A Dimension Hybrid Framework for Multimodal Medical Image Segmentation

Three-dimensional (3D) medical image segmentation plays a crucial role in medical care applications. Although various two-dimensional (2D) and 3D neural network models have been applied to 3D medical image segmentation and achieved impressive results, a trade-off remains between efficiency and accuracy. To address this issue, a novel mixture convolutional network (MixConvNet) is proposed, in which traditional 2D/3D convolutional blocks are replaced with novel MixConv blocks. In the MixConv block, 3D convolution is decomposed into a mixture of 2D convolutions from different views. Therefore, the MixConv block fully utilizes the advantages of 2D convolution and maintains the learning ability of 3D convolution. It acts as 3D convolutions and thus can process volumetric input directly and learn intra-slice features, which are absent in the traditional 2D convolutional block. By contrast, the proposed MixConv block only contains 2D convolutions; hence, it has significantly fewer trainable parameters and less computation budget than a block containing 3D convolutions. Furthermore, the proposed MixConvNet is pre-trained with small input patches and fine-tuned with large input patches to improve segmentation performance further. In experiments on the Decathlon Heart dataset and Sliver07 dataset, the proposed MixConvNet outperformed the state-of-the-art methods such as UNet3D, VNet, and nnUnet.

Three-dimensional (3D) medical image segmentation is used to segment the target (a lesion or an organ) in 3D medical images. Through this process, 3D target information is obtained; hence, this technology is an important auxiliary tool for medical diagnosis. Although some methods have proved to be successful for two-dimensional (2D) image segmentation, their direct use in the 3D case has been unsatisfactory. To obtain more precise tumor segmentation results from 3D MR images, in this paper, we propose a method known as the 3D shape-weighted level set method (3D-SLSM). The proposed method first converts the LSM, which is superior with respect to 2D image segmentation, into a 3D algorithm that is suitable for overall calculations in 3D image models, and which improves the efficiency and accuracy of calculations. A 3D shape-weighted value is then added for each 3D-SLSM iterative process according to the changes in volume. Besides increasing the convergence rate and eliminating background noise, this shape-weighted value also brings the segmented contour closer to the actual tumor margins. To perform a quantitative analysis of 3D-SLSM and to examine its feasibility in clinical applications, we have divided our experiments into computer-simulated sequence images and actual breast MRI cases. Subsequently, we simultaneously compared various existing 3D segmentation methods. The experimental results demonstrated that 3D-SLSM exhibited precise segmentation results for both types of experimental images. In addition, 3D-SLSM showed better results for quantitative data compared with existing 3D segmentation methods.

3D convolution neural networks (CNN) have been proved very successful in parsing organs or tumours in 3D medical images, but it remains sophisticated and time-consuming to choose or design proper 3D networks given different task contexts. Recently, Neural Architecture Search (NAS) is proposed to solve this problem by searching for the best network architecture automatically. However, the inconsistency between search stage and deployment stage often exists in NAS algorithms due to memory constraints and large search space, which could become more serious when applying NAS to some memory and time-consuming tasks, such as 3D medical image segmentation. In this paper, we propose a coarse-to-fine neural architecture search (C2FNAS) to automatically search a 3D segmentation network from scratch without inconsistency on network size or input size. Specifically, we divide the search procedure into two stages: 1) the coarse stage, where we search the macro-level topology of the network, i.e. how each convolution module is connected to other modules; 2) the fine stage, where we search at micro-level for operations in each cell based on previous searched macro-level topology. The coarse-to-fine manner divides the search procedure into two consecutive stages and meanwhile resolves the inconsistency. We evaluate our method on 10 public datasets from Medical Segmentation Decalthon (MSD) challenge, and achieve state-of-the-art performance with the network searched using one dataset, which demonstrates the effectiveness and generalization of our searched models.

Initialization of deformable models in 3D magnetic resonance images guided by automatically detected phase congruency point landmarks

Three-dimensional (3D) medical images are prone to overlap, and there are some problems, such as low detection efficiency and inconsistent with the actual situation. Therefore, a 3D medical image surface reconstruction method based on data mining and machine learning is proposed. The 3D medical images were classified according to different ways, the information frame of 3D medical images was established and the surface overlapping information model of 3D images was given. Based on this information framework, the nonlinear function of overlapping area information of 3D medical images was constructed. The weight of the nonlinear function was used to calculate the input and output results of overlapping area information. Combined with the input mode of 3D medical image information, the error between the information output and the expected output was set. The nonlinear function weight of the overlapping area information of 3D medical images was modified by using the learning rate and the use time of the overlapping area information, and the influence factors of the overlapping information detection were obtained by increasing the situation terms, so as to complete the detection of the surface reconstruction information of 3D medical images. The experimental results show that the information detection results of the proposed method fit well with the actual situation, and the information detection efficiency is high.

