/ClassWise-CRF.
This paper introduces GeloVec, a new CNN-based attention smoothing framework for semantic segmentation that addresses critical limitations in conventional approaches. While existing attention-backed segmentation methods suffer from boundary instability and contextual discontinuities during feature mapping, our framework implements a higher-dimensional geometric smoothing method to establish a robust manifold relationships between visually coherent regions. GeloVec combines modified Chebyshev distance metrics with multispatial transformations to enhance segmentation accuracy through stabilized feature extraction. The core innovation lies in the adaptive sampling weights system that calculates geometric distances in n-dimensional feature space, achieving superior edge preservation while maintaining intra-class homogeneity. The multispatial transformation matrix incorporates tensorial projections with orthogonal basis vectors, creating more discriminative feature representations without sacrificing computational efficiency. Experimental validation across multiple benchmark datasets demonstrates significant improvements in segmentation performance, with mean Intersection over Union (mIoU) gains of 2.1%, 2.7%, and 2.4% on Caltech Birds-200, LSDSC, and FSSD datasets respectively compared to state-of-the-art methods. GeloVec's mathematical foundation in Riemannian geometry provides theoretical guarantees on segmentation stability. Importantly, our framework maintains computational efficiency through parallelized implementation of geodesic transformations and exhibits strong generalization capabilities across disciplines due to the absence of information loss during transformations.
Interactive 3D segmentation has emerged as a promising solution for generating accurate object masks in complex 3D scenes by incorporating user-provided clicks. However, two critical challenges remain underexplored: (1) effectively generalizing from sparse user clicks to produce accurate segmentation, and (2) quantifying predictive uncertainty to help users identify unreliable regions. In this work, we propose NPISeg3D, a novel probabilistic framework that builds upon Neural Processes (NPs) to address these challenges. Specifically, NPISeg3D introduces a hierarchical latent variable structure with scene-specific and object-specific latent variables to enhance few-shot generalization by capturing both global context and object-specific characteristics. Additionally, we design a probabilistic prototype modulator that adaptively modulates click prototypes with object-specific latent variables, improving the model's ability to capture object-aware context and quantify predictive uncertainty. Experiments on four 3D point cloud datasets demonstrate that NPISeg3D achieves superior segmentation performance with fewer clicks while providing reliable uncertainty estimations.
Pancreatic cancer, characterized by its notable prevalence and mortality rates, demands accurate lesion delineation for effective diagnosis and therapeutic interventions. The generalizability of extant methods is frequently compromised due to the pronounced variability in imaging and the heterogeneous characteristics of pancreatic lesions, which may mimic normal tissues and exhibit significant inter-patient variability. Thus, we propose a generalization framework that synergizes pixel-level classification and regression tasks, to accurately delineate lesions and improve model stability. This framework not only seeks to align segmentation contours with actual lesions but also uses regression to elucidate spatial relationships between diseased and normal tissues, thereby improving tumor localization and morphological characterization. Enhanced by the reciprocal transformation of task outputs, our approach integrates additional regression supervision within the segmentation context, bolstering the model's generalization ability from a dual-task perspective. Besides, dual self-supervised learning in feature spaces and output spaces augments the model's representational capability and stability across different imaging views. Experiments on 594 samples composed of three datasets with significant imaging differences demonstrate that our generalized pancreas segmentation results comparable to mainstream in-domain validation performance (Dice: 84.07%). More importantly, it successfully improves the results of the highly challenging cross-lesion generalized pancreatic cancer segmentation task by 9.51%. Thus, our model constitutes a resilient and efficient foundational technological support for pancreatic disease management and wider medical applications. The codes will be released at https://github.com/SJTUBME-QianLab/Dual-Task-Seg.
