Neurofibromatosis Type 1 is a genetic disorder characterized by the development of neurofibromas (NFs), which exhibit significant variability in size, morphology, and anatomical location. Accurate and automated segmentation of these tumors in whole-body magnetic resonance imaging (WB-MRI) is crucial to assess tumor burden and monitor disease progression. In this study, we present and analyze a fully automated pipeline for NF segmentation in fat-suppressed T2-weighted WB-MRI, consisting of three stages: anatomy segmentation, NF segmentation, and tumor candidate classification. In the first stage, we use the MRSegmentator model to generate an anatomy segmentation mask, extended with a high-risk zone for NFs. This mask is concatenated with the input image as anatomical context information for NF segmentation. The second stage employs an ensemble of 3D anisotropic anatomy-informed U-Nets to produce an NF segmentation confidence mask. In the final stage, tumor candidates are extracted from the confidence mask and classified based on radiomic features, distinguishing tumors from non-tumor regions and reducing false positives. We evaluate the proposed pipeline on three test sets representing different conditions: in-domain data (test set 1), varying imaging protocols and field strength (test set 2), and low tumor burden cases (test set 3). Experimental results show a 68% improvement in per-scan Dice Similarity Coefficient (DSC), a 21% increase in per-tumor DSC, and a two-fold improvement in F1 score for tumor detection in high tumor burden cases by integrating anatomy information. The method is integrated into the 3D Slicer platform for practical clinical use, with the code publicly accessible.
With the rapid development of artificial intelligence (AI), AI-assisted medical imaging analysis demonstrates remarkable performance in early lung cancer screening. However, the costly annotation process and privacy concerns limit the construction of large-scale medical datasets, hampering the further application of AI in healthcare. To address the data scarcity in lung cancer screening, we propose Lung-DDPM, a thoracic CT image synthesis approach that effectively generates high-fidelity 3D synthetic CT images, which prove helpful in downstream lung nodule segmentation tasks. Our method is based on semantic layout-guided denoising diffusion probabilistic models (DDPM), enabling anatomically reasonable, seamless, and consistent sample generation even from incomplete semantic layouts. Our results suggest that the proposed method outperforms other state-of-the-art (SOTA) generative models in image quality evaluation and downstream lung nodule segmentation tasks. Specifically, Lung-DDPM achieved superior performance on our large validation cohort, with a Fr\'echet inception distance (FID) of 0.0047, maximum mean discrepancy (MMD) of 0.0070, and mean squared error (MSE) of 0.0024. These results were 7.4$\times$, 3.1$\times$, and 29.5$\times$ better than the second-best competitors, respectively. Furthermore, the lung nodule segmentation model, trained on a dataset combining real and Lung-DDPM-generated synthetic samples, attained a dice coefficient (Dice) of 0.3914 and sensitivity of 0.4393. This represents 8.8\% and 18.6\% improvements in DICE and sensitivity compared to the model trained solely on real samples. The experimental results highlight Lung-DDPM's potential for a broader range of medical imaging applications, such as general tumor segmentation, cancer survival estimation, and risk prediction.
Bird's Eye View (BEV) semantic maps have recently garnered a lot of attention as a useful representation of the environment to tackle assisted and autonomous driving tasks. However, most of the existing work focuses on the fully supervised setting, training networks on large annotated datasets. In this work, we present RendBEV, a new method for the self-supervised training of BEV semantic segmentation networks, leveraging differentiable volumetric rendering to receive supervision from semantic perspective views computed by a 2D semantic segmentation model. Our method enables zero-shot BEV semantic segmentation, and already delivers competitive results in this challenging setting. When used as pretraining to then fine-tune on labeled BEV ground-truth, our method significantly boosts performance in low-annotation regimes, and sets a new state of the art when fine-tuning on all available labels.
The significant effort required to annotate data for new training datasets hinders computer vision research and machine learning in the construction industry. This work explores adapting standard datasets and the latest transformer model architectures for point cloud semantic segmentation in the context of shell construction sites. Unlike common approaches focused on object segmentation of building interiors and furniture, this study addressed the challenges of segmenting complex structural components in Architecture, Engineering, and Construction (AEC). We establish a baseline through supervised training and a custom validation dataset, evaluate the cross-domain inference with large-scale indoor datasets, and utilize transfer learning to maximize segmentation performance with minimal new data. The findings indicate that with minimal fine-tuning, pre-trained transformer architectures offer an effective strategy for building component segmentation. Our results are promising for automating the annotation of new, previously unseen data when creating larger training resources and for the segmentation of frequently recurring objects.
