Medical Image Segmentation Methods Research Articles

A Hybrid CNN-TransXNet Approach for Advanced Glomerular Segmentation in Renal Histology Imaging

In the specialized field of renal histology, precise segmentation of glomeruli in microscopic images is crucial for accurate clinical diagnosis and pathological analysis. Facing the challenge of discerning complex visual features, such as shape, texture, and size within these images, we introduce a novel segmentation model that innovatively combines convolutional neural networks (CNNs) with the advanced TransXNet block, specifically tailored for glomerular segmentation. This innovative model is designed to capture the intricate details and broader contextual features within the images, ensuring a comprehensive and precise segmentation process. The model's architecture unfolds in two primary phases: the down-sampling phase, which utilizes CNNs structures within the TransXNet block for meticulous extraction of detailed features, and the up-sampling phase, which employs CNNs deconvolution techniques to restore spatial resolution and enhance macroscopic feature representation. A critical innovation in our model is the implementation of residual connections between these two phases, which facilitate the seamless integration of features and minimize loss of precision during image reconstruction. Experimental results demonstrate a significant improvement in our model’s performance compared to existing medical image segmentation methods. We report enhancements in mean Pixel Accuracy (mPA) and mean Intersection over Union (mIoU), with increases of approximately 3–5% and 3–8%, respectively. Additionally, the segmented outputs exhibit higher subjective visual quality with fewer noise artifacts. These findings suggest that our model offers promising applications in the segmentation of medical microscopic images, marking a significant contribution to the domain.

Hi-gMISnet: generalized medical image segmentation using DWT based multilayer fusion and dual mode attention into high resolution pGAN

Objective. Automatic medical image segmentation is crucial for accurately isolating target tissue areas in the image from background tissues, facilitating precise diagnoses and procedures. While the proliferation of publicly available clinical datasets led to the development of deep learning-based medical image segmentation methods, a generalized, accurate, robust, and reliable approach across diverse imaging modalities remains elusive. Approach. This paper proposes a novel high-resolution parallel generative adversarial network (pGAN)-based generalized deep learning method for automatic segmentation of medical images from diverse imaging modalities. The proposed method showcases better performance and generalizability by incorporating novel components such as partial hybrid transfer learning, discrete wavelet transform (DWT)-based multilayer and multiresolution feature fusion in the encoder, and a dual mode attention gate in the decoder of the multi-resolution U-Net-based GAN. With multi-objective adversarial training loss functions including a unique reciprocal loss for enforcing cooperative learning in pGANs, it further enhances the robustness and accuracy of the segmentation map. Main results. Experimental evaluations conducted on nine diverse publicly available medical image segmentation datasets, including PhysioNet ICH, BUSI, CVC-ClinicDB, MoNuSeg, GLAS, ISIC-2018, DRIVE, Montgomery, and PROMISE12, demonstrate the proposed method’s superior performance. The proposed method achieves mean F1 scores of 79.53%, 88.68%, 82.50%, 93.25%, 90.40%, 94.19%, 81.65%, 98.48%, and 90.79%, respectively, on the above datasets, surpass state-of-the-art segmentation methods. Furthermore, our proposed method demonstrates robust multi-domain segmentation capabilities, exhibiting consistent and reliable performance. The assessment of the model’s proficiency in accurately identifying small details indicates that the high-resolution generalized medical image segmentation network (Hi-gMISnet) is more precise in segmenting even when the target area is very small. Significance. The proposed method provides robust and reliable segmentation performance on medical images, and thus it has the potential to be used in a clinical setting for the diagnosis of patients.

TransDiff: medical image segmentation method based on Swin Transformer with diffusion probabilistic model

TransDiff: medical image segmentation method based on Swin Transformer with diffusion probabilistic model

A robust quality estimation method for medical image segmentation with small datasets

