Purpose: Automated ultrasound image analysis is challenging due to anatomical complexity and limited annotated data. To tackle this, we take a data-centric approach, assembling the largest public ultrasound segmentation dataset and training a versatile visual foundation model tailored for ultrasound. Methods: We compile US-43d, a large-scale collection of 43 open-access ultrasound datasets with over 280,000 images and segmentation masks for more than 50 anatomical structures. We then introduce UltraSam, an adaptation of the Segment Anything Model (SAM) that is trained on US-43d and supports both point- and box-prompts. Finally, we introduce a new use case for SAM-style models by using UltraSam as a model initialization that can be fine-tuned for various downstream analysis tasks, demonstrating UltraSam's foundational capabilities. Results: UltraSam achieves vastly improved performance over existing SAM-style models for prompt-based segmentation on three diverse public datasets. Moreover, an UltraSam-initialized Vision Transformer surpasses ImageNet-, SAM-, and MedSAM-initialized models in various downstream segmentation and classification tasks, highlighting UltraSam's effectiveness as a foundation model. Conclusion: We compile US-43d, a large-scale unified ultrasound dataset, and introduce UltraSam, a powerful multi-purpose SAM-style model for ultrasound images. We release our code and pretrained models at https://github.com/CAMMA-public/UltraSam and invite the community to further this effort by contributing high-quality datasets.
Implementing image-based machine learning in agriculture is often limited by scarce data and annotations, making it hard to achieve high-quality model predictions. This study tackles the issue of postharvest quality assessment of bananas in decentralized supply chains. We propose a method to detect and segment surface defects in banana images using panoptic segmentation to quantify defect size and number. Instead of time-consuming pixel-level annotations, we use weak supervision with coarse labels. A dataset of 476 smartphone images of bananas was collected under real-world field conditions and annotated for bruises and scars. Using the Segment Anything Model (SAM), a recently published foundation model for image segmentation, we generated dense annotations from coarse bounding boxes to train a segmentation model, significantly reducing manual effort while achieving a panoptic quality score of 77.6%. This demonstrates SAM's potential for low-effort, accurate segmentation in agricultural settings with limited data.
Existing 3D instance segmentation methods frequently encounter issues with over-segmentation, leading to redundant and inaccurate 3D proposals that complicate downstream tasks. This challenge arises from their unsupervised merging approach, where dense 2D instance masks are lifted across frames into point clouds to form 3D candidate proposals without direct supervision. These candidates are then hierarchically merged based on heuristic criteria, often resulting in numerous redundant segments that fail to combine into precise 3D proposals. To overcome these limitations, we propose a 3D-Aware 2D Mask Tracking module that uses robust 3D priors from a 2D mask segmentation and tracking foundation model (SAM-2) to ensure consistent object masks across video frames. Rather than merging all visible superpoints across views to create a 3D mask, our 3D Mask Optimization module leverages a dynamic programming algorithm to select an optimal set of views, refining the superpoints to produce a final 3D proposal for each object. Our approach achieves comprehensive object coverage within the scene while reducing unnecessary proposals, which could otherwise impair downstream applications. Evaluations on ScanNet200 and ScanNet++ confirm the effectiveness of our method, with improvements across Class-Agnostic, Open-Vocabulary, and Open-Ended 3D Instance Segmentation tasks.
Linear Text Segmentation is the task of automatically tagging text documents with topic shifts, i.e. the places in the text where the topics change. A well-established area of research in Natural Language Processing, drawing from well-understood concepts in linguistic and computational linguistic research, the field has recently seen a lot of interest as a result of the surge of text, video, and audio available on the web, which in turn require ways of summarising and categorizing the mole of content for which linear text segmentation is a fundamental step. In this survey, we provide an extensive overview of current advances in linear text segmentation, describing the state of the art in terms of resources and approaches for the task. Finally, we highlight the limitations of available resources and of the task itself, while indicating ways forward based on the most recent literature and under-explored research directions.
Wide-FoV cameras, like fisheye and panoramic setups, are essential for broader perception but introduce significant distortions in 180{\deg} and 360{\deg} images, complicating dense prediction tasks. For instance, existing MAMBA models lacking distortion-aware capacity cannot perform well in panoramic semantic segmentation. To address this problem, this work presents Deformable Mamba, a unified framework specifically designed to address imaging distortions within the context of panoramic and fisheye semantic segmentation. At the core is a decoder constructed with a series of Deformable Mamba Fusion (DMF) blocks, making the whole framework more deformable, efficient, and accurate, when handling extreme distortions. Extensive evaluations across five datasets demonstrate that our method consistently improves segmentation accuracy compared to the previous state-of-the-art methods tailored for specific FoVs. Notably, Deformable Mamba achieves a +2.5% performance improvement on the 360{\deg} Stanford2D3D dataset, and shows better results across FoVs from 60{\deg} to 360{\deg}.
