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arXiv2020

Robustness study of noisy annotation in deep learning based medical image segmentation

Partly due to the use of exhaustive-annotated data, deep networks have achieved impressive performance on medical image segmentation. Medical imaging data paired with noisy annotation are, however, ubiquitous, but little is known about the effect of noisy annotation on deep learning-based medical image segmentation. We studied the effects of noisy annotation in the context of mandible segmentation from CT images. First, 202 images of Head and Neck cancer patients were collected from our clinical database, where the organs-at-risk were annotated by one of 12 planning dosimetrists. The mandibles were roughly annotated as the planning avoiding structure. Then, mandible labels were checked and corrected by a physician to get clean annotations. At last, by varying the ratios of noisy labels in the training data, deep learning-based segmentation models were trained, one for each ratio. In general, a deep network trained with noisy labels had worse segmentation results than that trained with clean labels, and fewer noisy labels led to better segmentation. When using 20% or less noisy cases for training, no significant difference was found on the prediction performance between the models trained by noisy or clean. This study suggests that deep learning-based medical image segmentation is robust to noisy annotations to some extent. It also highlights the importance of labeling quality in deep learning

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arXiv2024

Leveraging Adaptive Implicit Representation Mapping for Ultra High-Resolution Image Segmentation

Implicit representation mapping (IRM) can translate image features to any continuous resolution, showcasing its potent capability for ultra-high-resolution image segmentation refinement. Current IRM-based methods for refining ultra-high-resolution image segmentation often rely on CNN-based encoders to extract image features and apply a Shared Implicit Representation Mapping Function (SIRMF) to convert pixel-wise features into segmented results. Hence, these methods exhibit two crucial limitations. Firstly, the CNN-based encoder may not effectively capture long-distance information, resulting in a lack of global semantic information in the pixel-wise features. Secondly, SIRMF is shared across all samples, which limits its ability to generalize and handle diverse inputs. To address these limitations, we propose a novel approach that leverages the newly proposed Adaptive Implicit Representation Mapping (AIRM) for ultra-high-resolution Image Segmentation. Specifically, the proposed method comprises two components: (1) the Affinity Empowered Encoder (AEE), a robust feature extractor that leverages the benefits of the transformer architecture and semantic affinity to model long-distance features effectively, and (2) the Adaptive Implicit Representation Mapping Function (AIRMF), which adaptively translates pixel-wise features without neglecting the global semantic information, allowing for flexible and precise feature translation. We evaluated our method on the commonly used ultra-high-resolution segmentation refinement datasets, i.e., BIG and PASCAL VOC 2012. The extensive experiments demonstrate that our method outperforms competitors by a large margin. The code is provided in supplementary material.

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arXiv2021

PoissonSeg: Semi-Supervised Few-Shot Medical Image Segmentation via Poisson Learning

The application of deep learning to medical image segmentation has been hampered due to the lack of abundant pixel-level annotated data. Few-shot Semantic Segmentation (FSS) is a promising strategy for breaking the deadlock. However, a high-performing FSS model still requires sufficient pixel-level annotated classes for training to avoid overfitting, which leads to its performance bottleneck in medical image segmentation due to the unmet need for annotations. Thus, semi-supervised FSS for medical images is accordingly proposed to utilize unlabeled data for further performance improvement. Nevertheless, existing semi-supervised FSS methods has two obvious defects: (1) neglecting the relationship between the labeled and unlabeled data; (2) using unlabeled data directly for end-to-end training leads to degenerated representation learning. To address these problems, we propose a novel semi-supervised FSS framework for medical image segmentation. The proposed framework employs Poisson learning for modeling data relationship and propagating supervision signals, and Spatial Consistency Calibration for encouraging the model to learn more coherent representations. In this process, unlabeled samples do not involve in end-to-end training, but provide supervisory information for query image segmentation through graph-based learning. We conduct extensive experiments on three medical image segmentation datasets (i.e. ISIC skin lesion segmentation, abdominal organs segmentation for MRI and abdominal organs segmentation for CT) to demonstrate the state-of-the-art performance and broad applicability of the proposed framework.

