Topological correctness is critical for segmentation of tubular structures. Existing topological segmentation loss functions are primarily based on the persistent homology of the image. They match the persistent features from the segmentation with the persistent features from the ground truth and minimize the difference between them. However, these methods suffer from an ambiguous matching problem since the matching only relies on the information in the topological space. In this work, we propose an effective and efficient Spatial-Aware Topological Loss Function that further leverages the information in the original spatial domain of the image to assist the matching of persistent features. Extensive experiments on images of various types of tubular structures show that the proposed method has superior performance in improving the topological accuracy of the segmentation compared with state-of-the-art methods.
In medical imaging, efficient segmentation of colon polyps plays a pivotal role in minimally invasive solutions for colorectal cancer. This study introduces a novel approach employing two parallel encoder branches within a network for polyp segmentation. One branch of the encoder incorporates the dual convolution blocks that have the capability to maintain feature information over increased depths, and the other block embraces the single convolution block with the addition of the previous layer's feature, offering diversity in feature extraction within the encoder, combining them before transpose layers with a depth-wise concatenation operation. Our model demonstrated superior performance, surpassing several established deep-learning architectures on the Kvasir and CVC-ClinicDB datasets, achieved a Dice score of 0.919, a mIoU of 0.866 for the Kvasir dataset, and a Dice score of 0.931 and a mIoU of 0.891 for the CVC-ClinicDB. The visual and quantitative results highlight the efficacy of our model, potentially setting a new model in medical image segmentation.
Adenoid hypertrophy stands as a common cause of obstructive sleep apnea-hypopnea syndrome in children. It is characterized by snoring, nasal congestion, and growth disorders. Computed Tomography (CT) emerges as a pivotal medical imaging modality, utilizing X-rays and advanced computational techniques to generate detailed cross-sectional images. Within the realm of pediatric airway assessments, CT imaging provides an insightful perspective on the shape and volume of enlarged adenoids. Despite the advances of deep learning methods for medical imaging analysis, there remains an emptiness in the segmentation of adenoid hypertrophy in CT scans. To address this research gap, we introduce TSUBF-Nett (Trans-Spatial UNet-like Network based on Bi-direction Fusion), a 3D medical image segmentation framework. TSUBF-Net is engineered to effectively discern intricate 3D spatial interlayer features in CT scans and enhance the extraction of boundary-blurring features. Notably, we propose two innovative modules within the U-shaped network architecture:the Trans-Spatial Perception module (TSP) and the Bi-directional Sampling Collaborated Fusion module (BSCF).These two modules are in charge of operating during the sampling process and strategically fusing down-sampled and up-sampled features, respectively. Furthermore, we introduce the Sobel loss term, which optimizes the smoothness of the segmentation results and enhances model accuracy. Extensive 3D segmentation experiments are conducted on several datasets. TSUBF-Net is superior to the state-of-the-art methods with the lowest HD95: 7.03, IoU:85.63, and DSC: 92.26 on our own AHSD dataset. The results in the other two public datasets also demonstrate that our methods can robustly and effectively address the challenges of 3D segmentation in CT scans.
Medical imaging is essential in healthcare to provide key insights into patient anatomy and pathology, aiding in diagnosis and treatment. Non-invasive techniques such as X-ray, Magnetic Resonance Imaging (MRI), Computed Tomography (CT), and Ultrasound (US), capture detailed images of organs, tissues, and abnormalities. Effective analysis of these images requires precise segmentation to delineate regions of interest (ROI), such as organs or lesions. Traditional segmentation methods, relying on manual feature-extraction, are labor-intensive and vary across experts. Recent advancements in Artificial Intelligence (AI) and Deep Learning (DL), particularly convolutional models such as U-Net and its variants (U-Net++ and U-Net 3+), have transformed medical image segmentation (MIS) by automating the process and enhancing accuracy. These models enable efficient, precise pixel-wise classification across various imaging modalities, overcoming the limitations of manual segmentation. This review explores various medical imaging techniques, examines the U-Net architectures and their adaptations, and discusses their application across different modalities. It also identifies common challenges in MIS and proposes potential solutions.
