Adversarial learning has been proven to be effective for capturing long-range and high-level label consistencies in semantic segmentation. Unique to medical imaging, capturing 3D semantics in an effective yet computationally efficient way remains an open problem. In this study, we address this computational burden by proposing a novel projective adversarial network, called PAN, which incorporates high-level 3D information through 2D projections. Furthermore, we introduce an attention module into our framework that helps for a selective integration of global information directly from our segmentor to our adversarial network. For the clinical application we chose pancreas segmentation from CT scans. Our proposed framework achieved state-of-the-art performance without adding to the complexity of the segmentor.
Automated and accurate 3D medical image segmentation plays an essential role in assisting medical professionals to evaluate disease progresses and make fast therapeutic schedules. Although deep convolutional neural networks (DCNNs) have widely applied to this task, the accuracy of these models still need to be further improved mainly due to their limited ability to 3D context perception. In this paper, we propose the 3D context residual network (ConResNet) for the accurate segmentation of 3D medical images. This model consists of an encoder, a segmentation decoder, and a context residual decod…
Johns Hopkins University（约翰斯·霍普金斯大学）；Johns Hopkins University School of Medicine（约翰斯·霍普金斯大学医学院）
Although deep neural networks have been a dominant method for many 2D vision tasks, it is still challenging to apply them to 3D tasks, such as medical image segmentation, due to the limited amount of annotated 3D data and limited computational resources. In this chapter, by rethinking the strategy to apply 3D Convolutional Neural Networks to segment medical images, we propose a novel 3D-based coarse-to-fine framework to efficiently tackle these challenges. The proposed 3D-based framework outperforms their 2D counterparts by a large margin since it can leverage the rich spatial information alon…
Deep learning highly relies on the quantity of annotated data. However, the annotations for 3D volumetric medical data require experienced physicians to spend hours or even days for investigation. Self-supervised learning is a potential solution to get rid of the strong requirement of training data by deeply exploiting raw data information. In this paper, we propose a novel self-supervised learning framework for volumetric medical images. Specifically, we propose a context restoration task, i.e., Rubik's cube++, to pre-train 3D neural networks. Different from the existing context-restoration-b…
Johns Hopkins University（约翰斯·霍普金斯大学）；Shanghai University（上海大学）；Johns Hopkins University School of Medicine（约翰斯·霍普金斯大学医学院）
In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial infor- mation along all three axes. We conduct ex…
SegDINO: Introducing Multi-Scale Structure into DINO for Efficient Medical Image Segmentation
The Hong Kong University of Science and Technology (Guangzhou)（香港科技大学（广州））；Sun Yat-sen University Cancer Center（中山大学肿瘤防治中心）；Imperial College London（帝国理工学院）
Federal Institute of Education, Science and Technology of Brasilia（巴西利亚联邦教育、科学与技术学院）
Telemedicine and mobile health applications, especially during the quarantine imposed by the covid-19 pandemic, led to an increase on the need of transferring health monitor readings from patients to specialists. Considering that most home medical devices use seven-segment displays, an automatic display reading algorithm should provide a more reliable tool for remote health care. This work proposes an end-to-end method for detection and reading seven-segment displays from medical devices based on deep learning object detection models. Two state of the art model families, EfficientDet and Effic…
Nagoya University（名古屋大学）；National Taiwan University（国立台湾大学）；NVIDIA Corporation（英伟达公司）；National Taiwan University Hospital（国立台湾大学医学院附设医院）
Federated learning (FL) for medical image segmentation becomes more challenging in multi-task settings where clients might have different categories of labels represented in their data. For example, one client might have patient data with "healthy'' pancreases only while datasets from other clients may contain cases with pancreatic tumors. The vanilla federated averaging algorithm makes it possible to obtain more generalizable deep learning-based segmentation models representing the training data from multiple institutions without centralizing datasets. However, it might be sub-optimal for the…
Background Matters: A Cross-view Bidirectional Modeling Framework for Semi-supervised Medical Image Segmentation