Camouflaged Object Segmentation (COS) remains challenging because camouflaged objects exhibit only subtle visual differences from their backgrounds and single-modality RGB methods provide limited cues, leading researchers to explore multimodal data to improve segmentation accuracy. In this work, we presenet MultiCOS, a novel framework that effectively leverages diverse data modalities to improve segmentation performance. MultiCOS comprises two modules: Bi-space Fusion Segmentor (BFSer), which employs a state space and a latent space fusion mechanism to integrate cross-modal features within a shared representation and employs a fusion-feedback mechanism to refine context-specific features, and Cross-modal Knowledge Learner (CKLer), which leverages external multimodal datasets to generate pseudo-modal inputs and establish cross-modal semantic associations, transferring knowledge to COS models when real multimodal pairs are missing. When real multimodal COS data are unavailable, CKLer yields additional segmentation gains using only non-COS multimodal sources. Experiments on standard COS benchmarks show that BFSer outperforms existing multimodal baselines with both real and pseudo-modal data. Code will be released at \href{https://github.com/cnyvfang/MultiCOS}{GitHub}.
Positron Emission Tomography (PET) imaging plays a crucial role in modern medical diagnostics by revealing the metabolic processes within a patient's body, which is essential for quantification of therapy response and monitoring treatment progress. However, the segmentation of PET images presents unique challenges due to their lower contrast and less distinct boundaries compared to other structural medical modalities. Recent developments in segmentation foundation models have shown superior versatility across diverse natural image segmentation tasks. Despite the efforts of medical adaptations, these works primarily focus on structural medical images with detailed physiological structural information and exhibit poor generalization ability when adapted to molecular PET imaging. In this paper, we collect and construct PETS-5k, the largest PET segmentation dataset to date, comprising 5,731 three-dimensional whole-body PET images and encompassing over 1.3M 2D images. Based on the established dataset, we develop SegAnyPET, a modality-specific 3D foundation model for universal promptable segmentation from PET images. To issue the challenge of discrepant annotation quality of PET images, we adopt a cross prompting confident learning (CPCL) strategy with an uncertainty-guided self-rectification process to robustly learn segmentation from high-quality labeled data and low-quality noisy labeled data. Experimental results demonstrate that SegAnyPET can correctly segment seen and unseen targets using only one or a few prompt points, outperforming state-of-the-art foundation models and task-specific fully supervised models with higher accuracy and strong generalization ability for universal segmentation. As the first foundation model for PET images, we believe that SegAnyPET will advance the applications to various downstream tasks for molecular imaging.
The rapid development of Vision Foundation Models (VFMs), particularly Vision Transformers (ViT) and Segment Anything Model (SAM), has sparked significant advances in the field of medical image analysis. These models have demonstrated exceptional capabilities in capturing long-range dependencies and achieving high generalization in segmentation tasks. However, adapting these large models to medical image analysis presents several challenges, including domain differences between medical and natural images, the need for efficient model adaptation strategies, and the limitations of small-scale medical datasets. This paper reviews the state-of-the-art research on the adaptation of VFMs to medical image segmentation, focusing on the challenges of domain adaptation, model compression, and federated learning. We discuss the latest developments in adapter-based improvements, knowledge distillation techniques, and multi-scale contextual feature modeling, and propose future directions to overcome these bottlenecks. Our analysis highlights the potential of VFMs, along with emerging methodologies such as federated learning and model compression, to revolutionize medical image analysis and enhance clinical applications. The goal of this work is to provide a comprehensive overview of current approaches and suggest key areas for future research that can drive the next wave of innovation in medical image segmentation.
Nasopharyngeal carcinoma (NPC) patients often undergo radiotherapy and chemotherapy, which can lead to postoperative complications such as limited mouth opening and joint stiffness, particularly in recurrent cases that require re-surgery. These complications can affect airway function, making accurate postoperative airway risk assessment essential for managing patient care. Accurate segmentation of airway-related structures in postoperative CT scans is crucial for assessing these risks. This study introduces TopoWMamba (Topology-aware Wavelet Mamba), a novel segmentation model specifically designed to address the challenges of postoperative airway risk evaluation in recurrent NPC patients. TopoWMamba combines wavelet-based multi-scale feature extraction, state-space sequence modeling, and topology-aware modules to segment airway-related structures in CT scans robustly. By leveraging the Wavelet-based Mamba Block (WMB) for hierarchical frequency decomposition and the Snake Conv VSS (SCVSS) module to preserve anatomical continuity, TopoWMamba effectively captures both fine-grained boundaries and global structural context, crucial for accurate segmentation in complex postoperative scenarios. Through extensive testing on the NPCSegCT dataset, TopoWMamba achieves an average Dice score of 88.02%, outperforming existing models such as UNet, Attention UNet, and SwinUNet. Additionally, TopoWMamba is tested on the SegRap 2023 Challenge dataset, where it shows a significant improvement in trachea segmentation with a Dice score of 95.26%. The proposed model provides a strong foundation for automated segmentation, enabling more accurate postoperative airway risk evaluation.