Medical image segmentation is a critical aspect of modern medical research and clinical practice. Despite the remarkable performance of Convolutional Neural Networks (CNNs) in this domain, they inherently struggle to capture long-range dependencies within images. Transformers, on the other hand, are naturally adept at modeling global context but often face challenges in capturing local features effectively. Therefore, we presents FAN-UNet, a novel architecture that combines the strengths of Fourier Analysis Network (FAN)-based vision backbones and the U-Net architecture, effectively addressing the challenges of long-range dependency and periodicity modeling in biomedical image segmentation tasks. The proposed Vision-FAN layer integrates the FAN layer and self-attention mechanisms, leveraging Fourier analysis to enable the model to effectively capture both long-range dependencies and periodic relationships. Extensive experiments on various medical imaging datasets demonstrate that FAN-UNet achieves a favorable balance between model complexity and performance, validating its effectiveness and practicality for medical image segmentation tasks.
Referring Image Segmentation (RIS) is an advanced vision-language task that involves identifying and segmenting objects within an image as described by free-form text descriptions. While previous studies focused on aligning visual and language features, exploring training techniques, such as data augmentation, remains underexplored. In this work, we explore effective data augmentation for RIS and propose a novel training framework called Masked Referring Image Segmentation (MaskRIS). We observe that the conventional image augmentations fall short of RIS, leading to performance degradation, while simple random masking significantly enhances the performance of RIS. MaskRIS uses both image and text masking, followed by Distortion-aware Contextual Learning (DCL) to fully exploit the benefits of the masking strategy. This approach can improve the model's robustness to occlusions, incomplete information, and various linguistic complexities, resulting in a significant performance improvement. Experiments demonstrate that MaskRIS can easily be applied to various RIS models, outperforming existing methods in both fully supervised and weakly supervised settings. Finally, MaskRIS achieves new state-of-the-art performance on RefCOCO, RefCOCO+, and RefCOCOg datasets. Code is available at https://github.com/naver-ai/maskris.
Most of current computer vision-based advanced driver assistance systems (ADAS) perform detection and tracking of objects quite successfully under regular conditions. However, under adverse weather and changing lighting conditions, and in complex situations with many overlapping objects, these systems are not completely reliable. The spectral reflectance of the different objects in a driving scene beyond the visible spectrum can offer additional information to increase the reliability of these systems, especially under challenging driving conditions. Furthermore, this information may be significant enough to develop vision systems that allow for a better understanding and interpretation of the whole driving scene. In this work we explore the use of snapshot, video-rate hyperspectral imaging (HSI) cameras in ADAS on the assumption that the near infrared (NIR) spectral reflectance of different materials can help to better segment the objects in real driving scenarios. To do this, we have used the HSI-Drive 1.1 dataset to perform various experiments on spectral classification algorithms. However, the information retrieval of hyperspectral recordings in natural outdoor scenarios is challenging, mainly because of deficient colour constancy and other inherent shortcomings of current snapshot HSI technology, which poses some limitations to the development of pure spectral classifiers. In consequence, in this work we analyze to what extent the spatial features codified by standard, tiny fully convolutional network (FCN) models can improve the performance of HSI segmentation systems for ADAS applications. The abstract above is truncated due to submission limits. For the full abstract, please refer to the published article.
