Guidewire segmentation during endovascular interventions holds the potential to significantly enhance procedural accuracy, improving visualization and providing critical feedback that can support both physicians and robotic systems in navigating complex vascular pathways. Unlike supervised segmentation networks, which need many expensive expert-annotated labels, sim-to-real domain adaptation approaches utilize synthetic data from simulations, offering a cost-effective solution. The success of models like Segment-Anything (SAM) has driven advancements in image segmentation foundation models with strong zero/few-shot generalization through prompt engineering. However, they struggle with medical images like X-ray fluoroscopy and the domain-shifts of the data. Given the challenges of acquiring annotation and the accessibility of labeled simulation data, we propose a sim-to-real domain adaption framework with a coarse-to-fine strategy to adapt SAM to X-ray fluoroscopy guidewire segmentation without any annotation on the target domain. We first generate the pseudo-labels by utilizing a simple source image style transfer technique that preserves the guidewire structure. Then, we develop a weakly supervised self-training architecture to fine-tune an end-to-end student SAM with the coarse labels by imposing consistency regularization and supervision from the teacher SAM network. We validate the effectiveness of the proposed method on a publicly available Cardiac dataset and an in-house Neurovascular dataset, where our method surpasses both pre-trained SAM and many state-of-the-art domain adaptation techniques by a large margin. Our code will be made public on GitHub soon.
Integrating grayscale and depth data in road inspection robots could enhance the accuracy, reliability, and comprehensiveness of road condition assessments, leading to improved maintenance strategies and safer infrastructure. However, these data sources are often compromised by significant background noise from the pavement. Recent advancements in Diffusion Probabilistic Models (DPM) have demonstrated remarkable success in image segmentation tasks, showcasing potent denoising capabilities, as evidenced in studies like SegDiff. Despite these advancements, current DPM-based segmentors do not fully capitalize on the potential of original image data. In this paper, we propose a novel DPM-based approach for crack segmentation, named CrackSegDiff, which uniquely fuses grayscale and range/depth images. This method enhances the reverse diffusion process by intensifying the interaction between local feature extraction via DPM and global feature extraction. Unlike traditional methods that utilize Transformers for global features, our approach employs Vm-unet to efficiently capture long-range information of the original data. The integration of features is further refined through two innovative modules: the Channel Fusion Module (CFM) and the Shallow Feature Compensation Module (SFCM). Our experimental evaluation on the three-class crack image segmentation tasks within the FIND dataset demonstrates that CrackSegDiff outperforms state-of-the-art methods, particularly excelling in the detection of shallow cracks. Code is available at https://github.com/sky-visionX/CrackSegDiff.
AI-based vascular segmentation is becoming increasingly common in enhancing the screening and treatment of ophthalmic diseases. Deep learning structures based on U-Net have achieved relatively good performance in vascular segmentation. However, small blood vessels and capillaries tend to be lost during segmentation when passed through the traditional U-Net downsampling module. To address this gap, this paper proposes a novel Kalman filter based Linear Deformable Diffusion (KLDD) model for retinal vessel segmentation. Our model employs a diffusion process that iteratively refines the segmentation, leveraging the flexible receptive fields of deformable convolutions in feature extraction modules to adapt to the detailed tubular vascular structures. More specifically, we first employ a feature extractor with linear deformable convolution to capture vascular structure information form the input images. To better optimize the coordinate positions of deformable convolution, we employ the Kalman filter to enhance the perception of vascular structures in linear deformable convolution. Subsequently, the features of the vascular structures extracted are utilized as a conditioning element within a diffusion model by the Cross-Attention Aggregation module (CAAM) and the Channel-wise Soft Attention module (CSAM). These aggregations are designed to enhance the diffusion model's capability to generate vascular structures. Experiments are evaluated on retinal fundus image datasets (DRIVE, CHASE_DB1) as well as the 3mm and 6mm of the OCTA-500 dataset, and the results show that the diffusion model proposed in this paper outperforms other methods.