With the rapid evolution of autonomous driving technology and intelligent transportation systems, semantic segmentation has become increasingly critical. Precise interpretation and analysis of real-world environments are indispensable for these advanced applications. However, traditional semantic segmentation approaches frequently face challenges in balancing model performance with computational efficiency, especially regarding the volume of model parameters. To address these constraints, we propose SegRet, a novel model employing the Retentive Network (RetNet) architecture coupled with a lightweight residual decoder that integrates zero-initialization. SegRet offers three distinctive advantages: (1) Lightweight Residual Decoder: by embedding a zero-initialization layer within the residual network structure, the decoder remains computationally streamlined without sacrificing essential information propagation; (2) Robust Feature Extraction: adopting RetNet as its backbone enables SegRet to effectively capture hierarchical image features, thereby enriching the representation quality of extracted features; (3) Parameter Efficiency: SegRet attains state-of-the-art (SOTA) segmentation performance while markedly decreasing the number of parameters, ensuring high accuracy without imposing additional computational burdens. Comprehensive empirical evaluations on prominent benchmarks, such as ADE20K, Citycapes, and COCO-Stuff, highlight the effectiveness and superiority of our method.
The complexity of scenes and variations in image quality result in significant variability in the performance of semantic segmentation methods of remote sensing imagery (RSI) in supervised real-world scenarios. This makes the evaluation of semantic segmentation quality in such scenarios an issue to be resolved. However, most of the existing evaluation metrics are developed based on expert-labeled object-level annotations, which are not applicable in such scenarios. To address this issue, we propose RS-SQA, an unsupervised quality assessment model for RSI semantic segmentation based on vision language model (VLM). This framework leverages a pre-trained RS VLM for semantic understanding and utilizes intermediate features from segmentation methods to extract implicit information about segmentation quality. Specifically, we introduce CLIP-RS, a large-scale pre-trained VLM trained with purified text to reduce textual noise and capture robust semantic information in the RS domain. Feature visualizations confirm that CLIP-RS can effectively differentiate between various levels of segmentation quality. Semantic features and low-level segmentation features are effectively integrated through a semantic-guided approach to enhance evaluation accuracy. To further support the development of RS semantic segmentation quality assessment, we present RS-SQED, a dedicated dataset sampled from four major RS semantic segmentation datasets and annotated with segmentation accuracy derived from the inference results of 8 representative segmentation methods. Experimental results on the established dataset demonstrate that RS-SQA significantly outperforms state-of-the-art quality assessment models. This provides essential support for predicting segmentation accuracy and high-quality semantic segmentation interpretation, offering substantial practical value.
This study introduces SEFI (SEgmentation-Free Integration), a novel method for integrating morphological features of cell nuclei with spatial transcriptomics data. Cell segmentation poses a significant challenge in the analysis of spatial transcriptomics data, as tissue-specific structural complexities and densely packed cells in certain regions make it difficult to develop a universal approach. SEFI addresses this by utilizing self-supervised learning to extract morphological features from fluorescent nuclear staining images, enhancing the clustering of gene expression data without requiring segmentation. We demonstrate SEFI on spatially resolved gene expression profiles of the developing retina, acquired using multiplexed single molecule Fluorescence In Situ Hybridization (smFISH). SEFI is publicly available at https://github.com/eduardchelebian/sefi.
We propose a novel approach that uses sparse annotations from clinical studies to train a 3D segmentation of the carotid artery wall. We use a centerline annotation to sample perpendicular cross-sections of the carotid artery and use an adversarial 2D network to segment them. These annotations are then transformed into 3D pseudo-labels for training of a 3D convolutional neural network, circumventing the creation of manual 3D masks. For pseudo-label creation in the bifurcation area we propose the use of cross-sections perpendicular to the bifurcation axis and show that this enhances segmentation performance. Different sampling distances had a lesser impact. The proposed method allows for efficient training of 3D segmentation, offering potential improvements in the assessment of carotid artery stenosis and allowing the extraction of 3D biomarkers such as plaque volume.