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arXiv2023

LViT: Language meets Vision Transformer in Medical Image Segmentation

Deep learning has been widely used in medical image segmentation and other aspects. However, the performance of existing medical image segmentation models has been limited by the challenge of obtaining sufficient high-quality labeled data due to the prohibitive data annotation cost. To alleviate this limitation, we propose a new text-augmented medical image segmentation model LViT (Language meets Vision Transformer). In our LViT model, medical text annotation is incorporated to compensate for the quality deficiency in image data. In addition, the text information can guide to generate pseudo labels of improved quality in the semi-supervised learning. We also propose an Exponential Pseudo label Iteration mechanism (EPI) to help the Pixel-Level Attention Module (PLAM) preserve local image features in semi-supervised LViT setting. In our model, LV (Language-Vision) loss is designed to supervise the training of unlabeled images using text information directly. For evaluation, we construct three multimodal medical segmentation datasets (image + text) containing X-rays and CT images. Experimental results show that our proposed LViT has superior segmentation performance in both fully-supervised and semi-supervised setting. The code and datasets are available at https://github.com/HUANGLIZI/LViT.

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arXiv2025

Towards Reliable Medical Image Segmentation by Modeling Evidential Calibrated Uncertainty

Medical image segmentation is critical for disease diagnosis and treatment assessment. However, concerns regarding the reliability of segmentation regions persist among clinicians, mainly attributed to the absence of confidence assessment, robustness, and calibration to accuracy. To address this, we introduce DEviS, an easily implementable foundational model that seamlessly integrates into various medical image segmentation networks. DEviS not only enhances the calibration and robustness of baseline segmentation accuracy but also provides high-efficiency uncertainty estimation for reliable predictions. By leveraging subjective logic theory, we explicitly model probability and uncertainty for medical image segmentation. Here, the Dirichlet distribution parameterizes the distribution of probabilities for different classes of the segmentation results. To generate calibrated predictions and uncertainty, we develop a trainable calibrated uncertainty penalty. Furthermore, DEviS incorporates an uncertainty-aware filtering module, which designs the metric of uncertainty-calibrated error to filter out-of-distribution data. We conducted validation studies on publicly available datasets, including ISIC2018, KiTS2021, LiTS2017, and BraTS2019, to assess the accuracy and robustness of different backbone segmentation models enhanced by DEviS, as well as the efficiency and reliability of uncertainty estimation.

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arXiv2025

CADFormer: Fine-Grained Cross-modal Alignment and Decoding Transformer for Referring Remote Sensing Image Segmentation

Referring Remote Sensing Image Segmentation (RRSIS) is a challenging task, aiming to segment specific target objects in remote sensing (RS) images based on a given language expression. Existing RRSIS methods typically employ coarse-grained unidirectional alignment approaches to obtain multimodal features, and they often overlook the critical role of language features as contextual information during the decoding process. Consequently, these methods exhibit weak object-level correspondence between visual and language features, leading to incomplete or erroneous predicted masks, especially when handling complex expressions and intricate RS image scenes. To address these challenges, we propose a fine-grained cross-modal alignment and decoding Transformer, CADFormer, for RRSIS. Specifically, we design a semantic mutual guidance alignment module (SMGAM) to achieve both vision-to-language and language-to-vision alignment, enabling comprehensive integration of visual and textual features for fine-grained cross-modal alignment. Furthermore, a textual-enhanced cross-modal decoder (TCMD) is introduced to incorporate language features during decoding, using refined textual information as context to enhance the relationship between cross-modal features. To thoroughly evaluate the performance of CADFormer, especially for inconspicuous targets in complex scenes, we constructed a new RRSIS dataset, called RRSIS-HR, which includes larger high-resolution RS image patches and semantically richer language expressions. Extensive experiments on the RRSIS-HR dataset and the popular RRSIS-D dataset demonstrate the effectiveness and superiority of CADFormer. Datasets and source codes will be available at https://github.com/zxk688.

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arXiv2016

3D Ultrasound image segmentation: A Survey

Three-dimensional Ultrasound image segmentation methods are surveyed in this paper. The focus of this report is to investigate applications of these techniques and a review of the original ideas and concepts. Although many two-dimensional image segmentation in the literature have been considered as a three-dimensional approach by mistake but we review them as a three-dimensional technique. We select the studies that have addressed the problem of medical three-dimensional Ultrasound image segmentation utilizing their proposed techniques. The evaluation methods and comparison between them are presented and tabulated in terms of evaluation techniques, interactivity, and robustness.