State Key Laboratory for Novel Software Technology, Nanjing University（新型软件技术国家重点实验室，南京大学）；College of Physics and Information Engineering, Fuzhou University（福州大学物理与信息工程学院）；National Institute of Healthcare Data Science, Nanjing University（健康数据科学国家研究院，南京大学）；Nanjing Drum Tower Hospital（南京鼓楼医院）
Image segmentation for video analysis plays an essential role in different research fields such as smart city, healthcare, computer vision and geoscience, and remote sensing applications. In this regard, a significant effort has been devoted recently to developing novel segmentation strategies; one of the latest outstanding achievements is panoptic segmentation. The latter has resulted from the fusion of semantic and instance segmentation. Explicitly, panoptic segmentation is currently under study to help gain a more nuanced knowledge of the image scenes for video surveillance, crowd counting,…
Hebei University of Technology（河北工业大学）；University of Macau（澳门大学）；University of Oxford（牛津大学）；Hospital of Joint Logistics Support Force（联勤保障部队第九八三医院）
Deep learning-based medical image segmentation technology aims at automatic recognizing and annotating objects on the medical image. Non-local attention and feature learning by multi-scale methods are widely used to model network, which drives progress in medical image segmentation. However, those attention mechanism methods have weakly non-local receptive fields' strengthened connection for small objects in medical images. Then, the features of important small objects in abstract or coarse feature maps may be deserted, which leads to unsatisfactory performance. Moreover, the existing multi-sc…
University of Toronto（多伦多大学）；Lunenfeld-Tanenbaum Research Institute, Sinai Health System（西奈卫生系统卢嫩菲尔德-塔南鲍姆研究所）；McMaster University（麦克马斯特大学）；Hamilton Health Sciences（汉密尔顿健康科学中心）；Sunnybrook Health Sciences Centre（桑尼布鲁克健康科学中心）；Sunnybrook Research Institute（桑尼布鲁克研究所）
Cox proportional hazard model (CPH) is commonly used in clinical research for survival analysis. In quantitative medical imaging (radiomics) studies, CPH plays an important role in feature reduction and modeling. However, the underlying linear assumption of CPH model limits the prognostic performance. In addition, the multicollinearity of radiomic features and multiple testing problem further impedes the CPH models performance. In this work, using transfer learning, a convolutional neural network (CNN) based survival model was built and tested on preoperative CT images of resectable Pancreatic…
Deep learning algorithms, in particular 2D and 3D fully convolutional neural networks (FCNs), have rapidly become the mainstream methodology for volumetric medical image segmentation. However, 2D convolutions cannot fully leverage the rich spatial information along the third axis, while 3D convolutions suffer from the demanding computation and high GPU memory consumption. In this paper, we propose to automatically search the network architecture tailoring to volumetric medical image segmentation problem. Concretely, we formulate the structure learning as differentiable neural architecture sear…
This work tackles the problem of generating a medical report for multi-image panels. We apply our solution to the Renal Direct Immunofluorescence (RDIF) assay which requires a pathologist to generate a report based on observations across the eight different WSI in concert with existing clinical features. To this end, we propose a novel attention-based multi-modal generative recurrent neural network (RNN) architecture capable of dynamically sampling image data concurrently across the RDIF panel. The proposed methodology incorporates text from the clinical notes of the requesting physician to re…
Pancreatic Tumor Segmentation as Anomaly Detection in CT Images Using Denoising Diffusion Models
School of Electrical and Computer Engineering, University of Oklahoma（俄克拉荷马大学电气与计算机工程学院）；University of Oklahoma Health Sciences Center（俄克拉荷马大学健康科学中心）；School of Computer Science, University of Oklahoma（俄克拉荷马大学计算机科学学院）
Technical University of Munich（慕尼黑工业大学）；Institute for Artificial Intelligence in Medicine and Healthcare, Technical University of Munich（慕尼黑工业大学医学与健康人工智能研究所）；OpenMined；Imperial College London（帝国理工学院）
For artificial intelligence-based image analysis methods to reach clinical applicability, the development of high-performance algorithms is crucial. For example, existent segmentation algorithms based on natural images are neither efficient in their parameter use nor optimized for medical imaging. Here we present MoNet, a highly optimized neural-network-based pancreatic segmentation algorithm focused on achieving high performance by efficient multi-scale image feature utilization.
