This study provides a comparative analysis of deep learning models including UNet, Res-UNet, Attention Res-UNet, and nnUNet, and evaluates their performance in brain tumour, polyp, and multi-class heart segmentation tasks. The analysis focuses on precision, accuracy, recall, Dice Similarity Coefficient (DSC), and Intersection over Union (IoU) to assess their clinical applicability. In brain tumour segmentation, Res-UNet and nnUNet significantly outperformed UNet, with Res-UNet leading in DSC and IoU scores, indicating superior accuracy in tumour delineation. Meanwhile, nnUNet excelled in recall and accuracy, which are crucial for reliable tumour detection in clinical diagnosis and planning. In polyp detection, nnUNet was the most effective, achieving the highest metrics across all categories and proving itself as a reliable diagnostic tool in endoscopy. In the complex task of heart segmentation, Res-UNet and Attention Res-UNet were outstanding in delineating the left ventricle, with Res-UNet also leading in right ventricle segmentation. nnUNet was unmatched in myocardium segmentation, achieving top scores in precision, recall, DSC, and IoU. The conclusion notes that although Res-UNet occasionally outperforms nnUNet in specific metrics, the differences are quite small. Moreover, nnUNet consistently shows superior overall performance across the experiments. Particularly noted for its high recall and accuracy, which are crucial in clinical settings to minimize misdiagnosis and ensure timely treatment, nnUNet's robust performance in crucial metrics across all tested categories establishes it as the most effective model for these varied and complex segmentation tasks.
Deep Learning-Based Cross-Anatomy CT Synthesis Using Adapted nnResU-Net with Anatomical Feature Prioritized Loss
Univ. Bordeaux, CNRS, LaBRI, UMR 5800, F-33400 Talence, France(波尔多大学,法国国家科学研究中心,LaBRI研究院,UMR 5800);Universidad Autónoma de Madrid, Madrid, 28049, Spain(马德里自治大学,西班牙);Pazmany Peter Catholic University, Budapest, 1083, Hungary(佩斯大学,匈牙利);RIKEN Center for Integrative Medical Sciences, Medical Data Deep Learning Team, Tokyo, Japan(日本再生医学科学中心,医学数据深度学习团队)
Retinal Optical Coherence Tomography (OCT), a noninvasive cross-sectional scan of the eye with qualitative 3D visualization of the retinal anatomy is use to study the retinal structure and the presence of pathogens. The advent of the retinal OCT has transformed ophthalmology and it is currently paramount for the diagnosis, monitoring and treatment of many eye pathogens including Macular Edema which impairs vision severely or Glaucoma that can cause irreversible blindness. However the quality of retinal OCT images varies among device manufacturers. Deep Learning methods have had their success i…
Xiamen University(厦门大学);The University of Hong Kong(香港大学)
Recent medical image segmentation models are mostly hybrid, which integrate self-attention and convolution layers into the non-isomorphic architecture. However, one potential drawback of these approaches is that they failed to provide an intuitive explanation of why this hybrid combination manner is beneficial, making it difficult for subsequent work to make improvements on top of them. To address this issue, we first analyze the differences between the weight allocation mechanisms of the self-attention and convolution. Based on this analysis, we propose to construct a parallel non-isomorphic …
There has been growing research interest in using deep learning based method to achieve fully automated segmentation of lesion in Positron emission tomography computed tomography(PET CT) scans for the prognosis of various cancers. Recent advances in the medical image segmentation shows the nnUNET is feasible for diverse tasks. However, lesion segmentation in the PET images is not straightforward, because lesion and physiological uptake has similar distribution patterns. The Distinction of them requires extra structural information in the CT images. The present paper introduces a nnUNet based m…
Comparative Analysis of nnUNet and MedNeXt for Head and Neck Tumor Segmentation in MRI-guided Radiotherapy
Sharif University of Technology(谢里夫理工大学);Institute for AI in Medicine (IKIM), University Medicine Essen(埃森大学医学中心人工智能医学研究所);Center Algoritmi / LASI, University of Minho(米尼奥大学Algoritmi中心/LASI);University Hospital RWTH Aachen(亚琛工业大学附属医院);Cancer Research Center Cologne Essen (CCCE), University Medicine Essen (AöR)(埃森大学医学中心(公法团体)科隆埃森癌症研究中心);German Cancer Consortium (DKTK), Partner Site Essen(德国癌症联盟埃森合作站点);TU Dortmund University(多特蒙德工业大学)