The quality check of automatic image analysis results is a necessity to eliminate poor outcomes. There are few work on segmentation quality estimation when there is no reference mask available. Generative-based and regression approaches generally have strict assumptions on shape/contrast of anatomical structures, which may fail when there are abnormalities in images or in the presence of domain shift. Ensemble approach promises more generalisability to various types of images; however, they are costly to train. Also, none of these methods were designed for small datasets. To address these shortcomings, this paper presents a segmentation quality estimation method for small datasets with arbitrary dimensions, which is validated with 2D, 3D and 4D image datasets with roughly 20 training images, and on the segmentation of retinal vessel and left atrium segmentation. Although our method uses an ensemble for image segmentation, its design reduces its parameter size. We describe possible scenarios relating the amount of agreement across the base models’ outputs in an ensemble to quality scores; then, present a technique to deal with high quality score estimation for poor segmentation as a result of the base models to largely agree on mistakes. We assess the performance of our method in the presence of different sources of domain shift, and compare it with methods selected from the aforementioned approaches. We found robust quality score estimation, generalisable to different datasets. Our code would be available upon acceptance.

Medical image segmentation data augmentation method based on channel weight and data-efficient features

In computer-aided medical diagnosis, obtaining labeled medical image data is expensive, while there is a high demand for model interpretability. However, most deep learning models currently require a large amount of data and lack interpretability. To address these challenges, this paper proposes a novel data augmentation method for medical image segmentation. The uniqueness and advantages of this method lie in the utilization of gradient-weighted class activation mapping to extract data efficient features, which are then fused with the original image. Subsequently, a new channel weight feature extractor is constructed to learn the weights between different channels. This approach achieves non-destructive data augmentation effects, enhancing the model's performance, data efficiency, and interpretability. Applying the method of this paper to the Hyper-Kvasir dataset, the intersection over union (IoU) and Dice of the U-net were improved, respectively; and on the ISIC-Archive dataset, the IoU and Dice of the DeepLabV3+ were also improved respectively. Furthermore, even when the training data is reduced to 70 %, the proposed method can still achieve performance that is 95 % of that achieved with the entire dataset, indicating its good data efficiency. Moreover, the data-efficient features used in the method have interpretable information built-in, which enhances the interpretability of the model. The method has excellent universality, is plug-and-play, applicable to various segmentation methods, and does not require modification of the network structure, thus it is easy to integrate into existing medical image segmentation method, enhancing the convenience of future research and applications.

A medical image segmentation method for rectal tumors based on multi-scale feature retention and multiple attention mechanisms.

With the continuous development of deep learning algorithms in the field of medical images, models for medical image processing based on convolutional neural networks have made great progress. Since medical images of rectal tumors are characterized by specific morphological features and complex edges that differ from natural images, achieving good segmentation results often requires a higher level of enrichment through the utilization of semantic features. The efficiency of feature extraction and utilization has been improved to some extent through enhanced hardware arithmetic and deeper networks in most models. However, problems still exist with detail loss and difficulty in feature extraction, arising from the extraction of high-level semantic features in deep networks. In this work, a novel medical image segmentation model has been proposed for Magnetic Resonance Imaging (MRI) image segmentation of rectal tumors. The model constructs a backbone architecture based on the idea of jump-connected feature fusion and solves the problems of detail feature loss and low segmentation accuracy using three novel modules: Multi-scale Feature Retention (MFR), Multi-branch Cross-channel Attention (MCA), and Coordinate Attention (CA). Compared with existing methods, our proposed model is able to segment the tumor region more effectively, achieving 97.4% and 94.9% in Dice and mIoU metrics, respectively, exhibiting excellent segmentation performance and computational speed. Our proposed model has improved the accuracy of both lesion region and tumor edge segmentation. In particular, the determination of the lesion region can help doctors identify the tumor location in clinical diagnosis, and the accurate segmentation of the tumor edge can assist doctors in judging the necessity and feasibility of surgery.

SASAN: Spectrum-Axial Spatial Approach Networks for Medical Image Segmentation.

