Retinal blood vessel segmentation is crucial for diagnosing ocular and cardiovascular diseases. Although the introduction of U-Net in 2015 by Olaf Ronneberger significantly advanced this field, yet issues like limited training data, imbalance data distribution, and inadequate feature extraction persist, hindering both the segmentation performance and optimal model generalization. Addressing these critical issues, the DEFFA-Unet is proposed featuring an additional encoder to process domain-invariant pre-processed inputs, thereby improving both richer feature encoding and enhanced model generalization. A feature filtering fusion module is developed to ensure the precise feature filtering and robust hybrid feature fusion. In response to the task-specific need for higher precision where false positives are very costly, traditional skip connections are replaced with the attention-guided feature reconstructing fusion module. Additionally, innovative data augmentation and balancing methods are proposed to counter data scarcity and distribution imbalance, further boosting the robustness and generalization of the model. With a comprehensive suite of evaluation metrics, extensive validations on four benchmark datasets (DRIVE, CHASEDB1, STARE, and HRF) and an SLO dataset (IOSTAR), demonstrate the proposed method's superiority over both baseline and state-of-the-art models. Particularly the proposed method significantly outperforms the compared methods in cross-validation model generalization.
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.
Accurate retinal vessel segmentation provides essential structural information for ophthalmic image analysis. However, existing methods struggle with challenges such as multi-scale vessel variability, complex curvatures, and ambiguous boundaries. While Convolutional Neural Networks (CNNs), Transformer-based models and Mamba-based architectures have advanced the field, they often suffer from vascular discontinuities or edge feature ambiguity. To address these limitations, we propose a novel hybrid framework that synergistically integrates CNNs and Mamba for high-precision retinal vessel segmentation. Our approach introduces three key innovations: 1) The proposed High-Resolution Edge Fuse Network is a high-resolution preserving hybrid segmentation framework that combines a multi-scale backbone with the Multi-scale Retina Edge Fusion (MREF) module to enhance edge features, ensuring accurate and robust vessel segmentation. 2) The Dynamic Snake Visual State Space block combines Dynamic Snake Convolution with Mamba to adaptively capture vessel curvature details and long-range dependencies. An improved eight-directional 2D Snake-Selective Scan mechanism and a dynamic weighting strategy enhance the perception of complex vascular topologies. 3) The MREF module enhances boundary precision through multi-scale edge feature aggregation, suppressing noise while emphasizing critical vessel structures across scales. Experiments on three public datasets demonstrate that our method achieves state-of-the-art performance, particularly in maintaining vascular continuity and effectively segmenting vessels in low-contrast regions. This work provides a robust method for clinical applications requiring accurate retinal vessel analysis. The code is available at https://github.com/frank-oy/HREFNet.
The U-Net architecture and its variants have remained state-of-the-art (SOTA) for retinal vessel segmentation over the past decade. In this study, we introduce a Full Scale Guided Network (FSG-Net), where the feature representation network with modernized convolution blocks extracts full-scale information and the guided convolution block refines that information. Attention-guided filter is introduced to the guided convolution block under the interpretation that the filter behaves like the unsharp mask filter. Passing full-scale information to the attention block allows for the generation of improved attention maps, which are then passed to the attention-guided filter, resulting in performance enhancement of the segmentation network. The structure preceding the guided convolution block can be replaced by any U-Net variant, which enhances the scalability of the proposed approach. For a fair comparison, we re-implemented recent studies available in public repositories to evaluate their scalability and reproducibility. Our experiments also show that the proposed network demonstrates competitive results compared to current SOTA models on various public datasets. Ablation studies demonstrate that the proposed model is competitive with much smaller parameter sizes. Lastly, by applying the proposed model to facial wrinkle segmentation, we confirmed the potential for scalability to similar tasks in other domains. Our code is available on https://github.com/ZombaSY/FSG-Net-pytorch.