RARE-UNet: Resolution-Aligned Routing Entry for Adaptive Medical Image Segmentation
Pioneer Centre for Artificial Intelligence, Department of Computer Science, University of Copenhagen, Copenhagen, Denmark(人工智能先锋中心、计算机科学系、哥本哈根大学、哥本哈根、丹麦)
University of Notre Dame(圣母大学);Guangdong Provincial People’s Hospital(广东省人民医院);IBM Thomas J. Watson Research Center(IBM托马斯·J·沃森研究中心)
Real-time cine magnetic resonance imaging (MRI) plays an increasingly important role in various cardiac interventions. In order to enable fast and accurate visual assistance, the temporal frames need to be segmented on-the-fly. However, state-of-the-art MRI segmentation methods are used either offline because of their high computation complexity, or in real-time but with significant accuracy loss and latency increase (causing visually noticeable lag). As such, they can hardly be adopted to assist visual guidance. In this work, inspired by a new interpretation of Independent Component Analysis …
Squeeze Excitation Embedded Attention UNet for Brain Tumor Segmentation
School of Electronics Engineering, Vellore Institute of Technology(韦洛尔理工大学电子工程学院);Centre for Advanced Data Science, Vellore Institute of Technology(韦洛尔理工大学高级数据科学中心)
Huazhong University of Science and Technology(华中科技大学);Shenzhen University(深圳大学)
Deep convolutional neural network (CNN) achieves remarkable performance for medical image analysis. UNet is the primary source in the performance of 3D CNN architectures for medical imaging tasks, including brain tumor segmentation. The skip connection in the UNet architecture concatenates features from both encoder and decoder paths to extract multi-contextual information from image data. The multi-scaled features play an essential role in brain tumor segmentation. However, the limited use of features can degrade the performance of the UNet approach for segmentation. In this paper, we propose…
Fudan University(复旦大学);Ruijin Hospital, Shanghai Jiaotong University(上海交通大学医学院附属瑞金医院);Tongji Hospital, Huazhong University of Science and Technology(华中科技大学同济医学院附属同济医院);Leiden University Medical Center(莱顿大学医学中心)
Convolutional neural network (CNN), in particular the Unet, is a powerful method for medical image segmentation. To date Unet has demonstrated state-of-art performance in many complex medical image segmentation tasks, especially under the condition when the training and testing data share the same distribution (i.e. come from the same source domain). However, in clinical practice, medical images are acquired from different vendors and centers. The performance of a U-Net trained from a particular source domain, when transferred to a different target domain (e.g. different vendor, acquisition pa…
HWA-UNETR: Hierarchical Window Aggregate UNETR for 3D Multimodal Gastric Lesion Segmentation
School of Computer Science and Engineering(计算机科学与工程学院);School of Future Technology(未来技术学院);South China University of Technology(华南理工大学);Department of Medical Imaging(医学影像科);Guangzhou Institute of Cancer Research(广州癌症研究所);the Affiliated Cancer Hospital(附属肿瘤医院);Guangzhou Medical University(广州医学院);Department of Radiology(放射科);Meizhou People’s Hospital(梅州市人民医院);School of Computer Science and Technology(计算机科学与技术学院);Hainan University(海南大学);Department of Oncology Institute(肿瘤研究所)
University of Copenhagen(哥本哈根大学);Copenhagen University Hospital, Bispebjerg and Frederiksberg(哥本哈根大学医院比斯佩布杰格和弗雷德里克斯堡院区)
UNet has become the gold standard method for segmenting 2D medical images that any new method must be validated against. However, in recent years, several variations of the seminal UNet have been proposed with promising results. However, there is no clear consensus on the generalisability of these architectures, and UNet currently remains the methodological gold standard. The purpose of this study was to evaluate some of the most promising UNet-inspired architectures for 3D segmentation. For the segmentation of 3D scans, UNet-inspired methods are also dominant, but there is a larger variety ac…
The George Washington University Medical Center(乔治华盛顿大学医学中心)