Ophthalmic diseases such as central serous chorioretinopathy (CSC) significantly impair the vision of millions of people globally. Precise segmentation of choroid and macular edema is critical for diagnosing and treating these conditions. However, existing 3D medical image segmentation methods often fall short due to the heterogeneous nature and blurry features of these conditions, compounded by medical image clarity issues and noise interference arising from equipment and environmental limitations. To address these challenges, we propose the Spectrum Analysis Synergy Axial-Spatial Network (SASAN), an approach that innovatively integrates spectrum features using the Fast Fourier Transform (FFT). SASAN incorporates two key modules: the Frequency Integrated Neural Enhancer (FINE), which mitigates noise interference, and the Axial-Spatial Elementum Multiplier (ASEM), which enhances feature extraction. Additionally, we introduce the Self-Adaptive Multi-Aspect Loss (LSM), which balances image regions, distribution, and boundaries, adaptively updating weights during training. We compiled and meticulously annotated the Choroid and Macular Edema OCT Mega Dataset (CMED-18k), currently the world's largest dataset of its kind. Comparative analysis against 13 baselines shows our method surpasses these benchmarks, achieving the highest Dice scores and lowest HD95 in the CMED and OIMHS datasets. Our code is publicly available at https://github.com/IMOP-lab/SASAN-Pytorch.

Semi-Supervised Medical Image Segmentation Using Cross-Style Consistency With Shape-Aware and Local Context Constraints.

Despite the remarkable progress in semi-supervised medical image segmentation methods based on deep learning, their application to real-life clinical scenarios still faces considerable challenges. For example, insufficient labeled data often makes it difficult for networks to capture the complexity and variability of the anatomical regions to be segmented. To address these problems, we design a new semi-supervised segmentation framework that aspires to produce anatomically plausible predictions. Our framework comprises two parallel networks: shape-agnostic and shape-aware networks. These networks learn from each other, enabling effective utilization of unlabeled data. Our shape-aware network implicitly introduces shape guidance to capture shape fine-grained information. Meanwhile, shape-agnostic networks employ uncertainty estimation to further obtain reliable pseudo-labels for the counterpart. We also employ a cross-style consistency strategy to enhance the network's utilization of unlabeled data. It enriches the dataset to prevent overfitting and further eases the coupling of the two networks that learn from each other. Our proposed architecture also incorporates a novel loss term that facilitates the learning of the local context of segmentation by the network, thereby enhancing the overall accuracy of prediction. Experiments on three different datasets of medical images show that our method outperforms many excellent semi-supervised segmentation methods and outperforms them in perceiving shape. The code can be seen at https://github.com/igip-liu/SLC-Net.

SDMI-Net: Spatially Dependent Mutual Information Network for semi-supervised medical image segmentation

Semi-supervised medical image segmentation strives to polish deep models with a small amount of labeled data and a large amount of unlabeled data. The efficiency of most semi-supervised medical image segmentation methods based on voxel-level consistency learning is affected by low-confidence voxels. In addition, voxel-level consistency learning fails to consider the spatial correlation between neighboring voxels. To encourage reliable voxel-level consistent learning, we propose a dual-teacher affine consistent uncertainty estimation method to filter out some voxels with high uncertainty. Moreover, we design the spatially dependent mutual information module, which enhances the spatial dependence between neighboring voxels by maximizing the mutual information between the local voxel blocks predicted from the dual-teacher models and the student model, enabling consistent learning at the block level. On two benchmark medical image segmentation datasets, including the Left Atrial Segmentation Challenge dataset and the BraTS-2019 dataset, our method achieves state-of-the-art performance in both quantitative and qualitative aspects.

Medical image segmentation network based on multi-scale frequency domain filter

With the development of deep learning, medical image segmentation in computer-aided diagnosis has become a research hotspot. Recently, UNet and its variants have become the most powerful medical image segmentation methods. However, these methods suffer from (1) insufficient sensing field and insufficient depth; (2) computational nonlinearity and redundancy of channel features; and (3) ignoring the interrelationships among feature channels. These problems lead to poor network segmentation performance and weak generalization ability. Therefore, first of all, we propose an effective replacement scheme of UNet base block, Double residual depthwise atrous convolution (DRDAC) block, to effectively improve the deficiency of receptive field and depth. Secondly, a new linear module, the Multi-scale frequency domain filter (MFDF), is designed to capture global information from the frequency domain. The high order multi-scale relationship is extracted by combining the depthwise atrous separable convolution with the frequency domain filter. Finally, a channel attention called Axial selection channel attention (ASCA) is redesigned to enhance the network’s ability to model feature channel interrelationships. Further, we design a novel frequency domain medical image segmentation baseline method FDFUNet based on the above modules. We conduct extensive experiments on five publicly available medical image datasets and demonstrate that the present method has stronger segmentation performance as well as generalization ability compared to other state-of-the-art baseline methods.

