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 comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively.
Dino-NestedUNet: Unlocking Foundation Vision Encoders for Pathology Tumor Bulk Segmentation via Dense Decoding
Department of Pathology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA（病理学系，医学学院，俄亥俄州立大学韦克斯纳医学中心，哥伦布，OH，USA）；Department of Biomedical Engineering, The Ohio State University, Columbus, OH, USA（生物医学工程系，俄亥俄州立大学，哥伦布，OH，USA）
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…
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…
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…
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.
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）
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…
Background and objective: Parotid gland tumors account for approximately 2% to 10% of head and neck tumors. Preoperative tumor localization, differential diagnosis, and subsequent selection of appropriate treatment for parotid gland tumors are critical. However, the relative rarity of these tumors and the highly dispersed tissue types have left an unmet need for a subtle differential diagnosis of such neoplastic lesions based on preoperative radiomics. Recently, deep learning methods have developed rapidly, especially Transformer beats the traditional convolutional neural network in computer v…
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…
Faculty of Computer Science, AGH University of Krakow（计算机科学系，克拉科夫AGH大学）；Department of Informatics, Universitas Pembangunan Nasional Veteran Yogyakarta（信息系，全国 veterans 大学 Yogya 市）
Jordan University of Science and Technology（约旦科技大学）；Staffordshire University（斯塔福德郡大学）
Pneumothorax, also called a collapsed lung, refers to the presence of the air in the pleural space between the lung and chest wall. It can be small (no need for treatment), or large and causes death if it is not identified and treated on time. It is easily seen and identified by experts using a chest X-ray. Although this method is mostly error-free, it is time-consuming and needs expert radiologists. Recently, Computer Vision has been providing great assistance in detecting and segmenting pneumothorax. In this paper, we propose a 2-Stage Training system (2ST-UNet) to segment images with pneumo…
xLSTM-UNet can be an Effective 2D & 3D Medical Image Segmentation Backbone with Vision-LSTM (ViL) better than its Mamba Counterpart
College of Computer Science and Technology, Zhejiang University（浙江大学计算机科学与技术学院）；KOKONI, Moxin (Huzhou) Tech. Co., LTD.（墨芯（湖州）科技有限公司KOKONI）；School of Information Engineering, Huzhou University（湖州师范学院信息工程学院）；Information Systems Technology and Design Pillar, Singapore University of Technology and Design（新加坡科技设计大学信息系统技术与设计 pillar）；School of Information Science and Technology, University of Science and Technology of China（中国科学技术大学信息科学技术学院）；School of Software Technology, Zhejiang University（浙江大学软件学院）
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）
Self-Prior Guided Mamba-UNet Networks for Medical Image Super-Resolution
School of Computer Science and Engineering, Central South University（中南大学计算机科学与工程学院）；Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Central South University（中南大学机器视觉与智能医学湖南省工程研究中心）；Department of Nuclear Medicine, Henri Becquerel Cancer Center（亨利·贝克勒尔癌症中心核医学科）；University of Rouen-Normandy（鲁昂-诺曼底大学）
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…
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…
College of Computer Science and Technology, Zhejiang University（浙江大学计算机科学与技术学院）；Sir Run Run Shaw Hospital（邵逸夫医院）；College of Information Science and Engineering, Ritsumeikan University（立命馆大学信息科学与工程学院）；Research Center for Healthcare Data Science, Zhejiang Lab（之江实验室医疗数据科学研究中心）
Recently, a growing interest has been seen in deep learning-based semantic segmentation. UNet, which is one of deep learning networks with an encoder-decoder architecture, is widely used in medical image segmentation. Combining multi-scale features is one of important factors for accurate segmentation. UNet++ was developed as a modified Unet by designing an architecture with nested and dense skip connections. However, it does not explore sufficient information from full scales and there is still a large room for improvement. In this paper, we propose a novel UNet 3+, which takes advantage of f…
East China Normal University（华东师范大学）；Ryerson University（瑞尔森大学）
Sturge-Weber syndrome (SWS) is a vascular malformation disease, and it may cause blindness if the patient's condition is severe. Clinical results show that SWS can be divided into two types based on the characteristics of scleral blood vessels. Therefore, how to accurately segment scleral blood vessels has become a significant problem in computer-aided diagnosis. In this research, we propose to continuously upsample the bottom layer's feature maps to preserve image details, and design a novel Claw UNet based on UNet for scleral blood vessel segmentation. Specifically, the residual structure is…
The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance…
George Mason University（乔治梅森大学）；The MITRE Corporation（MITRE公司）
In photoacoustic tomography (PAT), the acoustic pressure waves produced by optical excitation are measured by an array of detectors and used to reconstruct an image. Sparse spatial sampling and limited-view detection are two common challenges faced in PAT. Reconstructing from incomplete data using standard methods results in severe streaking artifacts and blurring. We propose a modified convolutional neural network (CNN) architecture termed Dense Dilation UNet (DD-UNet) for correcting artifacts in 3D PAT. The DD-Net leverages the benefits of dense connectivity and dilated convolutions to impro…