Hybrid-ctunet: a double complementation approach for 3D medical image segmentation

With advancements in technology, three-dimensional (3D) medical imaging has become vital in modern medicine, contributing to more accurate diagnosis, treatment planning, and personalized medicine. However, segmenting abdominal organs remains a challenging task due to anatomical variations, limited labeled data, and image noise. This study investigates the impact of deep learning-based architectures and preprocessing techniques on 3D organ segmentation using the publicly available Multi-Atlas Labeling Beyond the Cranial Vault (BTCV) dataset. To achieve this, 3D U-Net, UNETR, and SwinUNETR models were employed, and the effects of various preprocessing techniques and loss functions, including Dice Loss, Focal Loss, and Cross-Entropy Loss, were systematically analyzed. The findings reveal that combining Dice Loss with Cross-Entropy Loss significantly enhances segmentation performance. Additionally, preprocessing techniques improved segmentation accuracy by 1.19%, further optimizing model performance. Among the evaluated models, 3D U-Net achieved the highest overall segmentation performance, with an average Dice score of 0.8397, outperforming SwinUNETR and UNETR. These findings underscore the importance of selecting appropriate preprocessing methods and loss functions in 3D medical image segmentation. The results contribute to more precise and efficient medical image analysis, with potential applications in clinical decision support systems. Future research should focus on optimizing hybrid architectures, integrating advanced augmentation strategies, and expanding evaluation across multiple datasets to improve the robustness and real-world applicability of automated segmentation methods.

The current state of the art in three dimensional oncologic imaging: An overview

Chapter 4 - 4D medical image analysis: a systematic study on applications, challenges, and future research directions

This review examines the recent developments in deep learning (DL) techniques applied to multimodal fusion image segmentation for liver cancer. Hepatocellular carcinoma is a highly dangerous malignant tumor that requires accurate image segmentation for effective treatment and disease monitoring. Multimodal image fusion has the potential to offer more comprehensive information and more precise segmentation, and DL techniques have achieved remarkable progress in this domain. This paper starts with an introduction to liver cancer, then explains the preprocessing and fusion methods for multimodal images, then explores the application of DL methods in this area. Various DL architectures such as convolutional neural networks (CNN) and U-Net are discussed and their benefits in multimodal image fusion segmentation. Furthermore, various evaluation metrics and datasets currently used to measure the performance of segmentation models are reviewed. While reviewing the progress, the challenges of current research, such as data imbalance, model generalization, and model interpretability, are emphasized and future research directions are suggested. The application of DL in multimodal image segmentation for liver cancer is transforming the field of medical imaging and is expected to further enhance the accuracy and efficiency of clinical decision making. This review provides useful insights and guidance for medical practitioners.

Three-dimensional (3D) medical images, such as Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), are essential for clinical applications. However, the need for diverse and comprehensive representations is particularly pronounced when considering the variability across different organs, diagnostic tasks, and imaging modalities. How to effectively interpret the intricate contextual information and extract meaningful insights from these images remains an open challenge to the community. While current self-supervised learning methods have shown potential, they often consider an image as a whole thereby overlooking the extensive, complex relationships among local regions from one or multiple images. In this work, we introduce a pioneering method for learning 3D medical image representations through an autoregressive pre-training framework. Our approach sequences various 3D medical images based on spatial, contrast, and semantic correlations, treating them as interconnected visual tokens within a token sequence. By employing an autoregressive sequence modeling task, we predict the next visual token in the sequence, which allows our model to deeply understand and integrate the contextual information inherent in 3D medical images. Additionally, we implement a random startup strategy to avoid overestimating token relationships and to enhance the robustness of learning. The effectiveness of our approach is demonstrated by the superior performance over others on nine downstream tasks in public datasets.

Recently, 3D medical image reconstruction (MIR) and segmentation (MIS) based on deep neural networks have been developed with promising results, and attention mechanism has been further designed for performance enhancement. However, the large size of 3D volume images poses a great computational challenge to traditional attention methods. In this paper, we propose a folded attention (FA) approach to improve the computational efficiency of traditional attention methods on 3D medical images. The main idea is that we apply tensor folding and unfolding operations to construct four small sub-affinity matrices to approximate the original affinity matrix. Through four consecutive sub-attention modules of FA, each element in the feature tensor can aggregate spatial-channel information from all other elements. Compared to traditional attention methods, with the moderate improvement of accuracy, FA can substantially reduce the computational complexity and GPU memory consumption. We demonstrate the superiority of our method on two challenging tasks for 3D MIR and MIS, which are quantitative susceptibility mapping and multiple sclerosis lesion segmentation.