Purpose: This study investigated how nodule segmentation and surrounding peritumoral regions influence radionics-based lung cancer classification. Methods: Using 3D CT scans with bounding box annotated nodules, we generated 3D segmentations using four techniques: Otsu, Fuzzy C-Means (FCM), Gaussian Mixture Model (GMM), and K-Nearest Neighbors (KNN). Radiomics features were extracted using the PyRadiomics library, and multiple machine-learning-based classifiers, including Random Forest, Logistic Regression, and KNN, were employed to classify nodules as cancerous or non-cancerous. The best-performing segmentation and model were further analyzed by expanding the initial nodule segmentation into the peritumoral region (2, 4, 6, 8, 10, and 12 mm) to understand the influence of the surrounding area on classification. Additionally, we compared our results to deep learning-based feature extractors Foundation Model for Cancer Biomarkers (FMCB) and other state-of-the-art baseline models. Results: Incorporating peritumoral regions significantly enhanced performance, with the best result obtained at 8 mm expansion (AUC = 0.78). Compared to image-based deep learning models, such as FMCB (AUC = 0.71) and ResNet50-SWS++ (AUC = 0.71), our radiomics-based approach demonstrated superior classification accuracy. Conclusion: The study highlights the importance of peritumoral expansion in improving lung cancer classification using radiomics. These findings can inform the development of more robust AI-driven diagnostic tools.
The claustrum is a band-like gray matter structure located between putamen and insula whose exact functions are still actively researched. Its sheet-like structure makes it barely visible in in vivo Magnetic Resonance Imaging (MRI) scans at typical resolutions and neuroimaging tools for its study, including methods for automatic segmentation, are currently very limited. In this paper, we propose a contrast- and resolution-agnostic method for claustrum segmentation at ultra-high resolution (0.35 mm isotropic); the method is based on the SynthSeg segmentation framework (Billot et al., 2023), which leverages the use of synthetic training intensity images to achieve excellent generalization. In particular, SynthSeg requires only label maps to be trained, since corresponding intensity images are synthesized on the fly with random contrast and resolution. We trained a deep learning network for automatic claustrum segmentation, using claustrum manual labels obtained from 18 ultra-high resolution MRI scans (mostly ex vivo). We demonstrated the method to work on these 18 high resolution cases (Dice score = 0.632, mean surface distance = 0.458 mm, and volumetric similarity = 0.867 using 6-fold Cross Validation (CV)), and also on in vivo T1-weighted MRI scans at typical resolutions (~1 mm isotropic). We also demonstrated that the method is robust in a test-retest setting and when applied to multimodal imaging (T2-weighted, Proton Density and quantitative T1 scans). To the best of our knowledge this is the first accurate method for automatic ultra-high resolution claustrum segmentation, which is robust against changes in contrast and resolution. The method is released at https://github.com/chiara-mauri/claustrum_segmentation and as part of the neuroimaging package Freesurfer (Fischl, 2012).
Medical image segmentation is crucial for diagnosis and treatment planning. Traditional CNN-based models, like U-Net, have shown promising results but struggle to capture long-range dependencies and global context. To address these limitations, we propose a transformer-based architecture that jointly applies Channel Attention and Pyramid Attention mechanisms to improve multi-scale feature extraction and enhance segmentation performance for medical images. Increasing model complexity requires more training data, and we further improve model generalization with CutMix data augmentation. Our approach is evaluated on the Synapse multi-organ segmentation dataset, achieving a 6.9% improvement in Mean Dice score and a 39.9% improvement in Hausdorff Distance (HD95) over an implementation without our enhancements. Our proposed model demonstrates improved segmentation accuracy for complex anatomical structures, outperforming existing state-of-the-art methods.