It is a challenge to segment the location and size of rectal cancer tumours through deep learning. In this paper, in order to improve the ability of extracting suffi-cient feature information in rectal tumour segmentation, attention enlarged ConvNeXt UNet (AACN-UNet), is proposed. The network mainly includes two improvements: 1) the encoder stage of UNet is changed to ConvNeXt structure for encoding operation, which can not only integrate multi-scale semantic information on a large scale, but al-so reduce information loss and extract more feature information from CT images; 2) CBAM attention m…
Time-aware UNet and super-resolution deep residual networks for spatial downscaling
Department of Mathematics and Statistics（数学与统计学系）；University of Jyväskylä（于韦斯屈莱大学）；Department of Economic Sciences（经济科学系）；University of Salento（萨伦托大学）；National Centre for HPC, Big Data and Quantum Computing（高性能计算、大数据与量子计算国家中心）；National Biodiversity Future Center（国家生物多样性未来中心）；University of Helsinki（赫尔辛基大学）
Medical Image Segmentation Using Advanced Unet: VMSE-Unet and VM-Unet CBAM+
School of Computer Engineering, Kalinga Institute of Industrial Technology (KIIT) Deemed to be University（计算机工程学院，基灵加工业技术学院（KIIT）被认定为大学）；Department of Electrical and Electronics Engineering, BITS-Pilani, Pilani Campus（电气与电子工程系，BITS-帕利尼，帕利尼校区）
Shanghai University（上海大学）；Shanghai Jiao Tong University（上海交通大学）；University of Chinese Academy of Sciences（中国科学院大学）；Northeastern University（东北大学）
Liver tumor segmentation in CT images is a critical step in the diagnosis, surgical planning and postoperative evaluation of liver disease. An automatic liver and tumor segmentation method can greatly relieve physicians of the heavy workload of examining CT images and better improve the accuracy of diagnosis. In the last few decades, many modifications based on U-Net model have been proposed in the literature. However, there are relatively few improvements for the advanced UNet++ model. In our paper, we propose an encoding feature supervised UNet++(ES-UNet++) and apply it to the liver and tumo…
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 …
Robert Bosch Center of Data Science and AI, IIT Madras（印度理工学院马德拉斯分校罗伯特·博世数据科学与人工智能中心）；Indian Institute of Technology, Madras（印度理工学院马德拉斯分校）
In this work, we present our proposed method to segment the pulmonary arteries from the CT scans using Swin UNETR and U-Net-based deep neural network architecture. Six models, three models based on Swin UNETR, and three models based on 3D U-net with residual units were ensemble using a weighted average to make the final segmentation masks. Our team achieved a multi-level dice score of 84.36 percent through this method. The code of our work is available on the following link: https://github.com/akansh12/parse2022. This work is part of the MICCAI PARSE 2022 challenge.
Budapest University of Technology and Economics（布达佩斯技术与经济大学）；Jiangxi Normal University（江西师范大学）
The precise segmentation of retinal blood vessels is of great significance for early diagnosis of eye-related diseases such as diabetes and hypertension. In this work, we propose a lightweight network named Spatial Attention U-Net (SA-UNet) that does not require thousands of annotated training samples and can be utilized in a data augmentation manner to use the available annotated samples more efficiently. SA-UNet introduces a spatial attention module which infers the attention map along the spatial dimension, and multiplies the attention map by the input feature map for adaptive feature refin…
Imperial College London（帝国理工学院）；The University of Hong Kong（香港大学）
Transfer learning (TL) for medical image segmentation helps deep learning models achieve more accurate performances when there are scarce medical images. This study focuses on completing segmentation of the ribs from lung ultrasound images and finding the best TL technique with U-Net, a convolutional neural network for precise and fast image segmentation. Two approaches of TL were used, using a pre-trained VGG16 model to build the U-Net (V-Unet) and pre-training U-Net network with grayscale natural salient object dataset (X-Unet). Visual results and dice coefficients (DICE) of the models were …
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…
Nanjing University（南京大学）；National Institute of Healthcare Data Science at Nanjing University（南京大学医疗健康数据科学国家研究院）；Nanjing Drum Tower Hospital, Nanjing University Medical School（南京大学医学院附属鼓楼医院）；Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能科技有限公司）；Korea University（高丽大学）
Accurate segmentation of the prostate is a key step in external beam radiation therapy treatments. In this paper, we tackle the challenging task of prostate segmentation in CT images by a two-stage network with 1) the first stage to fast localize, and 2) the second stage to accurately segment the prostate. To precisely segment the prostate in the second stage, we formulate prostate segmentation into a multi-task learning framework, which includes a main task to segment the prostate, and an auxiliary task to delineate the prostate boundary. Here, the second task is applied to provide additional…
Eindhoven University of Technology（埃因霍温理工大学）；Shandong University of Science and Technology（山东科技大学）；Philips Research（飞利浦研究院）
Catheter segmentation in 3D ultrasound is important for computer-assisted cardiac intervention. However, a large amount of labeled images are required to train a successful deep convolutional neural network (CNN) to segment the catheter, which is expensive and time-consuming. In this paper, we propose a novel catheter segmentation approach, which requests fewer annotations than the supervised learning method, but nevertheless achieves better performance. Our scheme considers a deep Q learning as the pre-localization step, which avoids voxel-level annotation and which can efficiently localize t…