Recently, text-guided scalable vector graphics (SVG) synthesis has demonstrated significant potential in domains such as iconography and sketching. However, SVGs generated from existing Text-to-SVG methods often lack editability and exhibit deficiencies in visual quality and diversity. In this paper, we propose a novel text-guided vector graphics synthesis method to address these limitations. To enhance the editability of output SVGs, we introduce a Hierarchical Image VEctorization (HIVE) framework that operates at the semantic object level and supervises the optimization of components within the vector object. This approach facilitates the decoupling of vector graphics into distinct objects and component levels. Our proposed HIVE algorithm, informed by image segmentation priors, not only ensures a more precise representation of vector graphics but also enables fine-grained editing capabilities within vector objects. To improve the diversity of output SVGs, we present a Vectorized Particle-based Score Distillation (VPSD) approach. VPSD addresses over-saturation issues in existing methods and enhances sample diversity. A pre-trained reward model is incorporated to re-weight vector particles, improving aesthetic appeal and enabling faster convergence. Additionally, we design a novel adaptive vector primitives control strategy, which allows for the dynamic adjustment of the number of primitives, thereby enhancing the presentation of graphic details. Extensive experiments validate the effectiveness of the proposed method, demonstrating its superiority over baseline methods in terms of editability, visual quality, and diversity. We also show that our new method supports up to six distinct vector styles, capable of generating high-quality vector assets suitable for stylized vector design and poster design. Code and demo will be released at: http://ximinng.github.io/SVGDreamerV2Project/
This study introduces SAMatch, a SAM-guided Match-based framework for semi-supervised medical image segmentation, aimed at improving pseudo label quality in data-scarce scenarios. While Match-based frameworks are effective, they struggle with low-quality pseudo labels due to the absence of ground truth. SAM, pre-trained on a large dataset, generalizes well across diverse tasks and assists in generating high-confidence prompts, which are then used to refine pseudo labels via fine-tuned SAM. SAMatch is trained end-to-end, allowing for dynamic interaction between the models. Experiments on the ACDC cardiac MRI, BUSI breast ultrasound, and MRLiver datasets show SAMatch achieving state-of-the-art results, with Dice scores of 89.36%, 77.76%, and 80.04%, respectively, using minimal labeled data. SAMatch effectively addresses challenges in semi-supervised segmentation, offering a powerful tool for segmentation in data-limited environments. Code and data are available at https://github.com/apple1986/SAMatch.
The integration of machine learning in magnetic resonance imaging (MRI), specifically in neuroimaging, is proving to be incredibly effective, leading to better diagnostic accuracy, accelerated image analysis, and data-driven insights, which can potentially transform patient care. Deep learning models utilize multiple layers of processing to capture intricate details of complex data, which can then be used on a variety of tasks, including brain tumor classification, segmentation, image synthesis, and registration. Previous research demonstrates high accuracy in tumor segmentation using various model architectures, including nn-UNet and Swin-UNet. U-Mamba, which uses state space modeling, also achieves high accuracy in medical image segmentation. To leverage these models, we propose a deep learning framework that ensembles these state-of-the-art architectures to achieve accurate segmentation and produce finely synthesized images.
Segmenting 3D blood vessels is a critical yet challenging task in medical image analysis. This is due to significant imaging modality-specific variations in artifacts, vascular patterns and scales, signal-to-noise ratios, and background tissues. These variations, along with domain gaps arising from varying imaging protocols, limit the generalization of existing supervised learning-based methods, requiring tedious voxel-level annotations for each dataset separately. While foundation models promise to alleviate this limitation, they typically fail to generalize to the task of blood vessel segmentation, posing a unique, complex problem. In this work, we present vesselFM, a foundation model designed specifically for the broad task of 3D blood vessel segmentation. Unlike previous models, vesselFM can effortlessly generalize to unseen domains. To achieve zero-shot generalization, we train vesselFM on three heterogeneous data sources: a large, curated annotated dataset, data generated by a domain randomization scheme, and data sampled from a flow matching-based generative model. Extensive evaluations show that vesselFM outperforms state-of-the-art medical image segmentation foundation models across four (pre-)clinically relevant imaging modalities in zero-, one-, and few-shot scenarios, therefore providing a universal solution for 3D blood vessel segmentation.
Medical image segmentation often faces the challenge of prohibitively expensive annotation costs. While few-shot learning offers a promising solution to alleviate this burden, conventional approaches still rely heavily on pre-training with large volumes of labeled data from known categories. To address this issue, we propose leveraging the Segment Anything Model (SAM), pre-trained on over 1 billion masks, thus circumventing the need for extensive domain-specific annotated data. In light of this, we developed SAM-MPA, an innovative SAM-based framework for few-shot medical image segmentation using Mask Propagation-based Auto-prompting. Initially, we employ k-centroid clustering to select the most representative examples for labelling to construct the support set. These annotated examples are registered to other images yielding deformation fields that facilitate the propagation of the mask knowledge to obtain coarse masks across the dataset. Subsequently, we automatically generate visual prompts based on the region and boundary expansion of the coarse mask, including points, box and a coarse mask. Finally, we can obtain the segmentation predictions by inputting these prompts into SAM and refine the results by post refinement module. We validate the performance of the proposed framework through extensive experiments conducted on two medical image datasets with different modalities. Our method achieves Dices of 74.53%, 94.36% on Breast US, Chest X-ray, respectively. Experimental results substantiate that SAM-MPA yields high-accuracy segmentations within 10 labeled examples, outperforming other state-of-the-art few-shot auto-segmentation methods. Our method enables the customization of SAM for any medical image dataset with a small number of labeled examples.