Deep learning has seen remarkable advancements in machine learning, yet it often demands extensive annotated data. Tasks like 3D semantic segmentation impose a substantial annotation burden, especially in domains like medicine, where expert annotations drive up the cost. Active learning (AL) holds great potential to alleviate this annotation burden in 3D medical segmentation. The majority of existing AL methods, however, are not tailored to the medical domain. While weakly-supervised methods have been explored to reduce annotation burden, the fusion of AL with weak supervision remains unexplored, despite its potential to significantly reduce annotation costs. Additionally, there is little focus on slice-based AL for 3D segmentation, which can also significantly reduce costs in comparison to conventional volume-based AL. This paper introduces a novel metric learning method for Coreset to perform slice-based active learning in 3D medical segmentation. By merging contrastive learning with inherent data groupings in medical imaging, we learn a metric that emphasizes the relevant differences in samples for training 3D medical segmentation models. We perform comprehensive evaluations using both weak and full annotations across four datasets (medical and non-medical). Our findings demonstrate that our approach surpasses existing active learning techniques on both weak and full annotations and obtains superior performance with low-annotation budgets which is crucial in medical imaging. Source code for this project is available in the supplementary materials and on GitHub: https://github.com/arvindmvepa/al-seg.
Automated lumbar spine segmentation is very crucial for modern diagnosis systems. In this study, we introduce a novel machine-agnostic approach for segmenting lumbar vertebrae and intervertebral discs from MRI images, employing a cascaded model that synergizes an ROI detection and a Self-organized Operational Neural Network (Self-ONN)-based encoder-decoder network for segmentation. Addressing the challenge of diverse MRI modalities, our methodology capitalizes on a unique dataset comprising images from 12 scanners and 34 subjects, enhanced through strategic preprocessing and data augmentation techniques. The YOLOv8 medium model excels in ROI extraction, achieving an excellent performance of 0.916 mAP score. Significantly, our Self-ONN-based model, combined with a DenseNet121 encoder, demonstrates excellent performance in lumbar vertebrae and IVD segmentation with a mean Intersection over Union (IoU) of 83.66%, a sensitivity of 91.44%, and Dice Similarity Coefficient (DSC) of 91.03%, as validated through rigorous 10-fold cross-validation. This study not only showcases an effective approach to MRI segmentation in spine-related disorders but also sets the stage for future advancements in automated diagnostic tools, emphasizing the need for further dataset expansion and model refinement for broader clinical applicability.
In the diverse field of medical imaging, automatic segmentation has numerous applications and must handle a wide variety of input domains, such as different types of Computed Tomography (CT) scans and Magnetic Resonance (MR) images. This heterogeneity challenges automatic segmentation algorithms to maintain consistent performance across different modalities due to the requirement for spatially aligned and paired images. Typically, segmentation models are trained using a single modality, which limits their ability to generalize to other types of input data without employing transfer learning techniques. Additionally, leveraging complementary information from different modalities to enhance segmentation precision often necessitates substantial modifications to popular encoder-decoder designs, such as introducing multiple branched encoding or decoding paths for each modality. In this work, we propose a simple Multi-Modal Segmentation (MulModSeg) strategy to enhance medical image segmentation across multiple modalities, specifically CT and MR. It incorporates two key designs: a modality-conditioned text embedding framework via a frozen text encoder that adds modality awareness to existing segmentation frameworks without significant structural modifications or computational overhead, and an alternating training procedure that facilitates the integration of essential features from unpaired CT and MR inputs. Through extensive experiments with both Fully Convolutional Network and Transformer-based backbones, MulModSeg consistently outperforms previous methods in segmenting abdominal multi-organ and cardiac substructures for both CT and MR modalities. The code is available in this {\href{https://github.com/ChengyinLee/MulModSeg_2024}{link}}.
Organs-at-risk segmentation is critical for ensuring the safety and precision of radiotherapy and surgical procedures. However, existing methods for organs-at-risk image segmentation often suffer from uncertainties and biases in target selection, as well as insufficient model validation experiments, limiting their generality and reliability in practical applications. To address these issues, we propose an innovative cascaded network architecture called the Multi-scale Cascaded Fusing Network (MCFNet), which effectively captures complex multi-scale and multi-resolution features. MCFNet includes a Sharp Extraction Backbone and a Flexible Connection Backbone, which respectively enhance feature extraction in the downsampling and skip-connection stages. This design not only improves segmentation accuracy but also ensures computational efficiency, enabling precise detail capture even in low-resolution images. We conduct experiments using the A6000 GPU on diverse datasets from 671 patients, including 36,131 image-mask pairs across 10 different datasets. MCFNet demonstrates strong robustness, performing consistently well across 10 datasets. Additionally, MCFNet exhibits excellent generalizability, maintaining high accuracy in different clinical scenarios. We also introduce an adaptive loss aggregation strategy to further optimize the model training process, improving both segmentation accuracy and efficiency. Through extensive validation, MCFNet demonstrates superior performance compared to existing methods, providing more reliable image-guided support. Our solution aims to significantly improve the precision and safety of radiotherapy and surgical procedures, advancing personalized treatment. The code has been made available on GitHub:https://github.com/Henry991115/MCFNet.