Recent advances in transformer-based models have drawn attention to exploring these techniques in medical image segmentation, especially in conjunction with the U-Net model (or its variants), which has shown great success in medical image segmentation, under both 2D and 3D settings. Current 2D based methods either directly replace convolutional layers with pure transformers or consider a transformer as an additional intermediate encoder between the encoder and decoder of U-Net. However, these approaches only consider the attention encoding within one single slice and do not utilize the axial-a…
Although convolutional neural networks (CNNs) are promoting the development of medical image semantic segmentation, the standard model still has some shortcomings. First, the feature mapping from the encoder and decoder sub-networks in the skip connection operation has a large semantic difference. Second, the remote feature dependence is not effectively modeled. Third, the global context information of different scales is ignored. In this paper, we try to eliminate semantic ambiguity in skip connection operations by adding attention gates (AGs), and use attention mechanisms to combine local fe…
VinAI Research（VinAI研究院）；University of Arkansas（阿肯色大学）
Medical image segmentation has been so far achieving promising results with Convolutional Neural Networks (CNNs). However, it is arguable that in traditional CNNs, its pooling layer tends to discard important information such as positions. Moreover, CNNs are sensitive to rotation and affine transformation. Capsule network is a data-efficient network design proposed to overcome such limitations by replacing pooling layers with dynamic routing and convolutional strides, which aims to preserve the part-whole relationships. Capsule network has shown a great performance in image recognition and nat…
L-UNet: An LSTM Network for Remote Sensing Image Change Detection
College of Life Sciences and Oceanography, Shenzhen University（深圳大学生命科学与海洋学院）；School of Computer Science, China University of Geosciences（中国地质大学（武汉）计算机学院）
Erasmus MC（伊拉斯姆斯医学中心）；Erasmus MC-Sophia Children Hospital（伊拉斯姆斯医学中心索菲亚儿童医院）；University of Copenhagen（哥本哈根大学）；Herlev-Gentofte Hospital, Copenhagen University Hospital（哥本哈根大学医院海尔鲁夫-根措夫特医院）
We present an end-to-end deep learning segmentation method by combining a 3D UNet architecture with a graph neural network (GNN) model. In this approach, the convolutional layers at the deepest level of the UNet are replaced by a GNN-based module with a series of graph convolutions. The dense feature maps at this level are transformed into a graph input to the GNN module. The incorporation of graph convolutions in the UNet provides nodes in the graph with information that is based on node connectivity, in addition to the local features learnt through the downsampled paths. This information can…
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 …
Indian Institute of Information Technology Allahabad（阿拉哈巴德印度信息技术学院）
Deep learning has brought the most profound contribution towards biomedical image segmentation to automate the process of delineation in medical imaging. To accomplish such task, the models are required to be trained using huge amount of annotated or labelled data that highlights the region of interest with a binary mask. However, efficient generation of the annotations for such huge data requires expert biomedical analysts and extensive manual effort. It is a tedious and expensive task, while also being vulnerable to human error. To address this problem, a self-supervised learning framework, …
We propose an image-based cellular contractile force evaluation method using a machine learning technique. We use a special substrate that exhibits wrinkles when cells grab the substrate and contract, and the wrinkles can be used to visualize the force magnitude and direction. In order to extract wrinkles from the microscope images, we develop a new CNN (convolutional neural network) architecture SW-UNet (small-world U-Net), which is a CNN that reflects the concept of the small-world network. The SW-UNet shows better performance in wrinkle segmentation task compared to other methods: the error…
UNet [27] is widely used in semantic segmentation due to its simplicity and effectiveness. However, its manually-designed architecture is applied to a large number of problem settings, either with no architecture optimizations, or with manual tuning, which is time consuming and can be sub-optimal. In this work, firstly, we propose Markov Random Field Neural Architecture Search (MRF-NAS) that extends and improves the recent Adaptive and Optimal Network Width Search (AOWS) method [4] with (i) a more general MRF framework (ii) diverse M-best loopy inference (iii) differentiable parameter learning…
German Cancer Research Center (DKFZ)（德国癌症研究中心）；University of Heidelberg（海德堡大学）
Segmentation of endoscopic images is an essential processing step for computer and robotics-assisted interventions. The Robust-MIS challenge provides the largest dataset of annotated endoscopic images to date, with 5983 manually annotated images. Here we describe OR-UNet, our optimized robust residual 2D U-Net for endoscopic image segmentation. As the name implies, the network makes use of residual connections in the encoder. It is trained with the sum of Dice and cross-entropy loss and deep supervision. During training, extensive data augmentation is used to increase the robustness. In an 8-f…