Accurate segmentation of multiple organs and the differentiation of pathological tissues in medical imaging are crucial but challenging, especially for nuanced classifications and ambiguous organ boundaries. To tackle these challenges, we introduce GASA-UNet, a refined U-Net-like model featuring a novel Global Axial Self-Attention (GASA) block. This block processes image data as a 3D entity, with each 2D plane representing a different anatomical cross-section. Voxel features are defined within this spatial context, and a Multi-Head Self-Attention (MHSA) mechanism is utilized on extracted 1D patches to facilitate connections across these planes. Positional embeddings (PE) are incorporated into our attention framework, enriching voxel features with spatial context and enhancing tissue classification and organ edge delineation. Our model has demonstrated promising improvements in segmentation performance, particularly for smaller anatomical structures, as evidenced by enhanced Dice scores and Normalized Surface Dice (NSD) on three benchmark datasets, i.e., BTCV, AMOS, and KiTS23.
As remote sensing imaging technology continues to advance and evolve, processing high-resolution and diversified satellite imagery to improve segmentation accuracy and enhance interpretation efficiency emerg as a pivotal area of investigation within the realm of remote sensing. Although segmentation algorithms based on CNNs and Transformers achieve significant progress in performance, balancing segmentation accuracy and computational complexity remains challenging, limiting their wide application in practical tasks. To address this, this paper introduces state space model (SSM) and proposes a novel hybrid semantic segmentation network based on vision Mamba (CVMH-UNet). This method designs a cross-scanning visual state space block (CVSSBlock) that uses cross 2D scanning (CS2D) to fully capture global information from multiple directions, while by incorporating convolutional neural network branches to overcome the constraints of Vision Mamba (VMamba) in acquiring local information, this approach facilitates a comprehensive analysis of both global and local features. Furthermore, to address the issue of limited discriminative power and the difficulty in achieving detailed fusion with direct skip connections, a multi-frequency multi-scale feature fusion block (MFMSBlock) is designed. This module introduces multi-frequency information through 2D discrete cosine transform (2D DCT) to enhance information utilization and provides additional scale local detail information through point-wise convolution branches. Finally, it aggregates multi-scale information along the channel dimension, achieving refined feature fusion. Findings from experiments conducted on renowned datasets of remote sensing imagery demonstrate that proposed CVMH-UNet achieves superior segmentation performance while maintaining low computational complexity, outperforming surpassing current leading-edge segmentation algorithms.
Universal segmentation models offer significant potential in addressing a wide range of tasks by effectively leveraging discrete annotations. As the scope of tasks and modalities expands, it becomes increasingly important to generate and strategically position task- and modal-specific priors within the universal model. However, existing universal models often overlook the correlations between different priors, and the optimal placement and frequency of these priors remain underexplored. In this paper, we introduce MedUniSeg, a prompt-driven universal segmentation model designed for 2D and 3D multi-task segmentation across diverse modalities and domains. MedUniSeg employs multiple modal-specific prompts alongside a universal task prompt to accurately characterize the modalities and tasks. To generate the related priors, we propose the modal map (MMap) and the fusion and selection (FUSE) modules, which transform modal and task prompts into corresponding priors. These modal and task priors are systematically introduced at the start and end of the encoding process. We evaluate MedUniSeg on a comprehensive multi-modal upstream dataset consisting of 17 sub-datasets. The results demonstrate that MedUniSeg achieves superior multi-task segmentation performance, attaining a 1.2% improvement in the mean Dice score across the 17 upstream tasks compared to nnUNet baselines, while using less than 1/10 of the parameters. For tasks that underperform during the initial multi-task joint training, we freeze MedUniSeg and introduce new modules to re-learn these tasks. This approach yields an enhanced version, MedUniSeg*, which consistently outperforms MedUniSeg across all tasks. Moreover, MedUniSeg surpasses advanced self-supervised and supervised pre-trained models on six downstream tasks, establishing itself as a high-quality, highly generalizable pre-trained segmentation model.