Recently, deep learning has become much more popular in computer vision area. The Convolution Neural Network (CNN) has brought a breakthrough in images segmentation areas, especially, for medical images. In this regard, U-Net is the predominant approach to medical image segmentation task. The U-Net not only performs well in segmenting multimodal medical images generally, but also in some tough cases of them. However, we found that the classical U-Net architecture has limitation in several aspects. Therefore, we applied modifications: 1) designed efficient CNN architecture to replace encoder an…
Human veins are important for carrying the blood from the body-parts to the heart. The improper functioning of the human veins may arise from several venous diseases. Varicose vein is one such disease wherein back flow of blood can occur, often resulting in increased venous pressure or restricted blood flow due to changes in the structure of vein. To examine the functional characteristics of the varicose vein, it is crucial to study the physical and bio mechanical properties of the vein. This work proposes a segmentation model Opto-UNet, for segmenting the venous wall structure. Optical Cohere…
Ashford and St Peter’s Hospitals NHS Foundation Trust(阿什福德和圣彼得医院 NHS 基金会信托);University of Lincoln(林肯大学)
In this paper we propose a 2D deep residual Unet with 104 convolutional layers (DR-Unet104) for lesion segmentation in brain MRIs. We make multiple additions to the Unet architecture, including adding the 'bottleneck' residual block to the Unet encoder and adding dropout after each convolution block stack. We verified the effect of introducing the regularisation of dropout with small rate (e.g. 0.2) on the architecture, and found a dropout of 0.2 improved the overall performance compared to no dropout, or a dropout of 0.5. We evaluated the proposed architecture as part of the Multimodal Brain …
TTT-Unet: Enhancing U-Net with Test-Time Training Layers for Biomedical Image Segmentation
Lehigh University(里海大学);Northeastern University(东北大学);University of Notre Dame(圣母大学);University of Georgia(佐治亚大学);Massachusetts General Hospital(麻省总医院);Harvard Medical School(哈佛医学院)
CAD-Unet: A Capsule Network-Enhanced Unet Architecture for Accurate Segmentation of COVID-19 Lung Infections from CT Images
School of Information Engineering, Ningxia University(宁夏大学信息工程学院);Ningxia Key Laboratory of Artificial Intelligence and Information Security for Channeling Computing Resources from the East to the West, Ningxia University(宁夏人工智能与信息安全重点实验室);School of Mathematics and Computer Science, Ningxia Normal University(宁夏师范学院数学与计算机科学学院);School of Advanced Interdisciplinary Studies, Ningxia University(宁夏大学先进交叉学科学院)
New York University(纽约大学);Manipal Institute of Technology, Manipal Academy of Higher Education(马尼帕尔高等教育学院马尼帕尔理工学院);Columbia University(哥伦比亚大学)
Biomedical image segmentation is one of the fastest growing fields which has seen extensive automation through the use of Artificial Intelligence. This has enabled widespread adoption of accurate techniques to expedite the screening and diagnostic processes which would otherwise take several days to finalize. In this paper, we present an end-to-end pipeline to segment lungs from chest X-ray images, training the neural network model on the Japanese Society of Radiological Technology (JSRT) dataset, using UNet to enable faster processing of initial screening for various lung disorders. The pipel…
Convolutional neural networks (CNNs) have achieved remarkable success in automatically segmenting organs or lesions on 3D medical images. Recently, vision transformer networks have exhibited exceptional performance in 2D image classification tasks. Compared with CNNs, transformer networks have an appealing advantage of extracting long-range features due to their self-attention algorithm. Therefore, we propose a CNN-Transformer combined model, called BiTr-Unet, with specific modifications for brain tumor segmentation on multi-modal MRI scans. Our BiTr-Unet achieves good performance on the BraTS…
In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in compari…
In this paper, the Primal-Dual UNet for sparse view CT reconstruction is modified to be applicable to cone beam projections and perform reconstructions of entire volumes instead of slices. Experiments show that the PSNR of the proposed method is increased by 10dB compared to the direct FDK reconstruction and almost 3dB compared to the modified original Primal-Dual Network when using only 23 projections. The presented network is not optimized wrt. memory consumption or hyperparameters but merely serves as a proof of concept and is limited to low resolution projections and volumes.