Hyperspectral image (HSI) classification is a cornerstone of remote sensing, enabling precise material and land-cover identification through rich spectral information. While deep learning has driven significant progress in this task, small patch-based classifiers, which account for over 90% of the progress, face limitations: (1) the small patch (e.g., 7x7, 9x9)-based sampling approach considers a limited receptive field, resulting in insufficient spatial structural information critical for object-level identification and noise-like misclassifications even within uniform regions; (2) undefined optimal patch sizes lead to coarse label predictions, which degrade performance; and (3) a lack of multi-shape awareness around objects. To address these challenges, we draw inspiration from large-scale image segmentation techniques, which excel at handling object boundaries-a capability essential for semantic labeling in HSI classification. However, their application remains under-explored in this task due to (1) the prevailing notion that larger patch sizes degrade performance, (2) the extensive unlabeled regions in HSI groundtruth, and (3) the misalignment of input shapes between HSI data and segmentation models. Thus, in this study, we propose a novel paradigm and baseline, HSIseg, for HSI classification that leverages segmentation techniques combined with a novel Dynamic Shifted Regional Transformer (DSRT) to overcome these challenges. We also introduce an intuitive progressive learning framework with adaptive pseudo-labeling to iteratively incorporate unlabeled regions into the training process, thereby advancing the application of segmentation techniques. Additionally, we incorporate auxiliary data through multi-source data collaboration, promoting better feature interaction. Validated on five public HSI datasets, our proposal outperforms state-of-the-art methods.
Understanding how individuals perceive and recall information in their natural environments is critical to understanding potential failures in perception (e.g., sensory loss) and memory (e.g., dementia). Event segmentation, the process of identifying distinct events within dynamic environments, is central to how we perceive, encode, and recall experiences. This cognitive process not only influences moment-to-moment comprehension but also shapes event specific memory. Despite the importance of event segmentation and event memory, current research methodologies rely heavily on human judgements for assessing segmentation patterns and recall ability, which are subjective and time-consuming. A few approaches have been introduced to automate event segmentation and recall scoring, but validity with human responses and ease of implementation require further advancements. To address these concerns, we leverage Large Language Models (LLMs) to automate event segmentation and assess recall, employing chat completion and text-embedding models, respectively. We validated these models against human annotations and determined that LLMs can accurately identify event boundaries, and that human event segmentation is more consistent with LLMs than among humans themselves. Using this framework, we advanced an automated approach for recall assessments which revealed semantic similarity between segmented narrative events and participant recall can estimate recall performance. Our findings demonstrate that LLMs can effectively simulate human segmentation patterns and provide recall evaluations that are a scalable alternative to manual scoring. This research opens novel avenues for studying the intersection between perception, memory, and cognitive impairment using methodologies driven by artificial intelligence.
Medical image segmentation plays a crucial role in various clinical applications. A major challenge in medical image segmentation is achieving accurate delineation of regions of interest in the presence of noise, low contrast, or complex anatomical structures. Existing segmentation models often neglect the integration of multi-grained information and fail to preserve edge details, which are critical for precise segmentation. To address these challenges, we propose a novel image semantic segmentation model called the Multi-Grained Feature Integration Network (MGFI-Net). Our MGFI-Net is designed with two dedicated modules to tackle these issues. First, to enhance segmentation accuracy, we introduce a Multi-Grained Feature Extraction Module, which leverages hierarchical relationships between different feature scales to selectively focus on the most relevant information. Second, to preserve edge details, we incorporate an Edge Enhancement Module that effectively retains and integrates boundary information to refine segmentation results. Extensive experiments demonstrate that MGFI-Net not only outperforms state-of-the-art methods in terms of segmentation accuracy but also achieves superior time efficiency, establishing it as a leading solution for real-time medical image segmentation.
The accurate assessment of sperm morphology is crucial in andrological diagnostics, where the segmentation of sperm images presents significant challenges. Existing approaches frequently rely on large annotated datasets and often struggle with the segmentation of overlapping sperm and the presence of dye impurities. To address these challenges, this paper first analyzes the issue of overlapping sperm tails from a geometric perspective and introduces a novel clustering algorithm, Con2Dis, which effectively segments overlapping tails by considering three essential factors: CONnectivity, CONformity, and DIStance. Building on this foundation, we propose an unsupervised method, SpeHeatal, designed for the comprehensive segmentation of the SPErm HEAd and TAiL. SpeHeatal employs the Segment Anything Model(SAM) to generate masks for sperm heads while filtering out dye impurities, utilizes Con2Dis to segment tails, and then applies a tailored mask splicing technique to produce complete sperm masks. Experimental results underscore the superior performance of SpeHeatal, particularly in handling images with overlapping sperm.