Morphometric measures derived from spinal cord segmentations can serve as diagnostic and prognostic biomarkers in neurological diseases and injuries affecting the spinal cord. While robust, automatic segmentation methods to a wide variety of contrasts and pathologies have been developed over the past few years, whether their predictions are stable as the model is updated using new datasets has not been assessed. This is particularly important for deriving normative values from healthy participants. In this study, we present a spinal cord segmentation model trained on a multisite $(n=75)$ dataset, including 9 different MRI contrasts and several spinal cord pathologies. We also introduce a lifelong learning framework to automatically monitor the morphometric drift as the model is updated using additional datasets. The framework is triggered by an automatic GitHub Actions workflow every time a new model is created, recording the morphometric values derived from the model's predictions over time. As a real-world application of the proposed framework, we employed the spinal cord segmentation model to update a recently-introduced normative database of healthy participants containing commonly used measures of spinal cord morphometry. Results showed that: (i) our model outperforms previous versions and pathology-specific models on challenging lumbar spinal cord cases, achieving an average Dice score of $0.95 \pm 0.03$; (ii) the automatic workflow for monitoring morphometric drift provides a quick feedback loop for developing future segmentation models; and (iii) the scaling factor required to update the database of morphometric measures is nearly constant among slices across the given vertebral levels, showing minimum drift between the current and previous versions of the model monitored by the framework. The model is freely available in Spinal Cord Toolbox v7.0.
Accurate lung tumor segmentation is crucial for improving diagnosis, treatment planning, and patient outcomes in oncology. However, the complexity of tumor morphology, size, and location poses significant challenges for automated segmentation. This study presents a comprehensive benchmarking analysis of deep learning-based segmentation models, comparing traditional architectures such as U-Net and DeepLabV3, self-configuring models like nnUNet, and foundation models like MedSAM, and MedSAM~2. Evaluating performance across two lung tumor segmentation datasets, we assess segmentation accuracy and computational efficiency under various learning paradigms, including few-shot learning and fine-tuning. The results reveal that while traditional models struggle with tumor delineation, foundation models, particularly MedSAM~2, outperform them in both accuracy and computational efficiency. These findings underscore the potential of foundation models for lung tumor segmentation, highlighting their applicability in improving clinical workflows and patient outcomes.
The segmentation of cranial nerves (CNs) tract provides a valuable quantitative tool for the analysis of the morphology and trajectory of individual CNs. Multimodal CNs tract segmentation networks, e.g., CNTSeg, which combine structural Magnetic Resonance Imaging (MRI) and diffusion MRI, have achieved promising segmentation performance. However, it is laborious or even infeasible to collect complete multimodal data in clinical practice due to limitations in equipment, user privacy, and working conditions. In this work, we propose a novel arbitrary-modal fusion network for volumetric CNs tract segmentation, called CNTSeg-v2, which trains one model to handle different combinations of available modalities. Instead of directly combining all the modalities, we select T1-weighted (T1w) images as the primary modality due to its simplicity in data acquisition and contribution most to the results, which supervises the information selection of other auxiliary modalities. Our model encompasses an Arbitrary-Modal Collaboration Module (ACM) designed to effectively extract informative features from other auxiliary modalities, guided by the supervision of T1w images. Meanwhile, we construct a Deep Distance-guided Multi-stage (DDM) decoder to correct small errors and discontinuities through signed distance maps to improve segmentation accuracy. We evaluate our CNTSeg-v2 on the Human Connectome Project (HCP) dataset and the clinical Multi-shell Diffusion MRI (MDM) dataset. Extensive experimental results show that our CNTSeg-v2 achieves state-of-the-art segmentation performance, outperforming all competing methods.
To operate safely, autonomous vehicles (AVs) need to detect and handle unexpected objects or anomalies on the road. While significant research exists for anomaly detection and segmentation in 2D, research progress in 3D is underexplored. Existing datasets lack high-quality multimodal data that are typically found in AVs. This paper presents a novel dataset for anomaly segmentation in driving scenarios. To the best of our knowledge, it is the first publicly available dataset focused on road anomaly segmentation with dense 3D semantic labeling, incorporating both LiDAR and camera data, as well as sequential information to enable anomaly detection across various ranges. This capability is critical for the safe navigation of autonomous vehicles. We adapted and evaluated several baseline models for 3D segmentation, highlighting the challenges of 3D anomaly detection in driving environments. Our dataset and evaluation code will be openly available, facilitating the testing and performance comparison of different approaches.