An efficient neural network based method for medical image segmentation

Unsupervised domain adaption (UDA), which aims to enhance the segmentation performance of deep models on unlabeled data, has recently drawn much attention. In this paper, we propose a novel UDA method (namely DLaST) for medical image segmentation via disentanglement learning and self-training. Disentanglement learning factorizes an image into domain-invariant anatomy and domain-specific modality components. To make the best of disentanglement learning, we propose a novel shape constraint to boost the adaptation performance. The self-training strategy further adaptively improves the segmentation performance of the model for the target domain through adversarial learning and pseudo label, which implicitly facilitates feature alignment in the anatomy space. Experimental results demonstrate that the proposed method outperforms the state-of-the-art UDA methods for medical image segmentation on three public datasets, i.e., a cardiac dataset, an abdominal dataset and a brain dataset. The code will be released soon.

Aggregating multi-level feature representation plays a critical role in achieving robust volumetric medical image segmentation, which is important for the auxiliary diagnosis and treatment. Unlike the recent neural architecture search (NAS) methods that typically searched the optimal operators in each network layer, but missed a good strategy to search for feature aggregations, this paper proposes a novel NAS method for 3D medical image segmentation, named UXNet, which searches both the scale-wise feature aggregation strategies as well as the block-wise operators in the encoder-decoder network. UXNet has several appealing benefits. (1) It significantly improves flexibility of the classical UNet architecture, which only aggregates feature representations of encoder and decoder in equivalent resolution. (2) A continuous relaxation of UXNet is carefully designed, enabling its searching scheme performed in an efficient differentiable manner. (3) Extensive experiments demonstrate the effectiveness of UXNet compared with recent NAS methods for medical image segmentation. The architecture discovered by UXNet outperforms existing state-of-the-art models in terms of Dice on several public 3D medical image segmentation benchmarks, especially for the boundary locations and tiny tissues. The searching computational complexity of UXNet is cheap, enabling to search a network with best performance less than 1.5 days on two TitanXP GPUs.

Ultrasound (US) image segmentation is a difficult task because of its heavy speckle noise, low quality and blurry boundaries. In this paper, a new neural network based method is proposed for ultrasound images segmentation. A modified self organizing map (SOM) network, named finite impulse response SOM (FIR-SOM), is utilized to segment ultrasound images. A two dimensional (2D) discrete wavelet transform (DWT) is used to build the input feature space of the network. Experimental results show that FIR-SOM discovers the pattern of the input image properly and is robust against noise. Segmentation results of breast ultrasound images (BUS) demonstrate that there is a strong correlation between tumor region selected by a physician and the tumor region segmented by our proposed method.

Dense-sparse representation matters: A point-based method for volumetric medical image segmentation

A wavelet transform-based image segmentation method

Automatic superpixel-based segmentation method for breast ultrasound images

Medical image segmentation methods are generally designed as fully-supervised to guarantee model performance, which requires a significant amount of expert annotated samples that are high-cost and laborious. Semi-supervised image segmentation can alleviate the problem by utilizing a large number of unlabeled images along with limited labeled images. However, learning a robust representation from numerous unlabeled images remains challenging due to potential noise in pseudo labels and insufficient class separability in feature space, which undermines the performance of current semi-supervised segmentation approaches. To address the issues above, we propose a novel semi-supervised segmentation method named as Rectified Contrastive Pseudo Supervision (RCPS), which combines a rectified pseudo supervision and voxel-level contrastive learning to improve the effectiveness of semi-supervised segmentation. Particularly, we design a novel rectification strategy for the pseudo supervision method based on uncertainty estimation and consistency regularization to reduce the noise influence in pseudo labels. Furthermore, we introduce a bidirectional voxel contrastive loss in the network to ensure intra-class consistency and inter-class contrast in feature space, which increases class separability in the segmentation. The proposed RCPS segmentation method has been validated on two public datasets and an in-house clinical dataset. Experimental results reveal that the proposed method yields better segmentation performance compared with the state-of-the-art methods in semi-supervised medical image segmentation. The source code is available at https://github.com/hsiangyuzhao/RCPS.