Rolling-Unet: Revitalizing MLP’s Ability to Efficiently Extract Long-Distance Dependencies for Medical Image Segmentation

Medical image segmentation methods based on deep learning network are mainly divided into CNN and Transformer. However, CNN struggles to capture long-distance dependencies, while Transformer suffers from high computational complexity and poor local feature learning. To efficiently extract and fuse local features and long-range dependencies, this paper proposes Rolling-Unet, which is a CNN model combined with MLP. Specifically, we propose the core R-MLP module, which is responsible for learning the long-distance dependency in a single direction of the whole image. By controlling and combining R-MLP modules in different directions, OR-MLP and DOR-MLP modules are formed to capture long-distance dependencies in multiple directions. Further, Lo2 block is proposed to encode both local context information and long-distance dependencies without excessive computational burden. Lo2 block has the same parameter size and computational complexity as a 3×3 convolution. The experimental results on four public datasets show that Rolling-Unet achieves superior performance compared to the state-of-the-art methods.

Local–global pseudo-label correction for source-free domain adaptive medical image segmentation

Domain shift is a commonly encountered issue in medical imaging solutions, primarily caused by variations in imaging devices and data sources. To mitigate this problem, unsupervised domain adaptation techniques have been employed. However, concerns regarding patient privacy and potential degradation of image quality have led to an increased focus on source-free domain adaptation. In this study, we address the issue of false labels in self-training based source-free domain adaptive medical image segmentation methods. To correct erroneous pseudo-labels, we propose a novel approach called the local–global pseudo-label correction (LGDA) method for source-free domain adaptive medical image segmentation. Our method consists of two components: An offline local context-based pseudo-label correction method that utilizes local context similarity in image space. And an online global pseudo-label correction method based on class prototypes, which corrects erroneously predicted pseudo-labels by considering the relative distance between pixel-wise feature vectors and prototype vectors. We evaluate the performance of our method on three benchmark fundus image datasets for optic disc and cup segmentation. Our method achieves superior performance compared to the state-of-the-art approaches, even without using any source data.

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

Deep learning methods utilizing Convolutional Neural Networks (CNNs) and Transformers have achieved remarkable success in volumetric medical image analysis. While successful, the symmetrical structure of numerous networks pays insufficient attention to the encoding phase, and the large amount of memory occupied by voxels leads to unnecessary redundancy in the network. In this paper, we present a novel approach to handle volumetric medical images by converting them into point cloud and introduce a new asymmetrical segmentation architecture. We propose a dual-path encoder that fully captures both dense and sparse representations of the input point cloud sampled from volumes. Moreover, the two obtained representations are subtracted at the skip connection as a complementary feature during the decoding stage. Experimental results on the Brain Tumor Segmentation (BraTS) and the Multi-sequence Cardiac MR Segmentation tasks demonstrate the great potential of our point-based method for volumetric medical image segmentation.

CorrDiff: Corrective Diffusion Model for Accurate MRI Brain Tumor Segmentation.

Accurate segmentation of brain tumors in MRI images is imperative for precise clinical diagnosis and treatment. However, existing medical image segmentation methods exhibit errors, which can be categorized into two types: random errors and systematic errors. Random errors, arising from various unpredictable effects, pose challenges in terms of detection and correction. Conversely, systematic errors, attributable to systematic effects, can be effectively addressed through machine learning techniques. In this paper, we propose a corrective diffusion model for accurate MRI brain tumor segmentation by correcting systematic errors. This marks the first application of the diffusion model for correcting systematic segmentation errors. Additionally, we introduce the Vector Quantized Variational Autoencoder (VQ-VAE) to compress the original data into a discrete coding codebook. This not only reduces the dimensionality of the training data but also enhances the stability of the correction diffusion model. Furthermore, we propose the Multi-Fusion Attention Mechanism, which can effectively enhances the segmentation performance of brain tumor images, and enhance the flexibility and reliability of the corrective diffusion model. Our model is evaluated on the BRATS2019, BRATS2020, and Jun Cheng datasets. Experimental results demonstrate the effectiveness of our model over state-of-the-art methods in brain tumor segmentation.