Histopathology, the microscopic study of diseased tissue, is increasingly digitized, enabling improved visualization and streamlined workflows. An important task in histopathology is the segmentation of cells and glands, essential for determining shape and frequencies that can serve as indicators of disease. Deep learning tools are widely used in histopathology. However, variability in tissue appearance and cell morphology presents challenges for achieving reliable segmentation, often requiring manual correction to improve accuracy. This work introduces CellPilot, a framework that bridges the gap between automatic and interactive segmentation by providing initial automatic segmentation as well as guided interactive refinement. Our model was trained on over 675,000 masks of nine diverse cell and gland segmentation datasets, spanning 16 organs. CellPilot demonstrates superior performance compared to other interactive tools on three held-out histopathological datasets while enabling automatic segmentation. We make the model and a graphical user interface designed to assist practitioners in creating large-scale annotated datasets available as open-source, fostering the development of more robust and generalized diagnostic models.
Medical image segmentation data inherently contain uncertainty, often stemming from both imperfect image quality and variability in labeling preferences on ambiguous pixels, which depend on annotators' expertise and the clinical context of the annotations. For instance, a boundary pixel might be labeled as tumor in diagnosis to avoid under-assessment of severity, but as normal tissue in radiotherapy to prevent damage to sensitive structures. As segmentation preferences vary across downstream applications, it is often desirable for an image segmentation model to offer user-adaptable predictions rather than a fixed output. While prior uncertainty-aware and interactive methods offer adaptability, they are inefficient at test time: uncertainty-aware models require users to choose from numerous similar outputs, while interactive models demand significant user input through click or box prompts to refine segmentation. To address these challenges, we propose \textbf{SPA}, a segmentation framework that efficiently adapts to diverse test-time preferences with minimal human interaction. By presenting users a select few, distinct segmentation candidates that best capture uncertainties, it reduces clinician workload in reaching the preferred segmentation. To accommodate user preference, we introduce a probabilistic mechanism that leverages user feedback to adapt model's segmentation preference. The proposed framework is evaluated on a diverse range of medical image segmentation tasks: color fundus images, CT, and MRI. It demonstrates 1) a significant reduction in clinician time and effort compared with existing interactive segmentation approaches, 2) strong adaptability based on human feedback, and 3) state-of-the-art image segmentation performance across diverse modalities and semantic labels.
Accurate segmentation of blood vessels is essential for various clinical assessments and postoperative analyses. However, the inherent challenges of vascular imaging, such as sparsity, fine granularity, low contrast, data distribution variability, and the critical need for preserving topological structure, making generalized vessel segmentation particularly complex. While specialized segmentation methods have been developed for specific anatomical regions, their over-reliance on tailored models hinders broader applicability and generalization. General-purpose segmentation models introduced in medical imaging often fail to address critical vascular characteristics, including the connectivity of segmentation results. To overcome these limitations, we propose an optimized vessel segmentation framework: a structure-agnostic approach incorporating small vessel enhancement and morphological correction for multi-modality vessel segmentation. To train and validate this framework, we compiled a comprehensive multi-modality dataset spanning 17 datasets and benchmarked our model against six SAM-based methods and 17 expert models. The results demonstrate that our approach achieves superior segmentation accuracy, generalization, and a 34.6% improvement in connectivity, underscoring its clinical potential. An ablation study further validates the effectiveness of the proposed improvements. We will release the code and dataset at github following the publication of this work.
Surgical assessment of liver cancer patients requires identification of the vessel trees from medical images. Specifically, the venous trees - the portal (perfusing) and the hepatic (draining) trees are important for understanding the liver anatomy and disease state, and perform surgery planning. This research aims to improve the 3D segmentation, skeletonization, and subsequent analysis of vessel trees, by creating an automatic pipeline based on deep learning and image processing techniques. The first part of this work explores the impact of differentiable skeletonization methods such as ClDice and morphological skeletonization loss, on the overall liver vessel segmentation performance. To this aim, it studies how to improve vessel tree connectivity. The second part of this study converts a single class vessel segmentation into multi-class ones, separating the two venous trees. It builds on the previous two-class vessel segmentation model, which vessel tree outputs might be entangled, and on connected components and skeleton analyses of the trees. After providing sub-labeling of the specific anatomical branches of each venous tree, these algorithms also enable a morphometric analysis of the vessel trees by extracting various geometrical markers. In conclusion, we propose a method that successfully improves current skeletonization methods, for extensive vascular trees that contain vessels of different calibers. The separation algorithm creates a clean multi-class segmentation of the vessels, validated by surgeons to provide low error. A new, publicly shared high-quality liver vessel dataset of 77 cases is thus created. Finally a method to annotate vessel trees according to anatomy is provided, enabling a unique liver vessel morphometry analysis.