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arXiv2021

Topology-Preserving 3D Image Segmentation Based On Hyperelastic Regularization

Image segmentation is to extract meaningful objects from a given image. For degraded images due to occlusions, obscurities or noises, the accuracy of the segmentation result can be severely affected. To alleviate this problem, prior information about the target object is usually introduced. In [10], a topology-preserving registration-based segmentation model was proposed, which is restricted to segment 2D images only. In this paper, we propose a novel 3D topology-preserving registration-based segmentation model with the hyperelastic regularization, which can handle both 2D and 3D images. The existence of the solution of the proposed model is established. We also propose a converging iterative scheme to solve the proposed model. Numerical experiments have been carried out on the synthetic and real images, which demonstrate the effectiveness of our proposed model.

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arXiv2022

ProSFDA: Prompt Learning based Source-free Domain Adaptation for Medical Image Segmentation

The domain discrepancy existed between medical images acquired in different situations renders a major hurdle in deploying pre-trained medical image segmentation models for clinical use. Since it is less possible to distribute training data with the pre-trained model due to the huge data size and privacy concern, source-free unsupervised domain adaptation (SFDA) has recently been increasingly studied based on either pseudo labels or prior knowledge. However, the image features and probability maps used by pseudo label-based SFDA and the consistent prior assumption and the prior prediction network used by prior-guided SFDA may become less reliable when the domain discrepancy is large. In this paper, we propose a \textbf{Pro}mpt learning based \textbf{SFDA} (\textbf{ProSFDA}) method for medical image segmentation, which aims to improve the quality of domain adaption by minimizing explicitly the domain discrepancy. Specifically, in the prompt learning stage, we estimate source-domain images via adding a domain-aware prompt to target-domain images, then optimize the prompt via minimizing the statistic alignment loss, and thereby prompt the source model to generate reliable predictions on (altered) target-domain images. In the feature alignment stage, we also align the features of target-domain images and their styles-augmented counterparts to optimize the source model, and hence push the model to extract compact features. We evaluate our ProSFDA on two multi-domain medical image segmentation benchmarks. Our results indicate that the proposed ProSFDA outperforms substantially other SFDA methods and is even comparable to UDA methods. Code will be available at \url{https://github.com/ShishuaiHu/ProSFDA}.

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arXiv2025

Few-Shot Adaptation of Training-Free Foundation Model for 3D Medical Image Segmentation

Vision foundation models have achieved remarkable progress across various image analysis tasks. In the image segmentation task, foundation models like the Segment Anything Model (SAM) enable generalizable zero-shot segmentation through user-provided prompts. However, SAM primarily trained on natural images, lacks the domain-specific expertise of medical imaging. This limitation poses challenges when applying SAM to medical image segmentation, including the need for extensive fine-tuning on specialized medical datasets and a dependency on manual prompts, which are both labor-intensive and require intervention from medical experts. This work introduces the Few-shot Adaptation of Training-frEe SAM (FATE-SAM), a novel method designed to adapt the advanced Segment Anything Model 2 (SAM2) for 3D medical image segmentation. FATE-SAM reassembles pre-trained modules of SAM2 to enable few-shot adaptation, leveraging a small number of support examples to capture anatomical knowledge and perform prompt-free segmentation, without requiring model fine-tuning. To handle the volumetric nature of medical images, we incorporate a Volumetric Consistency mechanism that enhances spatial coherence across 3D slices. We evaluate FATE-SAM on multiple medical imaging datasets and compare it with supervised learning methods, zero-shot SAM approaches, and fine-tuned medical SAM methods. Results show that FATE-SAM delivers robust and accurate segmentation while eliminating the need for large annotated datasets and expert intervention. FATE-SAM provides a practical, efficient solution for medical image segmentation, making it more accessible for clinical applications.