The data-hungry approach of supervised classification drives the interest of the researchers toward unsupervised approaches, especially for problems such as medical image segmentation, where labeled data are difficult to get. Motivated by the recent success of Vision transformers (ViT) in various computer vision tasks, we propose an unsupervised segmentation framework with a pre-trained ViT. Moreover, by harnessing the graph structure inherent within the image, the proposed method achieves a notable performance in segmentation, especially in medical images. We further introduce a modularity-based loss function coupled with an Auto-Regressive Moving Average (ARMA) filter to capture the inherent graph topology within the image. Finally, we observe that employing Scaled Exponential Linear Unit (SELU) and SILU (Swish) activation functions within the proposed Graph Neural Network (GNN) architecture enhances the performance of segmentation. The proposed method provides state-of-the-art performance (even comparable to supervised methods) on benchmark image segmentation datasets such as ECSSD, DUTS, and CUB, as well as challenging medical image segmentation datasets such as KVASIR, CVC-ClinicDB, ISIC-2018. The github repository of the code is available on \url{https://github.com/ksgr5566/UnSeGArmaNet}.
The medical image processing field often encounters the critical issue of scarce annotated data. Transfer learning has emerged as a solution, yet how to select an adequate source task and effectively transfer the knowledge to the target task remains challenging. To address this, we propose a novel sequential transfer scheme with a task affinity metric tailored for medical images. Considering the characteristics of medical image segmentation tasks, we analyze the image and label similarity between tasks and compute the task affinity scores, which assess the relatedness among tasks. Based on this, we select appropriate source tasks and develop an effective sequential transfer strategy by incorporating intermediate source tasks to gradually narrow the domain discrepancy and minimize the transfer cost. Thereby we identify the best sequential transfer path for the given target task. Extensive experiments on three MRI medical datasets, FeTS 2022, iSeg-2019, and WMH, demonstrate the efficacy of our method in finding the best source sequence. Compared with directly transferring from a single source task, the sequential transfer results underline a significant improvement in target task performance, achieving an average of 2.58% gain in terms of segmentation Dice score, notably, 6.00% for FeTS 2022. Code is available at the git repository.
The disparity in healthcare personnel expertise and medical resources across different regions of the world is a pressing social issue. Artificial intelligence technology offers new opportunities to alleviate this issue. Segment Anything Model (SAM), which excels in intelligent image segmentation, has demonstrated exceptional performance in medical monitoring and assisted diagnosis. Unfortunately, the huge computational and storage overhead of SAM poses significant challenges for deployment on resource-limited edge devices. Quantization is an effective solution for model compression; however, traditional methods rely heavily on original data for calibration, which raises widespread concerns about medical data privacy and security. In this paper, we propose a data-free quantization framework for SAM, called DFQ-SAM, which learns and calibrates quantization parameters without any original data, thus effectively preserving data privacy during model compression. Specifically, we propose pseudo-positive label evolution for segmentation, combined with patch similarity, to fully leverage the semantic and distribution priors in pre-trained models, which facilitates high-quality data synthesis as a substitute for real data. Furthermore, we introduce scale reparameterization to ensure the accuracy of low-bit quantization. We perform extensive segmentation experiments on various datasets, and DFQ-SAM consistently provides significant performance on low-bit quantization. DFQ-SAM eliminates the need for data transfer in cloud-edge collaboration, thereby protecting sensitive data from potential attacks. It enables secure, fast, and personalized healthcare services at the edge, which enhances system efficiency and optimizes resource allocation, and thus facilitating the pervasive application of artificial intelligence in worldwide healthcare.
The Segment Anything Model (SAM) is a foundational model for image segmentation tasks, known for its strong generalization across diverse applications. However, its impressive performance comes with significant computational and resource demands, making it challenging to deploy in resource-limited environments such as edge devices. To address this, a variety of SAM variants have been proposed to enhance efficiency while keeping accuracy. This survey provides the first comprehensive review of these efficient SAM variants. We begin by exploring the motivations driving this research. We then present core techniques used in SAM and model acceleration. This is followed by a detailed exploration of SAM acceleration strategies, categorized by approach, and a discussion of several future research directions. Finally, we offer a unified and extensive evaluation of these methods across various hardware, assessing their efficiency and accuracy on representative benchmarks, and providing a clear comparison of their overall performance.