Recent breakthroughs in large foundation models have enabled the possibility of transferring knowledge pre-trained on vast datasets to domains with limited data availability. Agriculture is one of the domains that lacks sufficient data. This study proposes a framework to train effective, domain-specific, small models from foundation models without manual annotation. Our approach begins with SDM (Segmentation-Description-Matching), a stage that leverages two foundation models: SAM2 (Segment Anything in Images and Videos) for segmentation and OpenCLIP (Open Contrastive Language-Image Pretraining) for zero-shot open-vocabulary classification. In the second stage, a novel knowledge distillation mechanism is utilized to distill compact, edge-deployable models from SDM, enhancing both inference speed and perception accuracy. The complete method, termed SDM-D (Segmentation-Description-Matching-Distilling), demonstrates strong performance across various fruit detection tasks object detection, semantic segmentation, and instance segmentation) without manual annotation. It nearly matches the performance of models trained with abundant labels. Notably, SDM-D outperforms open-set detection methods such as Grounding SAM and YOLO-World on all tested fruit detection datasets. Additionally, we introduce MegaFruits, a comprehensive fruit segmentation dataset encompassing over 25,000 images, and all code and datasets are made publicly available at https://github.com/AgRoboticsResearch/SDM-D.git.
Recent works on Generalized Referring Expression Segmentation (GRES) struggle with handling complex expressions referring to multiple distinct objects. This is because these methods typically employ an end-to-end foreground-background segmentation and lack a mechanism to explicitly differentiate and associate different object instances to the text query. To this end, we propose InstAlign, a method that incorporates object-level reasoning into the segmentation process. Our model leverages both text and image inputs to extract a set of object-level tokens that capture both the semantic information in the input prompt and the objects within the image. By modeling the text-object alignment via instance-level supervision, each token uniquely represents an object segment in the image, while also aligning with relevant semantic information from the text. Extensive experiments on the gRefCOCO and Ref-ZOM benchmarks demonstrate that our method significantly advances state-of-the-art performance, setting a new standard for precise and flexible GRES.
Breast cancer remains the leading cause of cancer-related mortality among women worldwide, necessitating the meticulous examination of mammograms by radiologists to characterize abnormal lesions. This manual process demands high accuracy and is often time-consuming, costly, and error-prone. Automated image segmentation using artificial intelligence offers a promising alternative to streamline this workflow. However, most existing methods are supervised, requiring large, expertly annotated datasets that are not always available, and they experience significant generalization issues. Thus, unsupervised learning models can be leveraged for image segmentation, but they come at a cost of reduced accuracy, or require extensive computational resourcess. In this paper, we propose the first end-to-end quantum-enhanced framework for unsupervised mammography medical images segmentation that balances between performance accuracy and computational requirements. We first introduce a quantum-inspired image representation that serves as an initial approximation of the segmentation mask. The segmentation task is then formulated as a QUBO problem, aiming to maximize the contrast between the background and the tumor region while ensuring a cohesive segmentation mask with minimal connected components. We conduct an extensive evaluation of quantum and quantum-inspired methods for image segmentation, demonstrating that quantum annealing and variational quantum circuits achieve performance comparable to classical optimization techniques. Notably, quantum annealing is shown to be an order of magnitude faster than the classical optimization method in our experiments. Our findings demonstrate that this framework achieves performance comparable to state-of-the-art supervised methods, including UNet-based architectures, offering a viable unsupervised alternative for breast cancer image segmentation.
This paper presents an Open-Vocabulary Online 3D semantic mapping pipeline, that we denote by its acronym OVO. Given a sequence of posed RGB-D frames, we detect and track 3D segments, which we describe using CLIP vectors. These are computed from the viewpoints where they are observed by a novel CLIP merging method. Notably, our OVO has a significantly lower computational and memory footprint than offline baselines, while also showing better segmentation metrics than them. Along with superior segmentation performance, we also show experimental results of our mapping contributions integrated with two different SLAM backbones (Gaussian-SLAM and ORB-SLAM2), being the first ones demonstrating end-to-end open-vocabulary online 3D reconstructions without relying on ground-truth camera poses or scene geometry.