Recently, we introduced a novel Deep Learning (DL) based (semi-)automatic method for medical image segmentation. Unlike classical DL segmentation methods, it produces multiple segmentation variants (reflecting the variation of manual segmentations) instead of just one. Potentially, with this approach, there is a higher chance that a clinician prefers one of automatically produced segmentation variants. This work focuses on evaluating this method on prostate segmentation in MRI scans used for brachytherapy and investigating its potential clinical usefulness. Three experienced radiation oncologists graded (per-slice and per-scan) segmentations produced by our method, reference segmentations (manually created and used for brachytherapy treatment planning) and segmentations produced by a classical DL method. The study was retrospective and the way the segmentation was generated (our method, classical DL method, or manually) was blinded for the clinicians. The grades reflect the amount of manual correction required. Additionally, the clinicians were asked to rank segmentations to evaluate which one is preferred for each scan. The study was performed on 13 prostate cancer patients. Segmentations produced by our method are graded as requiring no manual correction in 292/576 (51%) slices compared to 240/576 (42%) slices in the case of the segmentations produced by a classical DL method. Furthermore, in fewer slices, 38 (6.6%) vs. 48 (8.3%), segmentations by our method were graded as unacceptable. Our study has demonstrated that deep-learning-based segmentation methods can produce high-quality segmentations. Our method was evaluated better than a classical DL method, indicating the potential for integration into clinical practice.

Segmentation of medical images is an important step in many clinical and diagnostic imaging applications. Medical images present many challenges for automated segmentation including poor contrast at tissue boundaries. Traditional segmentation methods based solely on information from the image do not work well in such cases. Statistical shape information for objects in medical images are easy to obtain. In this paper, we propose a graph cuts-based segmentation method for medical images that incorporates statistical shape priors to increase robustness. Our proposed method is able to deal with complex shapes and shape variations while taking advantage of the globally efficient optimization by graph cuts. We demonstrate the effectiveness of our method on kidney images without strong boundaries.

Medical image segmentation is a fundamental task in medical image analysis, playing a crucial role in disease diagnosis, treatment planning, and clinical decision-making. Accurate segmentation of anatomical structures, such as blood vessels, organs, and lesions, is essential for reliable medical interpretations. However, existing segmentation models often face challenges in effectively capturing both local and global features within medical images. Traditional convolutional neural networks (CNNs) excel at extracting fine-grained local features but struggle to model long-range dependencies due to their limited receptive fields. Conversely, transformer-based models can capture global contextual relationships but often fail to preserve detailed local structures, leading to suboptimal segmentation performance. The purpose of this study is to develop SEFormer, a novel hybrid network that integrates SENet, ResNet, and Transformer to enhance medical image segmentation. SEFormer aims to effectively capture both local and global features, addressing the limitations of traditional CNNs and transformer-based models.SENet is incorporated to recalibrate feature maps by adaptively emphasizing informative features, thereby compensating for the global representation limitations of CNNs. Meanwhile, the ResNet backbone ensures deep feature extraction while maintaining computational efficiency. Additionally, the Transformer module is introduced to capture long-range dependencies and enhance contextual awareness, complementing the local feature extraction capabilities of CNNs. This hybrid approach allows SEFormer to balance fine-grained spatial details with broader contextual information, leading to more precise segmentation results.Furthermore, to mitigate information loss during feature extraction and ensure a more complete and hierarchical representation of image information, we introduce a feature pyramid structure inspired by multi-scale image pyramid models. By progressively increasing the receptive field across different scales and employing skip connections, SEFormer effectively fuses multi-scale local and global features at each stage of the pyramid. This hierarchical fusion mechanism ensures a richer and more robust feature representation, which is particularly beneficial for segmenting complex medical structures such as blood vessels. We evaluate SEFormer on the CHASE_DB1 dataset, a widely used benchmark for retinal vessel segmentation. Experimental results demonstrate that SEFormer outperforms existing state-of-the-art segmentation methods, achieving a 3.25% improvement in segmentation accuracy. Additionally, we conduct ablation studies to verify the contributions of different components within SEFormer. The results show that incorporating SENet enhances feature recalibration and channel attention, while the Transformer module significantly improves global context awareness. The feature pyramid structure further contributes to performance gains by ensuring a multi-scale representation of vascular structures. Compared to conventional CNN-based methods, our approach achieves better segmentation accuracy with improved robustness to variations in vessel thickness, noise, and image contrast. Furthermore, SEFormer maintains computational efficiency, making it suitable for real-world clinical applications where both accuracy and processing speed are critical. SEFormer provides an efficient and accurate approach for medical image segmentation by leveraging the complementary strengths of CNNs, SENet, and Transformers while integrating a feature pyramid structure to maximize feature representation. Future research directions include extending SEFormer to other medical imaging modalities, such as CT and MRI scans, as well as exploring further optimization techniques to reduce computational costs while maintaining high segmentation performance. Additionally, integrating SEFormer with active learning frameworks could further improve segmentation performance by leveraging expert-annotated data more efficiently.