CrackMamba, a Mamba-based model, is designed for efficient and accurate crack segmentation for monitoring the structural health of infrastructure. Traditional Convolutional Neural Network (CNN) models struggle with limited receptive fields, and while Vision Transformers (ViT) improve segmentation accuracy, they are computationally intensive. CrackMamba addresses these challenges by utilizing the VMambaV2 with pre-trained ImageNet-1k weights as the encoder and a newly designed decoder for better performance. To handle the random and complex nature of crack development, a Snake Scan module is proposed to reshape crack feature sequences, enhancing feature extraction. Additionally, the three-branch Snake Conv VSS (SCVSS) block is proposed to target cracks more effectively. Experiments show that CrackMamba achieves state-of-the-art (SOTA) performance on the CrackSeg9k and SewerCrack datasets, and demonstrates competitive performance on the retinal vessel segmentation dataset CHASE\underline{~}DB1, highlighting its generalization capability. The code is publicly available at: {https://github.com/shengyu27/CrackMamba.}
Deep learning has shown remarkable performance in medical image segmentation. However, despite its promise, deep learning has many challenges in practice due to its inability to effectively transition to unseen domains, caused by the inherent data distribution shift and the lack of manual annotations to guide domain adaptation. To tackle this problem, we present an unsupervised domain adaptation (UDA) method named AdaptDiff that enables a retinal vessel segmentation network trained on fundus photography (FP) to produce satisfactory results on unseen modalities (e.g., OCT-A) without any manual labels. For all our target domains, we first adopt a segmentation model trained on the source domain to create pseudo-labels. With these pseudo-labels, we train a conditional semantic diffusion probabilistic model to represent the target domain distribution. Experimentally, we show that even with low quality pseudo-labels, the diffusion model can still capture the conditional semantic information. Subsequently, we sample on the target domain with binary vessel masks from the source domain to get paired data, i.e., target domain synthetic images conditioned on the binary vessel map. Finally, we fine-tune the pre-trained segmentation network using the synthetic paired data to mitigate the domain gap. We assess the effectiveness of AdaptDiff on seven publicly available datasets across three distinct modalities. Our results demonstrate a significant improvement in segmentation performance across all unseen datasets. Our code is publicly available at https://github.com/DeweiHu/AdaptDiff.
Children often suffer wrist trauma in daily life, while they usually need radiologists to analyze and interpret X-ray images before surgical treatment by surgeons. The development of deep learning has enabled neural networks to serve as computer-assisted diagnosis (CAD) tools to help doctors and experts in medical image diagnostics. Since YOLOv8 model has obtained the satisfactory success in object detection tasks, it has been applied to various fracture detection. This work introduces four variants of Feature Contexts Excitation-YOLOv8 (FCE-YOLOv8) model, each incorporating a different FCE module (i.e., modules of Squeeze-and-Excitation (SE), Global Context (GC), Gather-Excite (GE), and Gaussian Context Transformer (GCT)) to enhance the model performance. Experimental results on GRAZPEDWRI-DX dataset demonstrate that our proposed YOLOv8+GC-M3 model improves the mAP@50 value from 65.78% to 66.32%, outperforming the state-of-the-art (SOTA) model while reducing inference time. Furthermore, our proposed YOLOv8+SE-M3 model achieves the highest mAP@50 value of 67.07%, exceeding the SOTA performance. The implementation of this work is available at https://github.com/RuiyangJu/FCE-YOLOv8.
We introduce VascX models, a comprehensive set of model ensembles for analyzing retinal vasculature from color fundus images (CFIs). Annotated CFIs were aggregated from public datasets . Additional CFIs, mainly from the population-based Rotterdam Study were annotated by graders for arteries and veins at pixel level, resulting in a dataset diverse in patient demographics and imaging conditions. VascX models demonstrated superior segmentation performance across datasets, image quality levels, and anatomic regions when compared to existing, publicly available models, likely due to the increased size and variety of our training set. Important improvements were observed in artery-vein and disc segmentation performance, particularly in segmentations of these structures on CFIs of intermediate quality, common in large cohorts and clinical datasets. Importantly, these improvements translated into significantly more accurate vascular features when we compared features extracted from VascX segmentation masks with features extracted from segmentation masks generated by previous models. With VascX models we provide a robust, ready-to-use set of model ensembles and inference code aimed at simplifying the implementation and enhancing the quality of automated retinal vasculature analyses. The precise vessel parameters generated by the model can serve as starting points for the identification of disease patterns in and outside of the eye.
Recent works have introduced methods to estimate segmentation performance without ground truth, relying solely on neural network softmax outputs. These techniques hold potential for intuitive output quality control. However, such performance estimates rely on calibrated softmax outputs, which is often not the case in modern neural networks. Moreover, the estimates do not take into account inherent uncertainty in segmentation tasks. These limitations may render precise performance predictions unattainable, restricting the practical applicability of performance estimation methods. To address these challenges, we develop a novel approach for predicting performance ranges with statistical guarantees of containing the ground truth with a user specified probability. Our method leverages sampling-based segmentation uncertainty estimation to derive heuristic performance ranges, and applies split conformal prediction to transform these estimates into rigorous prediction ranges that meet the desired guarantees. We demonstrate our approach on the FIVES retinal vessel segmentation dataset and compare five commonly used sampling-based uncertainty estimation techniques. Our results show that it is possible to achieve the desired coverage with small prediction ranges, highlighting the potential of performance range prediction as a valuable tool for output quality control.