Recently, there have been explorations of generalist segmentation models that can effectively tackle a variety of image segmentation tasks within a unified in-context learning framework. However, these methods still struggle with task ambiguity in in-context segmentation, as not all in-context examples can accurately convey the task information. In order to address this issue, we present SINE, a simple image Segmentation framework utilizing in-context examples. Our approach leverages a Transformer encoder-decoder structure, where the encoder provides high-quality image representations, and the decoder is designed to yield multiple task-specific output masks to effectively eliminate task ambiguity. Specifically, we introduce an In-context Interaction module to complement in-context information and produce correlations between the target image and the in-context example and a Matching Transformer that uses fixed matching and a Hungarian algorithm to eliminate differences between different tasks. In addition, we have further perfected the current evaluation system for in-context image segmentation, aiming to facilitate a holistic appraisal of these models. Experiments on various segmentation tasks show the effectiveness of the proposed method.
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.
The UNet architecture has transformed image segmentation. UNet's versatility and accuracy have driven its widespread adoption, significantly advancing fields reliant on machine learning problems with images. In this work, we give a clear and concise mathematical explanation of UNet. We explain what is the meaning and function of each of the components of UNet. We will show that UNet is solving a control problem. We decompose the control variables using multigrid methods. Then, operator-splitting techniques is used to solve the problem, whose architecture exactly recovers the UNet architecture. Our result shows that UNet is a one-step operator-splitting algorithm for the control problem.
Recently, the Segment Anything Model (SAM) has demonstrated promising segmentation capabilities in a variety of downstream segmentation tasks. However in the context of universal medical image segmentation there exists a notable performance discrepancy when directly applying SAM due to the domain gap between natural and 2D/3D medical data. In this work, we propose a dual-branch adapted SAM framework, named DB-SAM, that strives to effectively bridge this domain gap. Our dual-branch adapted SAM contains two branches in parallel: a ViT branch and a convolution branch. The ViT branch incorporates a learnable channel attention block after each frozen attention block, which captures domain-specific local features. On the other hand, the convolution branch employs a light-weight convolutional block to extract domain-specific shallow features from the input medical image. To perform cross-branch feature fusion, we design a bilateral cross-attention block and a ViT convolution fusion block, which dynamically combine diverse information of two branches for mask decoder. Extensive experiments on large-scale medical image dataset with various 3D and 2D medical segmentation tasks reveal the merits of our proposed contributions. On 21 3D medical image segmentation tasks, our proposed DB-SAM achieves an absolute gain of 8.8%, compared to a recent medical SAM adapter in the literature. The code and model are available at https://github.com/AlfredQin/DB-SAM.
U-Net is widely used in medical image segmentation due to its simple and flexible architecture design. To address the challenges of scale and complexity in medical tasks, several variants of U-Net have been proposed. In particular, methods based on Vision Transformer (ViT), represented by Swin UNETR, have gained widespread attention in recent years. However, these improvements often focus on the encoder, overlooking the crucial role of the decoder in optimizing segmentation details. This design imbalance limits the potential for further enhancing segmentation performance. To address this issue, we analyze the roles of various decoder components, including upsampling method, skip connection, and feature extraction module, as well as the shortcomings of existing methods. Consequently, we propose Swin DER (i.e., Swin UNETR Decoder Enhanced and Refined) by specifically optimizing the design of these three components. Swin DER performs upsampling using learnable interpolation algorithm called offset coordinate neighborhood weighted up sampling (Onsampling) and replaces traditional skip connection with spatial-channel parallel attention gate (SCP AG). Additionally, Swin DER introduces deformable convolution along with attention mechanism in the feature extraction module of the decoder. Our model design achieves excellent results, surpassing other state-of-the-art methods on both the Synapse and the MSD brain tumor segmentation task. Code is available at: https://github.com/WillBeanYang/Swin-DER
We develop confidence sets which provide spatial uncertainty guarantees for the output of a black-box machine learning model designed for image segmentation. To do so we adapt conformal inference to the imaging setting, obtaining thresholds on a calibration dataset based on the distribution of the maximum of the transformed logit scores within and outside of the ground truth masks. We prove that these confidence sets, when applied to new predictions of the model, are guaranteed to contain the true unknown segmented mask with desired probability. We show that learning appropriate score transformations on a learning dataset before performing calibration is crucial for optimizing performance. We illustrate and validate our approach on a polpys tumor dataset. To do so we obtain the logit scores from a deep neural network trained for polpys segmentation and show that using distance transformed scores to obtain outer confidence sets and the original scores for inner confidence sets enables tight bounds on tumor location whilst controlling the false coverage rate.