LumVertCancNet: A novel 3D lumbar vertebral body cancellous bone location and segmentation method based on hybrid Swin-transformer

Lumbar vertebral body cancellous bone location and segmentation is crucial in an automated lumbar spine processing pipeline. Accurate and reliable analysis of lumbar spine image is expected to advantage practical medical diagnosis and population-based analysis of bone strength. However, the design of automated algorithms for lumbar spine processing is demanding due to significant anatomical variations and scarcity of publicly available data. In recent years, convolutional neural network (CNN) and vision transformers (Vits) have been the de facto standard in medical image segmentation. Although adept at capturing global features, the inherent bias of locality and weight sharing of CNN constrains its capacity to model long-range dependency. In contrast, Vits excel at long-range dependency modeling, but they may not generalize well with limited datasets due to the lack of inductive biases inherent to CNN. In this paper, we propose a deep learning-based two-stage coarse-to-fine solution to address the problem of automatic location and segmentation of lumbar vertebral body cancellous bone. Specifically, in the first stage, a Swin-transformer based model is applied to predict the heatmap of lumbar vertebral body centroids. Considering the characteristic anatomical structure of lumbar spine, we propose a novel loss function called LumAnatomy loss, which enforces the order and bend of the predicted vertebral body centroids. To inherit the excellence of CNN and Vits while preventing their respective limitations, in the second stage, we propose an encoder–decoder network to segment the identified lumbar vertebral body cancellous bone, which consists of two parallel encoders, i.e., a Swin-transformer encoder and a CNN encoder. To enhance the combination of CNNs and Vits, we propose a novel multi-scale attention feature fusion module (MSA-FFM), which address issues that arise when fusing features given at different encoders. To tackle the issue of lack of data, we raise the first large-scale lumbar vertebral body cancellous bone segmentation dataset called LumVBCanSeg containing a total of 185 CT scans annotated at voxel level by 3 physicians. Extensive experimental results on the LumVBCanSeg dataset demonstrate the proposed algorithm outperform other state-of-the-art medical image segmentation methods. The data is publicly available at: https://zenodo.org/record/8181250. The implementation of the proposed method is available at: https://github.com/sia405yd/LumVertCancNet.

Weakly supervised learning for multi-class medical image segmentation via feature decomposition

Weakly supervised learning with image-level labels, releasing deep learning from highly labor-intensive pixel-wise annotation, has gained great attention for medical image segmentation. However, existing weakly supervised methods are mainly designed for single-class segmentation while leaving multi-class medical image segmentation rarely-explored. Different from natural images, label symbiosis, together with location adjacency, are much more common in medical images, making it more challenging for multi-class segmentation. In this paper, we propose a novel weakly supervised learning method for multi-class medical image segmentation with image-level labels. In terms of the multi-class classification backbone, a multi-level classification network encoding multi-scale features is proposed to produce binary predictions, together with the corresponding CAMs, of each class separately. To address the above issues (i.e., label symbiosis and location adjacency), a feature decomposition module based on semantic affinity is first proposed to learn both class-independent and class-dependent features by maximizing the inter-class feature distance. Through a cross-guidance loss to jointly utilize the above features, label symbiosis is largely alleviated. In terms of location adjacency, a mutually exclusive loss is constructed to minimize the overlap among regions corresponding to different classes. Experimental results on three datasets demonstrate the superior performance of the proposed weakly-supervised framework for both single-class and multi-class medical image segmentation. We believe the analysis in this paper would shed new light on future work for multi-class medical image segmentation. The source code of this paper is publicly available at https://github.com/HustAlexander/MCWSS.

RKSeg+: make full use of Runge–Kutta methods in medical image segmentation

RKSeg+: make full use of Runge–Kutta methods in medical image segmentation

MDT: semi-supervised medical image segmentation with mixup-decoupling training.