Breast lesions segmentation is an important step of computer-aided diagnosis system, and it has attracted much attention. However, accurate segmentation of malignant breast lesions is a challenging task due to the effects of heterogeneous structure and similar intensity distributions. In this paper, a novel bidirectional aware guidance network (BAGNet) is proposed to segment the malignant lesion from breast ultrasound images. Specifically, the bidirectional aware guidance network is used to capture the context between global (low-level) and local (high-level) features from the input coarse saliency map. The introduction of the global feature map can reduce the interference of surrounding tissue (background) on the lesion regions. To evaluate the segmentation performance of the network, we compared with several state-of-the-art medical image segmentation methods on the public breast ultrasound dataset using six commonly used evaluation metrics. Extensive experimental results indicate that our method achieves the most competitive segmentation results on malignant breast ultrasound images.

We systematically evaluate a Deep Learning model in a 3D medical image segmentation task. With our model, we address the flaws of manual segmentation: high inter-rater contouring variability and time consumption of the contouring process. The main extension over the existing evaluations is the careful and detailed analysis that could be further generalized on other medical image segmentation tasks. Firstly, we analyze the changes in the inter-rater detection agreement. We show that the model reduces the number of detection disagreements by [Formula: see text] [Formula: see text]. Secondly, we show that the model improves the inter-rater contouring agreement from [Formula: see text] to [Formula: see text] surface Dice Score [Formula: see text]. Thirdly, we show that the model accelerates the delineation process between [Formula: see text] and [Formula: see text] times [Formula: see text]. Finally, we design the setup of the clinical experiment to either exclude or estimate the evaluation biases; thus, preserving the significance of the results. Besides the clinical evaluation, we also share intuitions and practical ideas for building an efficient DL-based model for 3D medical image segmentation.

Histogram-based level set methods for medical image segmentation

Statistical shape modelling is an efficient and robust method for medical image segmentation in computer-aided diagnosis. The key step in building a statistical shape model is to find corresponding landmarks in each instance of a training set. In this paper, a novel landmark correspondence estimation method that uses edge collapse surface simplification and the sphere registration is proposed. All the landmarks are selected and transformed by spherical conformal mapping from the instances of the training set and the associated correspondence are automatically found on the spheres. We applied our method on 21 cases of 3-D right lung shapes. The results of image segmentation experiment indicate that our method has a positive influence on the accuracy of segmentation result.

Active learning is considered a viable solution to alleviate the contradiction between the high dependency of deep learning-based segmentation methods on annotated data and the expensive pixel-level annotation cost of medical images. However, most existing methods suffer from unreliable uncertainty assessment and the struggle to balance diversity and informativeness, leading to poor performance in segmentation tasks. In response, we propose an efficient Predictive Accuracy-based Active Learning (PAAL) method for medical image segmentation, first introducing predictive accuracy to define uncertainty. Specifically, PAAL mainly consists of an Accuracy Predictor (AP) and a Weighted Polling Strategy (WPS). The former is an attached learnable module that can accurately predict the segmentation accuracy of unlabeled samples relative to the target model with the predicted posterior probability. The latter provides an efficient hybrid querying scheme by combining predicted accuracy and feature representation, aiming to ensure the uncertainty and diversity of the acquired samples. Extensive experiment results on multiple datasets demonstrate the superiority of PAAL. PAAL achieves comparable accuracy to fully annotated data while reducing annotation costs by approximately 50% to 80%, showcasing significant potential in clinical applications. The code is available at https://github.com/shijun18/PAAL-MedSeg.