National Taiwan University（台湾大学）；Nagoya University（名古屋大学）；NVIDIA Corporation（英伟达公司）；Aichi Cancer Center（爱知癌症中心）；National Taiwan University Hospital（台湾大学医学院附设医院）
The performance of deep learning-based methods strongly relies on the number of datasets used for training. Many efforts have been made to increase the data in the medical image analysis field. However, unlike photography images, it is hard to generate centralized databases to collect medical images because of numerous technical, legal, and privacy issues. In this work, we study the use of federated learning between two institutions in a real-world setting to collaboratively train a model without sharing the raw data across national boundaries. We quantitatively compare the segmentation models…
School of Computer Science（计算机科学学院）；The University of Adelaide（阿德莱德大学）
Spatially varying warps are increasingly popular for image alignment. In particular, as-projective-as-possible (APAP) warps have been proven effective for accurate panoramic stitching, especially in cases with significant depth parallax that defeat standard homographic warps. However, estimating spatially varying warps requires a sufficient number of feature matches. In image regions where feature detection or matching fail, the warp loses guidance and is unable to accurately model the true underlying warp, thus resulting in poor registration. In this paper, we propose a correspondence inserti…
Pyramid Attention Network for Medical Image Registration
School of Biomedical Engineering, Shenzhen University（深圳大学生物医学工程学院）；Medical UltraSound Image Computing (MUSIC) Lab（医学超声图像计算实验室）；Smart Medical Imaging, Learning and Engineering (SMILE) Lab（智能医学影像、学习与工程实验室）
Technical University of Berlin, Germany（柏林工业大学（德国））；Hasso Plattner Institute for Digital Engineering, University of Potsdam, Germany（波茨坦大学哈索普拉特纳数字工程研究所（德国））；Hasso Plattner Institute for Digital Health at the Icahn School of Medicine at Mount Sinai, NYC, USA（西奈山伊坎医学院哈索普拉特纳数字健康研究所（美国纽约市））
Self-supervised learning methods can be used to learn meaningful representations from unlabeled data that can be transferred to supervised downstream tasks to reduce the need for labeled data. In this paper, we propose a 3D self-supervised method that is based on the contrastive (SimCLR) method. Additionally, we show that employing Bayesian neural networks (with Monte-Carlo Dropout) during the inference phase can further enhance the results on the downstream tasks. We showcase our models on two medical imaging segmentation tasks: i) Brain Tumor Segmentation from 3D MRI, ii) Pancreas Tumor Segm…
Deepwise AI Lab（深睿人工智能实验室）；The University of Hong Kong（香港大学）；Sun Yat-sen University（中山大学）
Recently 3D volumetric organ segmentation attracts much research interest in medical image analysis due to its significance in computer aided diagnosis. This paper aims to address the pancreas segmentation task in 3D computed tomography volumes. We propose a novel end-to-end network, Globally Guided Progressive Fusion Network, as an effective and efficient solution to volumetric segmentation, which involves both global features and complicated 3D geometric information. A progressive fusion network is devised to extract 3D information from a moderate number of neighboring slices and predict a p…
Shanghai Jiao Tong University（上海交通大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；East China Normal University（华东师范大学）
Shape information is a strong and valuable prior in segmenting organs in medical images. However, most current deep learning based segmentation algorithms have not taken shape information into consideration, which can lead to bias towards texture. We aim at modeling shape explicitly and using it to help medical image segmentation. Previous methods proposed Variational Autoencoder (VAE) based models to learn the distribution of shape for a particular organ and used it to automatically evaluate the quality of a segmentation prediction by fitting it into the learned shape distribution. Based on w…
Centre for Research and Technology Hellas (CERTH)（希腊研究与技术中心（CERTH））；Information Technologies Institute (ITI)（信息技术研究所（ITI））
Recent work on depth estimation up to now has only focused on projective images ignoring 360 content which is now increasingly and more easily produced. We show that monocular depth estimation models trained on traditional images produce sub-optimal results on omnidirectional images, showcasing the need for training directly on 360 datasets, which however, are hard to acquire. In this work, we circumvent the challenges associated with acquiring high quality 360 datasets with ground truth depth annotations, by re-using recently released large scale 3D datasets and re-purposing them to 360 via r…
Segmentation of pancreas is important for medical image analysis, yet it faces great challenges of class imbalance, background distractions and non-rigid geometrical features. To address these difficulties, we introduce a Deep Q Network(DQN) driven approach with deformable U-Net to accurately segment the pancreas by explicitly interacting with contextual information and extract anisotropic features from pancreas. The DQN based model learns a context-adaptive localization policy to produce a visually tightened and precise localization bounding box of the pancreas. Furthermore, deformable U-Net …
3DGAUnet: 3D generative adversarial networks with a 3D U-Net based generator to achieve the accurate and effective synthesis of clinical tumor image data for pancreatic cancer
University of Nebraska-Lincoln（内布拉斯加大学林肯分校）；University of Nebraska Medical Center（内布拉斯加大学医学中心）；University of Rochester Medical Center（罗切斯特大学医学中心）