Accurate retinal vessel (RV) segmentation is a crucial step in the quantitative assessment of retinal vasculature, which is needed for the early detection of retinal diseases and other conditions. Numerous studies have been conducted to tackle the problem of segmenting vessels automatically using a pixel-wise classification approach. The common practice of creating ground truth labels is to categorize pixels as foreground and background. This approach is, however, biased, and it ignores the uncertainty of a human annotator when it comes to annotating e.g. thin vessels. In this work, we propose a simple and effective method that casts the RV segmentation task as an image-level regression. For this purpose, we first introduce a novel Segmentation Annotation Uncertainty-Aware (SAUNA) transform, which adds pixel uncertainty to the ground truth using the pixel's closeness to the annotation boundary and vessel thickness. To train our model with soft labels, we generalize the earlier proposed Jaccard metric loss to arbitrary hypercubes for soft Jaccard index (Intersection-over-Union) optimization. Additionally, we employ a stable version of the Focal-L1 loss for pixel-wise regression. We conduct thorough experiments and compare our method to a diverse set of baselines across 5 retinal image datasets. Our empirical results indicate that the integration of the SAUNA transform and these segmentation losses led to significant performance boosts for different segmentation models. Particularly, our methodology enables UNet-like architectures to substantially outperform computational-intensive baselines. Our implementation is available at \url{https://github.com/Oulu-IMEDS/SAUNA}.
Precision in identifying and differentiating micro and macro blood vessels in the retina is crucial for the diagnosis of retinal diseases, although it poses a significant challenge. Current autoencoding-based segmentation approaches encounter limitations as they are constrained by the encoder and undergo a reduction in resolution during the encoding stage. The inability to recover lost information in the decoding phase further impedes these approaches. Consequently, their capacity to extract the retinal microvascular structure is restricted. To address this issue, we introduce Swin-Res-Net, a specialized module designed to enhance the precision of retinal vessel segmentation. Swin-Res-Net utilizes the Swin transformer which uses shifted windows with displacement for partitioning, to reduce network complexity and accelerate model convergence. Additionally, the model incorporates interactive fusion with a functional module in the Res2Net architecture. The Res2Net leverages multi-scale techniques to enlarge the receptive field of the convolutional kernel, enabling the extraction of additional semantic information from the image. This combination creates a new module that enhances the localization and separation of micro vessels in the retina. To improve the efficiency of processing vascular information, we've added a module to eliminate redundant information between the encoding and decoding steps. Our proposed architecture produces outstanding results, either meeting or surpassing those of other published models. The AUC reflects significant enhancements, achieving values of 0.9956, 0.9931, and 0.9946 in pixel-wise segmentation of retinal vessels across three widely utilized datasets: CHASE-DB1, DRIVE, and STARE, respectively. Moreover, Swin-Res-Net outperforms alternative architectures, demonstrating superior performance in both IOU and F1 measure metrics.
In recent years, medical image segmentation has become an important application in the field of computer-aided diagnosis. In this paper, we are the first to propose a new graph convolution-based decoder namely, Cascaded Graph Convolutional Attention Decoder (G-CASCADE), for 2D medical image segmentation. G-CASCADE progressively refines multi-stage feature maps generated by hierarchical transformer encoders with an efficient graph convolution block. The encoder utilizes the self-attention mechanism to capture long-range dependencies, while the decoder refines the feature maps preserving long-range information due to the global receptive fields of the graph convolution block. Rigorous evaluations of our decoder with multiple transformer encoders on five medical image segmentation tasks (i.e., Abdomen organs, Cardiac organs, Polyp lesions, Skin lesions, and Retinal vessels) show that our model outperforms other state-of-the-art (SOTA) methods. We also demonstrate that our decoder achieves better DICE scores than the SOTA CASCADE decoder with 80.8% fewer parameters and 82.3% fewer FLOPs. Our decoder can easily be used with other hierarchical encoders for general-purpose semantic and medical image segmentation tasks.
Optical coherence tomography angiography (OCTA) is a noninvasive imaging technique that can reveal high-resolution retinal vessels. In this work, we propose an accurate and efficient neural network for retinal vessel segmentation in OCTA images. The proposed network achieves accuracy comparable to other SOTA methods, while having fewer parameters and faster inference speed (e.g. 110x lighter and 1.3x faster than U-Net), which is very friendly for industrial applications. This is achieved by applying the modified Recurrent ConvNeXt Block to a full resolution convolutional network. In addition, we create a new dataset containing 918 OCTA images and their corresponding vessel annotations. The data set is semi-automatically annotated with the help of Segment Anything Model (SAM), which greatly improves the annotation speed. For the benefit of the community, our code and dataset can be obtained from https://github.com/nhjydywd/OCTA-FRNet.