This study presents a unified deep learning (DL) framework, MultiFlowSeg, for classification and segmentation of velocity-encoded phase-contrast magnetic resonance imaging data, and MultiFlowDTC for temporal clustering of flow phenotypes. Applied to the FORCE registry of Fontan procedure patients, MultiFlowSeg achieved 100% classification accuracy for the aorta, SVC, and IVC, and 94% for the LPA and RPA. It demonstrated robust segmentation with a median Dice score of 0.91 (IQR: 0.86-0.93). The automated pipeline processed registry data, achieving high segmentation success despite challenges like poor image quality and dextrocardia. Temporal clustering identified five distinct patient subgroups, with significant differences in clinical outcomes, including ejection fraction, exercise tolerance, liver disease, and mortality. These results demonstrate the potential of combining DL and time-varying flow data for improved CHD prognosis and personalized care.
Open-vocabulary semantic segmentation enables models to identify novel object categories beyond their training data. While this flexibility represents a significant advancement, current approaches still rely on manually specified class names as input, creating an inherent bottleneck in real-world applications. This work proposes a Vocabulary-Free Semantic Segmentation pipeline, eliminating the need for predefined class vocabularies. Specifically, we address the chicken-and-egg problem where users need knowledge of all potential objects within a scene to identify them, yet the purpose of segmentation is often to discover these objects. The proposed approach leverages Vision-Language Models to automatically recognize objects and generate appropriate class names, aiming to solve the challenge of class specification and naming quality. Through extensive experiments on several public datasets, we highlight the crucial role of the text encoder in model performance, particularly when the image text classes are paired with generated descriptions. Despite the challenges introduced by the sensitivity of the segmentation text encoder to false negatives within the class tagging process, which adds complexity to the task, we demonstrate that our fully automated pipeline significantly enhances vocabulary-free segmentation accuracy across diverse real-world scenarios.
Accurately restoring topology is both challenging and crucial in tubular structure extraction tasks, such as blood vessel segmentation and road network extraction. Diverging from traditional approaches based on pixel-level classification, our proposed method, named GraphMorph, focuses on branch-level features of tubular structures to achieve more topologically accurate predictions. GraphMorph comprises two main components: a Graph Decoder and a Morph Module. Utilizing multi-scale features extracted from an image patch by the segmentation network, the Graph Decoder facilitates the learning of branch-level features and generates a graph that accurately represents the tubular structure in this patch. The Morph Module processes two primary inputs: the graph and the centerline probability map, provided by the Graph Decoder and the segmentation network, respectively. Employing a novel SkeletonDijkstra algorithm, the Morph Module produces a centerline mask that aligns with the predicted graph. Furthermore, we observe that employing centerline masks predicted by GraphMorph significantly reduces false positives in the segmentation task, which is achieved by a simple yet effective post-processing strategy. The efficacy of our method in the centerline extraction and segmentation tasks has been substantiated through experimental evaluations across various datasets. Source code will be released soon.
Medical image registration is a fundamental task in medical image analysis, aiming to establish spatial correspondences between paired images. However, existing unsupervised deformable registration methods rely solely on intensity-based similarity metrics, lacking explicit anatomical knowledge, which limits their accuracy and robustness. Vision foundation models, such as the Segment Anything Model (SAM), can generate high-quality segmentation masks that provide explicit anatomical structure knowledge, addressing the limitations of traditional methods that depend only on intensity similarity. Based on this, we propose a novel SAM-assisted registration framework incorporating prototype learning and contour awareness. The framework includes: (1) Explicit anatomical information injection, where SAM-generated segmentation masks are used as auxiliary inputs throughout training and testing to ensure the consistency of anatomical information; (2) Prototype learning, which leverages segmentation masks to extract prototype features and aligns prototypes to optimize semantic correspondences between images; and (3) Contour-aware loss, a contour-aware loss is designed that leverages the edges of segmentation masks to improve the model's performance in fine-grained deformation fields. Extensive experiments demonstrate that the proposed framework significantly outperforms existing methods across multiple datasets, particularly in challenging scenarios with complex anatomical structures and ambiguous boundaries. Our code is available at https://github.com/HaoXu0507/IPMI25-SAM-Assisted-Registration.