Gliomas, the most aggressive primary tumors in the central nervous system, are characterized by high morphological heterogeneity and diffusely infiltrating boundaries. Such complexity poses significant challenges for accurate segmentation in clinical practice. Although deep learning methods have shown promising results, they often struggle to achieve a satisfactory trade-off among precise boundary delineation, robust multi-scale feature representation, and computational efficiency, particularly when processing high-resolution three-dimensional (3D) magnetic resonance imaging (MRI) data. Therefore, the aim of this study is to develop a novel 3D segmentation framework that specifically addresses these challenges, thereby improving clinical utility in brain tumor analysis. To accomplish this, we propose a multi-level channel-spatial attention and light-weight scale-fusion network (MCSLF-Net), which integrates a multi-level channel-spatial attention mechanism (MCSAM) and a light-weight scale-fusion module. By strategically enhancing subtle boundary features while maintaining a compact network design, our approach seeks to achieve high accuracy in delineating complex glioma morphologies, reduce computational burden, and provide a more clinically feasible segmentation solution. We propose MCSLF-Net, a network integrating two key components: (I) MCSAM: by strategically inserting a 3D channel-spatial attention module at critical semantic layers, the network progressively emphasizes subtle, infiltrative edges and small, easily overlooked contours. This avoids reliance on an additional edge detection branch while enabling fine-grained localization in ambiguous transitional regions. (II) Light-weight scale fusion unit (LSFU): leveraging depth-wise separable convolutions combined with multi-scale atrous (dilated) convolutions, LSFU enhances computational efficiency and adapts to varying feature requirements at different network depths. In doing so, it effectively captures small infiltrative lesions as well as extensive tumor areas. By coupling these two modules, MCSLF-Net balances global contextual information with local fine-grained features, simultaneously reducing the computational burden typically associated with 3D medical image segmentation. Extensive experiments on the BraTS 2019, BraTS 2020, and BraTS 2021 datasets validated the effectiveness of our approach. On BraTS 2021, MCSLF-Net achieved a mean Dice similarity coefficient (DSC) of 0.8974 and a mean 95th percentile Hausdorff distance (HD95) of 2.52 mm. Notably, it excels in segmenting intricate transitional areas, including the enhancing tumor (ET) region and the tumor core (TC), thereby demonstrating superior boundary delineation and multi-scale feature fusion capabilities relative to existing methods. These findings underscore the clinical potential of deploying multi-level channel-spatial attention and light-weight multi-scale fusion strategies in high-precision 3D glioma segmentation. By striking an optimal balance among boundary accuracy, multi-scale feature capture, and computational efficiency, the proposed MCSLF-Net offers a practical framework for further advancements in automated brain tumor analysis and can be extended to a range of 3D medical image segmentation tasks.

Objective. Over the past years, convolutional neural networks based methods have dominated the field of medical image segmentation. But the main drawback of these methods is that they have difficulty representing long-range dependencies. Recently, the Transformer has demonstrated super performance in computer vision and has also been successfully applied to medical image segmentation because of the self-attention mechanism and long-range dependencies encoding on images. To the best of our knowledge, only a few works focus on cross-modalities of image segmentation using the Transformer. Hence, the main objective of this study was to design, propose and validate a deep learning method to extend the application of Transformer to multi-modality medical image segmentation. Approach. This paper proposes a novel automated multi-modal Transformer network termed AMTNet for 3D medical image segmentation. Especially, the network is a well-modeled U-shaped network architecture where many effective and significant changes have been made in the feature encoding, fusion, and decoding parts. The encoding part comprises 3D embedding, 3D multi-modal Transformer, and 3D Co-learn down-sampling blocks. Symmetrically, the 3D Transformer block, upsampling block, and 3D-expanding blocks are included in the decoding part. In addition, a Transformer-based adaptive channel interleaved Transformer feature fusion module is designed to fully fuse features of different modalities. Main results. We provide a comprehensive experimental analysis of the Prostate and BraTS2021 datasets. The results show that our method achieves an average DSC of 0.907 and 0.851 (0.734 for ET, 0.895 for TC, and 0.924 for WT) on these two datasets, respectively. These values show that AMTNet yielded significant improvements over the state-of-the-art segmentation networks. Significance. The proposed 3D segmentation network exploits complementary features of different modalities during the feature extraction process at multiple scales to increase the 3D feature representations and improve the segmentation efficiency. This powerful network enriches the research of the Transformer to multi-modal medical image segmentation.

Segmentation of organs of interest in 3D medical images is necessary for accurate diagnosis and longitudinal studies. Though recent advances using deep learning have shown success for many segmentation tasks, large datasets are required for high performance and the annotation process is both time consuming and labor intensive. In this paper, we propose a 3D few shot segmentation framework for accurate organ segmentation using limited training samples of the target organ annotation. To achieve this, a U-Net like network is designed to predict segmentation by learning the relationship between 2D slices of support data and a query image, including a bidirectional gated recurrent unit (GRU) that learns consistency of encoded features between adjacent slices. Also, we introduce a transfer learning method to adapt the characteristics of the target image and organ by updating the model before testing with arbitrary support and query data sampled from the support data. We evaluate our proposed model using three 3D CT datasets with annotations of different organs. Our model yielded significantly improved performance over state-of-the-art few shot segmentation models and was comparable to a fully supervised model trained with more target training data.