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arXiv2026

Exploiting DINOv3-Based Self-Supervised Features for Robust Few-Shot Medical Image Segmentation

Deep learning-based automatic medical image segmentation plays a critical role in clinical diagnosis and treatment planning but remains challenging in few-shot scenarios due to the scarcity of annotated training data. Recently, self-supervised foundation models such as DINOv3, which were trained on large natural image datasets, have shown strong potential for dense feature extraction that can help with the few-shot learning challenge. Yet, their direct application to medical images is hindered by domain differences. In this work, we propose DINO-AugSeg, a novel framework that leverages DINOv3 features to address the few-shot medical image segmentation challenge. Specifically, we introduce WT-Aug, a wavelet-based feature-level augmentation module that enriches the diversity of DINOv3-extracted features by perturbing frequency components, and CG-Fuse, a contextual information-guided fusion module that exploits cross-attention to integrate semantic-rich low-resolution features with spatially detailed high-resolution features. Extensive experiments on six public benchmarks spanning five imaging modalities, including MRI, CT, ultrasound, endoscopy, and dermoscopy, demonstrate that DINO-AugSeg consistently outperforms existing methods under limited-sample conditions. The results highlight the effectiveness of incorporating wavelet-domain augmentation and contextual fusion for robust feature representation, suggesting DINO-AugSeg as a promising direction for advancing few-shot medical image segmentation. Code and data will be made available on https://github.com/apple1986/DINO-AugSeg.

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arXiv2024

I-MedSAM: Implicit Medical Image Segmentation with Segment Anything

With the development of Deep Neural Networks (DNNs), many efforts have been made to handle medical image segmentation. Traditional methods such as nnUNet train specific segmentation models on the individual datasets. Plenty of recent methods have been proposed to adapt the foundational Segment Anything Model (SAM) to medical image segmentation. However, they still focus on discrete representations to generate pixel-wise predictions, which are spatially inflexible and scale poorly to higher resolution. In contrast, implicit methods learn continuous representations for segmentation, which is crucial for medical image segmentation. In this paper, we propose I-MedSAM, which leverages the benefits of both continuous representations and SAM, to obtain better cross-domain ability and accurate boundary delineation. Since medical image segmentation needs to predict detailed segmentation boundaries, we designed a novel adapter to enhance the SAM features with high-frequency information during Parameter-Efficient Fine-Tuning (PEFT). To convert the SAM features and coordinates into continuous segmentation output, we utilize Implicit Neural Representation (INR) to learn an implicit segmentation decoder. We also propose an uncertainty-guided sampling strategy for efficient learning of INR. Extensive evaluations on 2D medical image segmentation tasks have shown that our proposed method with only 1.6M trainable parameters outperforms existing methods including discrete and implicit methods. The code will be available at: https://github.com/ucwxb/I-MedSAM.

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arXiv2025

On Splitting Lightweight Semantic Image Segmentation for Wireless Communications

Semantic communication represents a promising technique towards reducing communication costs, especially when dealing with image segmentation, but it still lacks a balance between computational efficiency and bandwidth requirements while maintaining high image segmentation accuracy, particularly in resource-limited environments and changing channel conditions. On the other hand, the more complex and larger semantic image segmentation models become, the more stressed the devices are when processing data. This paper proposes a novel approach to implementing semantic communication based on splitting the semantic image segmentation process between a resource constrained transmitter and the receiver. This allows saving bandwidth by reducing the transmitted data while maintaining the accuracy of the semantic image segmentation. Additionally, it reduces the computational requirements at the resource constrained transmitter compared to doing all the semantic image segmentation in the transmitter. The proposed approach is evaluated by means of simulation-based experiments in terms of different metrics such as computational resource usage, required bit rate and segmentation accuracy. The results when comparing the proposal with the full semantic image segmentation in the transmitter show that up to 72% of the bit rate was reduced in the transmission process. In addition, the computational load of the transmitter is reduced by more than 19%. This reflects the interest of this technique for its application in communication systems, particularly in the upcoming 6G systems.

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arXiv2025

Diversity-enhanced Collaborative Mamba for Semi-supervised Medical Image Segmentation

Acquiring high-quality annotated data for medical image segmentation is tedious and costly. Semi-supervised segmentation techniques alleviate this burden by leveraging unlabeled data to generate pseudo labels. Recently, advanced state space models, represented by Mamba, have shown efficient handling of long-range dependencies. This drives us to explore their potential in semi-supervised medical image segmentation. In this paper, we propose a novel Diversity-enhanced Collaborative Mamba framework (namely DCMamba) for semi-supervised medical image segmentation, which explores and utilizes the diversity from data, network, and feature perspectives. Firstly, from the data perspective, we develop patch-level weak-strong mixing augmentation with Mamba's scanning modeling characteristics. Moreover, from the network perspective, we introduce a diverse-scan collaboration module, which could benefit from the prediction discrepancies arising from different scanning directions. Furthermore, from the feature perspective, we adopt an uncertainty-weighted contrastive learning mechanism to enhance the diversity of feature representation. Experiments demonstrate that our DCMamba significantly outperforms other semi-supervised medical image segmentation methods, e.g., yielding the latest SSM-based method by 6.69% on the Synapse dataset with 20% labeled data.