The retina is the only part of the human body in which blood vessels can be accessed non-invasively using imaging techniques such as digital fundus images (DFI). The spatial distribution of the retinal microvasculature may change with cardiovascular diseases and thus the eyes may be regarded as a window to our hearts. Computerized segmentation of the retinal arterioles and venules (A/V) is essential for automated microvasculature analysis. Using active learning, we created a new DFI dataset containing 240 crowd-sourced manual A/V segmentations performed by fifteen medical students and reviewed by an ophthalmologist, and developed LUNet, a novel deep learning architecture for high resolution A/V segmentation. LUNet architecture includes a double dilated convolutional block that aims to enhance the receptive field of the model and reduce its parameter count. Furthermore, LUNet has a long tail that operates at high resolution to refine the segmentation. The custom loss function emphasizes the continuity of the blood vessels. LUNet is shown to significantly outperform two state-of-the-art segmentation algorithms on the local test set as well as on four external test sets simulating distribution shifts across ethnicity, comorbidities, and annotators. We make the newly created dataset open access (upon publication).
Driven by the latest trend towards self-supervised learning (SSL), the paradigm of "pretraining-then-finetuning" has been extensively explored to enhance the performance of clinical applications with limited annotations. Previous literature on model finetuning has mainly focused on regularization terms and specific policy models, while the misalignment of channels between source and target models has not received sufficient attention. In this work, we revisited the dynamics of batch normalization (BN) layers and observed that the trainable affine parameters of BN serve as sensitive indicators of domain information. Therefore, Affine Collaborative Normalization (AC-Norm) is proposed for finetuning, which dynamically recalibrates the channels in the target model according to the cross-domain channel-wise correlations without adding extra parameters. Based on a single-step backpropagation, AC-Norm can also be utilized to measure the transferability of pretrained models. We evaluated AC-Norm against the vanilla finetuning and state-of-the-art fine-tuning methods on transferring diverse pretrained models to the diabetic retinopathy grade classification, retinal vessel segmentation, CT lung nodule segmentation/classification, CT liver-tumor segmentation and MRI cardiac segmentation tasks. Extensive experiments demonstrate that AC-Norm unanimously outperforms the vanilla finetuning by up to 4% improvement, even under significant domain shifts where the state-of-the-art methods bring no gains. We also prove the capability of AC-Norm in fast transferability estimation. Our code is available at https://github.com/EndoluminalSurgicalVision-IMR/ACNorm.
Optical coherence tomography angiography (OCTA) is a non-invasive imaging modality that can acquire high-resolution volumes of the retinal vasculature and aid the diagnosis of ocular, neurological and cardiac diseases. Segmenting the visible blood vessels is a common first step when extracting quantitative biomarkers from these images. Classical segmentation algorithms based on thresholding are strongly affected by image artifacts and limited signal-to-noise ratio. The use of modern, deep learning-based segmentation methods has been inhibited by a lack of large datasets with detailed annotations of the blood vessels. To address this issue, recent work has employed transfer learning, where a segmentation network is trained on synthetic OCTA images and is then applied to real data. However, the previously proposed simulations fail to faithfully model the retinal vasculature and do not provide effective domain adaptation. Because of this, current methods are unable to fully segment the retinal vasculature, in particular the smallest capillaries. In this work, we present a lightweight simulation of the retinal vascular network based on space colonization for faster and more realistic OCTA synthesis. We then introduce three contrast adaptation pipelines to decrease the domain gap between real and artificial images. We demonstrate the superior segmentation performance of our approach in extensive quantitative and qualitative experiments on three public datasets that compare our method to traditional computer vision algorithms and supervised training using human annotations. Finally, we make our entire pipeline publicly available, including the source code, pretrained models, and a large dataset of synthetic OCTA images.