The proliferation of digital microscopy images, driven by advances in automated whole slide scanning, presents significant opportunities for biomedical research and clinical diagnostics. However, accurately annotating densely packed information in these images remains a major challenge. To address this, we introduce DiffKillR, a novel framework that reframes cell annotation as the combination of archetype matching and image registration tasks. DiffKillR employs two complementary neural networks: one that learns a diffeomorphism-invariant feature space for robust cell matching and another that computes the precise warping field between cells for annotation mapping. Using a small set of annotated archetypes, DiffKillR efficiently propagates annotations across large microscopy images, reducing the need for extensive manual labeling. More importantly, it is suitable for any type of pixel-level annotation. We will discuss the theoretical properties of DiffKillR and validate it on three microscopy tasks, demonstrating its advantages over existing supervised, semi-supervised, and unsupervised methods.
Convolutional neural networks (CNNs) have shown great effectiveness in medical image segmentation. However, they may be limited in modeling large inter-subject variations in organ shapes and sizes and exploiting global long-range contextual information. This is because CNNs typically employ convolutions with fixed-sized local receptive fields and lack the mechanisms to utilize global information. To address these limitations, we developed Dynamic Multi-Resolution Convolution (DMRC) and Dynamic Multi-Scale Convolution (DMSC) modules. Both modules enhance the representation capabilities of single convolutions to capture varying scaled features and global contextual information. This is achieved in the DMRC module by employing a convolutional filter on images with different resolutions and subsequently utilizing dynamic mechanisms to model global inter-dependencies between features. In contrast, the DMSC module extracts features at different scales by employing convolutions with different kernel sizes and utilizing dynamic mechanisms to extract global contextual information. The utilization of convolutions with different kernel sizes in the DMSC module may increase computational complexity. To lessen this burden, we propose to use a lightweight design for convolution layers with a large kernel size. Thus, DMSC and DMRC modules are designed as lightweight drop-in replacements for single convolutions, and they can be easily integrated into general CNN architectures for end-to-end training. The segmentation network was proposed by incorporating our DMSC and DMRC modules into a standard U-Net architecture, termed Dynamic Multi-scale and Multi-resolution Convolution network (DMC-Net). The results demonstrate that our proposed DMSC and DMRC can enhance the representation capabilities of single convolutions and improve segmentation accuracy.
In the domain of battery research, the processing of high-resolution microscopy images is a challenging task, as it involves dealing with complex images and requires a prior understanding of the components involved. The utilization of deep learning methodologies for image analysis has attracted considerable interest in recent years, with multiple investigations employing such techniques for image segmentation and analysis within the realm of battery research. However, the automated analysis of high-resolution microscopy images for detecting phases and components in composite materials is still an underexplored area. This work proposes a novel workflow for detecting components and phase segmentation from raw high resolution transmission electron microscopy (TEM) images using a trained U-Net segmentation model. The developed model can expedite the detection of components and phase segmentation, diminishing the temporal and cognitive demands associated with scrutinizing an extensive array of TEM images, thereby mitigating the potential for human errors. This approach presents a novel and efficient image analysis approach with broad applicability beyond the battery field and holds potential for application in other related domains characterized by phase and composition distribution, such as alloy production.
The evaluation of segmentation performance is a common task in biomedical image analysis, with its importance emphasized in the recently released metrics selection guidelines and computing frameworks. To quantitatively evaluate the alignment of two segmentations, researchers commonly resort to counting metrics, such as the Dice similarity coefficient, or distance-based metrics, such as the Hausdorff distance, which are usually computed by publicly available open-source tools with an inherent assumption that these tools provide consistent results. In this study we questioned this assumption, and performed a systematic implementation analysis along with quantitative experiments on real-world clinical data to compare 11 open-source tools for distance-based metrics computation against our highly accurate mesh-based reference implementation. The results revealed that statistically significant differences among all open-source tools are both surprising and concerning, since they question the validity of existing studies. Besides identifying the main sources of variation, we also provide recommendations for distance-based metrics computation.