Visual Search Patterns in 3D Pancreatic Imaging: An Eye Tracking Study
Department of Computer Science, University of Copenhagen（哥本哈根大学计算机科学系）；Department of Radiology, Herlev Hospital（赫尔勒夫医院放射科）；Department of Radiology, University of Iowa（爱荷华大学放射科）
Medical Image Classification on Imbalanced Data Using ProGAN and SMA-Optimized ResNet: Application to COVID-19
Department of Mechatronics, School of Intelligent Systems College of Interdisciplinary Science and Technology University of Tehran（塔里克大学机械工程系、智能系统学院跨学科科学与技术学院）；School of Science and Technology Faculty of Science, Agriculture, Business and Law University of New England（新英格兰大学科学与技术学院科学、农业、商业与法学院）
University of California Los Angeles（加利福尼亚大学洛杉矶分校）
Due to the fact that pancreas is an abdominal organ with very large variations in shape and size, automatic and accurate pancreas segmentation can be challenging for medical image analysis. In this work, we proposed a fully automated two stage framework for pancreas segmentation based on convolutional neural networks (CNN). In the first stage, a U-Net is trained for the down-sampled 3D volume segmentation. Then a candidate region covering the pancreas is extracted from the estimated labels. Motivated by the superior performance reported by renowned region based CNN, in the second stage, anothe…
In medical imaging, there are clinically relevant segmentation tasks where the output mask is a projection to a subset of input image dimensions. In this work, we propose a novel convolutional neural network architecture that can effectively learn to produce a lower-dimensional segmentation mask than the input image. The network restores encoded representation only in a subset of input spatial dimensions and keeps the representation unchanged in the others. The newly proposed projective skip-connections allow linking the encoder and decoder in a UNet-like structure. We evaluated the proposed m…
Accurate automatic organ segmentation is an important yet challenging problem for medical image analysis. The pancreas is an abdominal organ with very high anatomical variability. This inhibits traditional segmentation methods from achieving high accuracies, especially compared to other organs such as the liver, heart or kidneys. In this paper, we present a holistic learning approach that integrates semantic mid-level cues of deeply-learned organ interior and boundary maps via robust spatial aggregation using random forest. Our method generates boundary preserving pixel-wise class labels for p…
Differentiable rendering is a technique to connect 3D scenes with corresponding 2D images. Since it is differentiable, processes during image formation can be learned. Previous approaches to differentiable rendering focus on mesh-based representations of 3D scenes, which is inappropriate for medical applications where volumetric, voxelized models are used to represent anatomy. We propose a novel Projective Spatial Transformer module that generalizes spatial transformers to projective geometry, thus enabling differentiable volume rendering. We demonstrate the usefulness of this architecture on …
Pancreatic cancer is one of the deadliest types of cancer, with 25% of the diagnosed patients surviving for only one year and 6% of them for five. Computed tomography (CT) screening trials have played a key role in improving early detection of pancreatic cancer, which has shown significant improvement in patient survival rates. However, advanced analysis of such images often requires manual segmentation of the pancreas, which is a time-consuming task. Moreover, pancreas presents high variability in shape, while occupying only a very small area of the entire abdominal CT scans, which increases …
Compositional Reward Models for Conditional Medical Image Generation
Yardi School of Artificial Intelligence（亚尔迪人工智能学院）；Indian Institute Of Technology, Delhi（德里印度理工学院）；Indian Institute of Science（印度科学学院）；Department of Computer Science and Engineering（计算机科学与工程系）
LIPN-UMR-CNRS 7030（法国国家科学研究中心7030联合研究单元LIPN实验室）；Sorbonne University Paris Nord（巴黎北索邦大学）；Amirkabir University of Technology（阿米尔卡比尔理工大学）；Laboratory of Images, Signals and Intelligent Systems（图像、信号与智能系统实验室）；Université Paris-Est Créteil（巴黎东克雷泰伊大学）
Manual segmentation of medical images (e.g., segmenting tumors in CT scans) is a high-effort task that can be accelerated with machine learning techniques. However, selecting the right segmentation approach depends on the evaluation function, particularly in medical image segmentation where we must deal with dependency between voxels. For instance, in contrast to classical systems where the predictions are either correct or incorrect, predictions in medical image segmentation may be partially correct and incorrect simultaneously. In this paper, we explore this expressiveness to extract the use…
Beihang University（北京航空航天大学）；University of Oxford（牛津大学）；The Affiliated Hospital of Qingdao University（青岛大学附属医院）
As Deep Convolutional Neural Networks (DCNNs) have shown robust performance and results in medical image analysis, a number of deep-learning-based tumor detection methods were developed in recent years. Nowadays, the automatic detection of pancreatic tumors using contrast-enhanced Computed Tomography (CT) is widely applied for the diagnosis and staging of pancreatic cancer. Traditional hand-crafted methods only extract low-level features. Normal convolutional neural networks, however, fail to make full use of effective context information, which causes inferior detection results. In this paper…