We present the updated version of the HSI-Drive dataset aimed at developing automated driving systems (ADS) using hyperspectral imaging (HSI). The v2.0 version includes new annotated images from videos recorded during winter and fall in real driving scenarios. Added to the spring and summer images included in the previous v1.1 version, the new dataset contains 752 images covering the four seasons. In this paper, we show the improvements achieved over previously published results obtained on the v1.1 dataset, showcasing the enhanced performance of models trained on the new v2.0 dataset. We also show the progress made in comprehensive scene understanding by experimenting with more capable image segmentation models. These models include new segmentation categories aimed at the identification of essential road safety objects such as the presence of vehicles and road signs, as well as highly vulnerable groups like pedestrians and cyclists. In addition, we provide evidence of the performance and robustness of the models when applied to segmenting HSI video sequences captured in various environments and conditions. Finally, for a correct assessment of the results described in this work, the constraints imposed by the processing platforms that can sensibly be deployed in vehicles for ADS must be taken into account. Thus, and although implementation details are out of the scope of this paper, we focus our research on the development of computationally efficient, lightweight ML models that can eventually operate at high throughput rates. The dataset and some examples of segmented videos are available in https://ipaccess.ehu.eus/HSI-Drive/.
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.
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.
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.
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.
Advancements in image segmentation play an integral role within the broad scope of Deep Learning-based Computer Vision. Furthermore, their widespread applicability in critical real-world tasks has resulted in challenges related to the reliability of such algorithms. Hence, uncertainty quantification has been extensively studied within this context, enabling the expression of model ignorance (epistemic uncertainty) or data ambiguity (aleatoric uncertainty) to prevent uninformed decision-making. Due to the rapid adoption of Convolutional Neural Network (CNN)-based segmentation models in high-stake applications, a substantial body of research has been published on this very topic, causing its swift expansion into a distinct field. This work provides a comprehensive overview of probabilistic segmentation, by discussing fundamental concepts of uncertainty quantification, governing advancements in the field as well as the application to various tasks. Moreover, literature on both types of uncertainties trace back to four key applications: (1) to quantify statistical inconsistencies in the annotation process due ambiguous images, (2) correlating prediction error with uncertainty, (3) expanding the model hypothesis space for better generalization, and (4) Active Learning. An extensive discussion follows that includes an overview of utilized datasets for each of the applications and evaluation of the available methods. We also highlight challenges related to architectures, uncertainty quantification methods, standardization and benchmarking, and finally end with recommendations for future work such as methods based on single forward passes and models that appropriately leverage volumetric data.
Computed Tomography (CT) is one of the most popular modalities for medical imaging. By far, CT images have contributed to the largest publicly available datasets for volumetric medical segmentation tasks, covering full-body anatomical structures. Large amounts of full-body CT images provide the opportunity to pre-train powerful models, e.g., STU-Net pre-trained in a supervised fashion, to segment numerous anatomical structures. However, it remains unclear in which conditions these pre-trained models can be transferred to various downstream medical segmentation tasks, particularly segmenting the other modalities and diverse targets. To address this problem, a large-scale benchmark for comprehensive evaluation is crucial for finding these conditions. Thus, we collected 87 public datasets varying in modality, target, and sample size to evaluate the transfer ability of full-body CT pre-trained models. We then employed a representative model, STU-Net with multiple model scales, to conduct transfer learning across modalities and targets. Our experimental results show that (1) there may be a bottleneck effect concerning the dataset size in fine-tuning, with more improvement on both small- and large-scale datasets than medium-size ones. (2) Models pre-trained on full-body CT demonstrate effective modality transfer, adapting well to other modalities such as MRI. (3) Pre-training on the full-body CT not only supports strong performance in structure detection but also shows efficacy in lesion detection, showcasing adaptability across target tasks. We hope that this large-scale open evaluation of transfer learning can direct future research in volumetric medical image segmentation.