WAVE-UNET: Wavelength based Image Reconstruction method using attention UNET for OCT images
Institute of Optical Materials and Technologies, Bulgarian Academy of Sciences(保加利亚科学院光学材料与技术研究所);Faculty of Information Technology and Communication Sciences, Tampere University(坦佩雷大学信息技术与通信科学学院);Electronics and Telecommunications Research Institute(电子与电信研究所)
Shanghai Jiao Tong University(上海交通大学);Ruijin Hospital, Shanghai Jiao Tong University School of Medicine(上海交通大学医学院附属瑞金医院);Rutgers University(罗格斯大学)
Pancreas segmentation in medical imaging data is of great significance for clinical pancreas diagnostics and treatment. However, the large population variations in the pancreas shape and volume cause enormous segmentation difficulties, even for state-of-the-art algorithms utilizing fully-convolutional neural networks (FCNs). Specifically, pancreas segmentation suffers from the loss of spatial information in 2D methods, and the high computational cost of 3D methods. To alleviate these problems, we propose a probabilistic-map-guided bi-directional recurrent UNet (PBR-UNet) architecture, which fu…
Automatic extraction of liver and tumor from CT volumes is a challenging task due to their heterogeneous and diffusive shapes. Recently, 2D and 3D deep convolutional neural networks have become popular in medical image segmentation tasks because of the utilization of large labeled datasets to learn hierarchical features. However, 3D networks have some drawbacks due to their high cost on computational resources. In this paper, we propose a 3D hybrid residual attention-aware segmentation method, named RA-UNet, to precisely extract the liver volume of interests (VOI) and segment tumors from the l…
LAW & ORDER: Adaptive Spatial Weighting for Medical Diffusion and Segmentation
Elmore Family School of Electrical and Computer Engineering(埃尔莫尔电气与计算机工程学院);Purdue University(普渡大学);Sesame AI;Department of Computer Science(计算机科学系);Department of Agricultural and Biological Engineering (ABE)(农业与生物工程系);Department of Agricultural Sciences Education and Communication (ASEC)(农业科学教育与交流系)
Autopet III challenge: Incorporating anatomical knowledge into nnUNet for lesion segmentation in PET/CT
Institute for AI in Medicine (IKIM)(医学人工智能研究所);University Hospital Essen (AöR)(埃森大学医院);Department of Nuclear Medicine(核医学科);Cancer Research Center Cologne Essen (CCCE)(科隆埃森癌症研究中心);West German Cancer Center Essen University Hospital Essen (AöR)(埃森大学医院西德癌症中心);TU Dortmund(多特蒙德工业大学);German Cancer Consortium (DKTK, Partner site Essen)(德国癌症联盟(埃森合作站点))
本研究针对 PET/CT 病变分割,提出基于示踪剂分类和集成 nnUNet 的方法,融合解剖标签,在 autoPET III 挑战中取得高 Dice 分数。
As an essential prerequisite for developing a medical intelligent assistant system, medical image segmentation has received extensive research and concentration from the neural network community. A series of UNet-like networks with encoder-decoder architecture has achieved extraordinary success, in which UNet2+ and UNet3+ redesign skip connections, respectively proposing dense skip connection and full-scale skip connection and dramatically improving compared with UNet in medical image segmentation. However, UNet2+ lacks sufficient information explored from the full scale, which will affect the…
Beijing Zoezen Robot Co Ltd(北京佐伊森机器人有限公司);Beihang University(北京航空航天大学)
Medical image segmentation have drawn massive attention as it is important in biomedical image analysis. Good segmentation results can assist doctors with their judgement and further improve patients' experience. Among many available pipelines in medical image analysis, Unet is one of the most popular neural networks as it keeps raw features by adding concatenation between encoder and decoder, which makes it still widely used in industrial field. In the mean time, as a popular model which dominates natural language process tasks, transformer is now introduced to computer vision tasks and have …