Objective. In the field of medicine, semi-supervised segmentation algorithms hold crucial research significance while also facing substantial challenges, primarily due to the extreme scarcity of expert-level annotated medical image data. However, many existing semi-supervised methods still process labeled and unlabeled data in inconsistent ways, which can lead to knowledge learned from labeled data being discarded to some extent. This not only lacks a variety of perturbations to explore potential robust information in unlabeled data but also ignores the confirmation bias and class imbalance issues in pseudo-labeling methods.Approach. To solve these problems, this paper proposes a semi-supervised medical image segmentation method 'mixup-decoupling training (MDT)' that combines the idea of consistency and pseudo-labeling. Firstly, MDT introduces a new perturbation strategy 'mixup-decoupling' to fully regularize training data. It not only mixes labeled and unlabeled data at the data level but also performs decoupling operations between the output predictions of mixed target data and labeled data at the feature level to obtain strong version predictions of unlabeled data. Then it establishes a dual learning paradigm based on consistency and pseudo-labeling. Secondly, MDT employs a novel categorical entropy filtering approach to pick high-confidence pseudo-labels for unlabeled data, facilitating more refined supervision.Main results. This paper compares MDT with other advanced semi-supervised methods on 2D and 3D datasets separately. A large number of experimental results show that MDT achieves competitive segmentation performance and outperforms other state-of-the-art semi-supervised segmentation methods.Significance. This paper proposes a semi-supervised medical image segmentation method MDT, which greatly reduces the demand for manually labeled data and eases the difficulty of data annotation to a great extent. In addition, MDT not only outperforms many advanced semi-supervised image segmentation methods in quantitative and qualitative experimental results, but also provides a new and developable idea for semi-supervised learning and computer-aided diagnosis technology research.

Unsupervised Domain Adaptation for Medical Image Segmentation Using Transformer With Meta Attention.

Image segmentation is essential to medical image analysis as it provides the labeled regions of interest for the subsequent diagnosis and treatment. However, fully-supervised segmentation methods require high-quality annotations produced by experts, which is laborious and expensive. In addition, when performing segmentation on another unlabeled image modality, the segmentation performance will be adversely affected due to the domain shift. Unsupervised domain adaptation (UDA) is an effective way to tackle these problems, but the performance of the existing methods is still desired to improve. Also, despite the effectiveness of recent Transformer-based methods in medical image segmentation, the adaptability of Transformers is rarely investigated. In this paper, we present a novel UDA framework using a Transformer for building a cross-modality segmentation method with the advantages of learning long-range dependencies and transferring attentive information. To fully utilize the attention learned by the Transformer in UDA, we propose Meta Attention (MA) and use it to perform a fully attention-based alignment scheme, which can learn the hierarchical consistencies of attention and transfer more discriminative information between two modalities. We have conducted extensive experiments on cross-modality segmentation using three datasets, including a whole heart segmentation dataset (MMWHS), an abdominal organ segmentation dataset, and a brain tumor segmentation dataset. The promising results show that our method can significantly improve performance compared with the state-of-the-art UDA methods.

SG-MIAN: Self-guided multiple information aggregation network for image-level weakly supervised skin lesion segmentation

Nowadays, skin disease is becoming one of the most malignant diseases that threaten people’s health. Computer aided diagnosis based on deep learning has become a widely used technology to assist medical professionals in diagnosis, and segmentation of lesion areas is one of the most important steps in it. However, traditional medical image segmentation methods rely on numerous pixel-level labels for fully supervised training, and such labeling process is time-consuming and requires professional competence. In order to reduce the costs of pixel-level labeling, we proposed a method only using image-level label to segment skin lesion areas. Due to the lack of lesion’s spatial and intensity information in image-level labels, and the wide distribution range of irregular shape and different texture on skin lesions, the algorithm must pay great attention to the automatic lesion localization and perception of lesion boundary. In this paper, we proposed a Self-Guided Multiple Information Aggregation Network (SG-MIAN). Our backbone network MIAN utilizes the Multiple Spatial Perceptron (MSP) solely using classification information as guidance to discriminate the key classification features of lesion areas, and thereby performing more accurate localization and activation of lesion areas. Additionally, adjunct to MSP, we also proposed an Auxiliary Activation Structure (AAS) and two auxiliary loss functions to further self-guided boundary correction, achieving the goal of accurate boundary activation. To verify the effectiveness of the proposed method, we conducted extensive experiments using the HAM10000 dataset and the PH2dataset, which demonstrated superior performance compared to most existing weakly supervised segmentation methods.