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arXiv2023

Post-Train Adaptive U-Net for Image Segmentation

Typical neural network architectures used for image segmentation cannot be changed without further training. This is quite limiting as the network might not only be executed on a powerful server, but also on a mobile or edge device. Adaptive neural networks offer a solution to the problem by allowing certain adaptivity after the training process is complete. In this work for the first time, we apply Post-Train Adaptive (PTA) approach to the task of image segmentation. We introduce U-Net+PTA neural network, which can be trained once, and then adapted to different device performance categories. The two key components of the approach are PTA blocks and PTA-sampling training strategy. The post-train configuration can be done at runtime on any inference device including mobile. Also, the PTA approach has allowed to improve image segmentation Dice score on the CamVid dataset. The final trained model can be switched at runtime between 6 PTA configurations, which differ by inference time and quality. Importantly, all of the configurations have better quality than the original U-Net (No PTA) model.

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arXiv2015

Evolving Fuzzy Image Segmentation with Self-Configuration

Current image segmentation techniques usually require that the user tune several parameters in order to obtain maximum segmentation accuracy, a computationally inefficient approach, especially when a large number of images must be processed sequentially in daily practice. The use of evolving fuzzy systems for designing a method that automatically adjusts parameters to segment medical images according to the quality expectation of expert users has been proposed recently (Evolving fuzzy image segmentation EFIS). However, EFIS suffers from a few limitations when used in practice mainly due to some fixed parameters. For instance, EFIS depends on auto-detection of the object of interest for feature calculation, a task that is highly application-dependent. This shortcoming limits the applicability of EFIS, which was proposed with the ultimate goal of offering a generic but adjustable segmentation scheme. In this paper, a new version of EFIS is proposed to overcome these limitations. The new EFIS, called self-configuring EFIS (SC-EFIS), uses available training data to self-estimate the parameters that are fixed in EFIS. As well, the proposed SC-EFIS relies on a feature selection process that does not require auto-detection of an ROI. The proposed SC-EFIS was evaluated using the same segmentation algorithms and the same dataset as for EFIS. The results show that SC-EFIS can provide the same results as EFIS but with a higher level of automation.

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arXiv2022

Less Is More: A Comparison of Active Learning Strategies for 3D Medical Image Segmentation

Since labeling medical image data is a costly and labor-intensive process, active learning has gained much popularity in the medical image segmentation domain in recent years. A variety of active learning strategies have been proposed in the literature, but their effectiveness is highly dependent on the dataset and training scenario. To facilitate the comparison of existing strategies and provide a baseline for evaluating novel strategies, we evaluate the performance of several well-known active learning strategies on three datasets from the Medical Segmentation Decathlon. Additionally, we consider a strided sampling strategy specifically tailored to 3D image data. We demonstrate that both random and strided sampling act as strong baselines and discuss the advantages and disadvantages of the studied methods. To allow other researchers to compare their work to our results, we provide an open-source framework for benchmarking active learning strategies on a variety of medical segmentation datasets.

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arXiv2016

Image Segmentation Using Hierarchical Merge Tree

This paper investigates one of the most fundamental computer vision problems: image segmentation. We propose a supervised hierarchical approach to object-independent image segmentation. Starting with over-segmenting superpixels, we use a tree structure to represent the hierarchy of region merging, by which we reduce the problem of segmenting image regions to finding a set of label assignment to tree nodes. We formulate the tree structure as a constrained conditional model to associate region merging with likelihoods predicted using an ensemble boundary classifier. Final segmentations can then be inferred by finding globally optimal solutions to the model efficiently. We also present an iterative training and testing algorithm that generates various tree structures and combines them to emphasize accurate boundaries by segmentation accumulation. Experiment results and comparisons with other very recent methods on six public data sets demonstrate that our approach achieves the state-of-the-art region accuracy and is very competitive in image segmentation without semantic priors.

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