Clinical screening with low-quality fundus images is challenging and significantly leads to misdiagnosis. This paper addresses the issue of improving the retinal image quality and vessel segmentation through retinal image restoration. More specifically, a cycle-consistent generative adversarial network (CycleGAN) with a convolution block attention module (CBAM) is used for retinal image restoration. A modified UNet is used for retinal vessel segmentation for the restored retinal images (CBAM-UNet). The proposed model consists of two generators and two discriminators. Generators translate images from one domain to another, i.e., from low to high quality and vice versa. Discriminators classify generated and original images. The retinal vessel segmentation model uses downsampling, bottlenecking, and upsampling layers to generate segmented images. The CBAM has been used to enhance the feature extraction of these models. The proposed method does not require paired image datasets, which are challenging to produce. Instead, it uses unpaired data that consists of low- and high-quality fundus images retrieved from publicly available datasets. The restoration performance of the proposed method was evaluated using full-reference evaluation metrics, e.g., peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM). The retinal vessel segmentation performance was compared with the ground-truth fundus images. The proposed method can significantly reduce the degradation effects caused by out-of-focus blurring, color distortion, low, high, and uneven illumination. Experimental results show the effectiveness of the proposed method for retinal image restoration and vessel segmentation.
Convolutional neural networks have been widely applied to medical image segmentation and have achieved considerable performance. However, the performance may be significantly affected by the domain gap between training data (source domain) and testing data (target domain). To address this issue, we propose a data manipulation based domain generalization method, called Automated Augmentation for Domain Generalization (AADG). Our AADG framework can effectively sample data augmentation policies that generate novel domains and diversify the training set from an appropriate search space. Specifically, we introduce a novel proxy task maximizing the diversity among multiple augmented novel domains as measured by the Sinkhorn distance in a unit sphere space, making automated augmentation tractable. Adversarial training and deep reinforcement learning are employed to efficiently search the objectives. Quantitative and qualitative experiments on 11 publicly-accessible fundus image datasets (four for retinal vessel segmentation, four for optic disc and cup (OD/OC) segmentation and three for retinal lesion segmentation) are comprehensively performed. Two OCTA datasets for retinal vasculature segmentation are further involved to validate cross-modality generalization. Our proposed AADG exhibits state-of-the-art generalization performance and outperforms existing approaches by considerable margins on retinal vessel, OD/OC and lesion segmentation tasks. The learned policies are empirically validated to be model-agnostic and can transfer well to other models. The source code is available at https://github.com/CRazorback/AADG.
Efficient medical image segmentation aims to provide accurate pixel-wise predictions for medical images with a lightweight implementation framework. However, lightweight frameworks generally fail to achieve superior performance and suffer from poor generalizable ability on cross-domain tasks. In this paper, we explore the generalizable knowledge distillation for the efficient segmentation of cross-domain medical images. Considering the domain gaps between different medical datasets, we propose the Model-Specific Alignment Networks (MSAN) to obtain the domain-invariant representations. Meanwhile, a customized Alignment Consistency Training (ACT) strategy is designed to promote the MSAN training. Considering the domain-invariant representative vectors in MSAN, we propose two generalizable knowledge distillation schemes for cross-domain distillation, Dual Contrastive Graph Distillation (DCGD) and Domain-Invariant Cross Distillation (DICD). Specifically, in DCGD, two types of implicit contrastive graphs are designed to represent the intra-coupling and inter-coupling semantic correlations from the perspective of data distribution. In DICD, the domain-invariant semantic vectors from the two models (i.e., teacher and student) are leveraged to cross-reconstruct features by the header exchange of MSAN, which achieves improvement in the generalization of both the encoder and decoder in the student model. Furthermore, a metric named Frechet Semantic Distance (FSD) is tailored to verify the effectiveness of the regularized domain-invariant features. Extensive experiments conducted on the Liver and Retinal Vessel Segmentation datasets demonstrate the superiority of our method, in terms of performance and generalization on lightweight frameworks.
While there have been increased researches using deep learning techniques for the extraction of vascular structure from the 2D en face OCTA, for such approach, it is known that the data annotation process on the curvilinear structure like the retinal vasculature is very costly and time consuming, albeit few tried to address the annotation problem. In this work, we propose the application of the scribble-base weakly-supervised learning method to automate the pixel-level annotation. The proposed method, called OCTAve, combines the weakly-supervised learning using scribble-annotated ground truth augmented with an adversarial and a novel self-supervised deep supervision. Our novel mechanism is designed to utilize the discriminative outputs from the discrimination layer of a UNet-like architecture where the Kullback-Liebler Divergence between the aggregate discriminative outputs and the segmentation map predicate is minimized during the training. This combined method leads to the better localization of the vascular structure as shown in our experiments. We validate our proposed method on the large public datasets i.e., ROSE, OCTA-500. The segmentation performance is compared against both state-of-the-art fully-supervised and scribble-based weakly-supervised approaches. The implementation of our work used in the experiments is located at [LINK].