SelfReg-UNet: Self-Regularized UNet for Medical Image Segmentation
School of Computing and Augmented Intelligence, Arizona State University(亚利桑那州立大学计算与增强智能学院);McKeley School of Engineering, Washington University in St. Louis(圣路易斯华盛顿大学麦凯莱工程学院);School of Computing, Clemson University(克莱姆森大学计算学院)
LightM-UNet: Mamba Assists in Lightweight UNet for Medical Image Segmentation
School of Computer Science, Peking University(北京大学计算机学院);Institute of Artificial Intelligence, Beihang University(北京航空航天大学人工智能研究院);Key Laboratory of High Confidence Software Technologies, Ministry of Education(教育部高可信软件技术重点实验室);National Engineering Research Center for Software Engineering, Peking University(北京大学国家软件工程研究中心)
nnSAM2: nnUNet-Enhanced One-Prompt SAM2 for Few-shot Multi-Modality Segmentation and Composition Analysis of Lumbar Paraspinal Muscles
School of Information and Communication Technology, Griffith University(格里菲斯大学信息与通信技术学院);School of Allied Health, Sport and Social Work, Griffith University(格里菲斯大学联合健康、体育与社会工作学院);Center for Neuroplasticity and Pain (CNAP), Department of Health Science and Technology, Aalborg University(奥尔堡大学健康科学与技术系神经可塑性与疼痛中心)
The manual ground truth of abdominal multi-organ is labor-intensive. In order to make full use of CT data, we developed a semi-supervised learning based dual-light UNet. In the training phase, it consists of two light UNets, which make full use of label and unlabeled data simultaneously by using consistent-based learning. Moreover, separable convolution and residual concatenation was introduced light UNet to reduce the computational cost. Further, a robust segmentation loss was applied to improve the performance. In the inference phase, only a light UNet is used, which required low time cost a…
Technische Universität München(慕尼黑工业大学);Fudan University(复旦大学);Huawei Technologies(华为技术有限公司)
In the past few years, convolutional neural networks (CNNs) have achieved milestones in medical image analysis. Especially, the deep neural networks based on U-shaped architecture and skip-connections have been widely applied in a variety of medical image tasks. However, although CNN has achieved excellent performance, it cannot learn global and long-range semantic information interaction well due to the locality of the convolution operation. In this paper, we propose Swin-Unet, which is an Unet-like pure Transformer for medical image segmentation. The tokenized image patches are fed into the …
College of Medicine and Biological Information Engineering, Northeastern University(东北大学生物医学与信息工程学院);Department of Electrical and Computer Engineering, Steven Institute of Technology(史蒂文斯理工学院电气与计算机工程系);Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education(医学影像智能计算教育部重点实验室)
Whole-body PET/CT scan is an important tool for diagnosing various malignancies (e.g., malignant melanoma, lymphoma, or lung cancer), and accurate segmentation of tumors is a key part for subsequent treatment. In recent years, CNN-based segmentation methods have been extensively investigated. However, these methods often give inaccurate segmentation results, such as over-segmentation and under-segmentation. Therefore, to address such issues, we propose a post-processing method based on a graph convolutional neural network (GCN) to refine inaccurate segmentation parts and improve the overall se…
VM-UNet: Vision Mamba UNet for Medical Image Segmentation
School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University(上海交通大学电子信息与电气工程学院);School of Biomedical Engineering, Shanghai Jiao Tong University(上海交通大学生物医学工程学院)