Existing techniques to encode spatial invariance within deep convolutional neural networks (CNNs) apply the same warping field to all the feature channels. This does not account for the fact that the individual feature channels can represent different semantic parts, which can undergo different spatial transformations w.r.t. a canonical configuration. To overcome this limitation, we introduce a learnable module, the volumetric transformer network (VTN), that predicts channel-wise warping fields so as to reconfigure intermediate CNN features spatially and channel-wisely. We design our VTN as an encoder-decoder network, with modules dedicated to letting the information flow across the feature channels, to account for the dependencies between the semantic parts. We further propose a loss function defined between the warped features of pairs of instances, which improves the localization ability of VTN. Our experiments show that VTN consistently boosts the features' representation power and consequently the networks' accuracy on fine-grained image recognition and instance-level image retrieval.
3D shape models that directly classify objects from 3D information have become more widely implementable. Current state of the art models rely on deep convolutional and inception models that are resource intensive. Residual neural networks have been demonstrated to be easier to optimize and do not suffer from vanishing/exploding gradients observed in deep networks. Here we implement a residual neural network for 3D object classification of the 3D Princeton ModelNet dataset. Further, we show that widening network layers dramatically improves accuracy in shallow residual nets, and residual neura…
Department of Statistics, University of Chicago, Chicago, USA（统计系，芝加哥大学，芝加哥，美国）；Department of Computer Science, University of Chicago, Chicago, USA（计算机科学系，芝加哥大学，芝加哥，美国）
Xiamen University（厦门大学）；The University of Hong Kong（香港大学）；Shenzhen Research Institute of Big Data, The Chinese University of Hong Kong (Shenzhen)（香港中文大学（深圳）深圳大数据研究院）
Transformer, the model of choice for natural language processing, has drawn scant attention from the medical imaging community. Given the ability to exploit long-term dependencies, transformers are promising to help atypical convolutional neural networks to overcome their inherent shortcomings of spatial inductive bias. However, most of recently proposed transformer-based segmentation approaches simply treated transformers as assisted modules to help encode global context into convolutional representations. To address this issue, we introduce nnFormer, a 3D transformer for volumetric medical i…
VolDiT: Controllable Volumetric Medical Image Synthesis with Diffusion Transformers
Institute for Artificial Intelligence in Cardiovascular Medicine, Medical Faculty of Heidelberg University, Heidelberg University（海德堡大学医学院心血管医学人工智能研究所）；Department of Cardiology, Angiology, Pneumology, Heidelberg University Hospital（海德堡大学医院心脏病学、血管学、肺病学系）；DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim（德国心血管研究中心（DZHK）海德堡/曼海姆合作站点）；University Medical Center of the Johannes Gutenberg-University Mainz（美因茨约翰内斯·古腾堡大学医学中心）
Hybrid Transformer-Mamba for Weakly Supervised Volumetric Medical Segmentation
University of Western Australia（西澳大学）；Harry Perkins Institute of Medical Research（哈利·佩金斯医学研究所）；National Imaging Facility（国家成像设施）；Fiona Stanley Hospital（菲奥娜·斯蒂尔医院）；Victor Chang Cardiac Research Institute（维多利亚·张心脏研究中心）
The recent 3D medical ViTs (e.g., SwinUNETR) achieve the state-of-the-art performances on several 3D volumetric data benchmarks, including 3D medical image segmentation. Hierarchical transformers (e.g., Swin Transformers) reintroduced several ConvNet priors and further enhanced the practical viability of adapting volumetric segmentation in 3D medical datasets. The effectiveness of hybrid approaches is largely credited to the large receptive field for non-local self-attention and the large number of model parameters. In this work, we propose a lightweight volumetric ConvNet, termed 3D UX-Net, w…
We propose a Transformer architecture for volumetric segmentation, a challenging task that requires keeping a complex balance in encoding local and global spatial cues, and preserving information along all axes of the volume. Encoder of the proposed design benefits from self-attention mechanism to simultaneously encode local and global cues, while the decoder employs a parallel self and cross attention formulation to capture fine details for boundary refinement. Empirically, we show that the proposed design choices result in a computationally efficient model, with competitive and promising res…
University of California, Santa Barbara（加州大学圣巴巴拉分校）
Recent volumetric 3D reconstruction methods can produce very accurate results, with plausible geometry even for unobserved surfaces. However, they face an undesirable trade-off when it comes to multi-view fusion. They can fuse all available view information by global averaging, thus losing fine detail, or they can heuristically cluster views for local fusion, thus restricting their ability to consider all views jointly. Our key insight is that greater detail can be retained without restricting view diversity by learning a view-fusion function conditioned on camera pose and image content. We pr…
Johns Hopkins University（约翰斯·霍普金斯大学）；Johns Hopkins Medical Institutes（约翰斯·霍普金斯医学研究所）
In the last decade, convolutional neural networks (ConvNets) have dominated and achieved state-of-the-art performances in a variety of medical imaging applications. However, the performances of ConvNets are still limited by lacking the understanding of long-range spatial relations in an image. The recently proposed Vision Transformer (ViT) for image classification uses a purely self-attention-based model that learns long-range spatial relations to focus on the relevant parts of an image. Nevertheless, ViT emphasizes the low-resolution features because of the consecutive downsamplings, result i…
Infervision Medical Technology Co., Ltd.（推想医疗科技有限公司）；UCLA（加州大学洛杉矶分校）
In clinical practice, anisotropic volumetric medical images with low through-plane resolution are commonly used due to short acquisition time and lower storage cost. Nevertheless, the coarse resolution may lead to difficulties in medical diagnosis by either physicians or computer-aided diagnosis algorithms. Deep learning-based volumetric super-resolution (SR) methods are feasible ways to improve resolution, with convolutional neural networks (CNN) at their core. Despite recent progress, these methods are limited by inherent properties of convolution operators, which ignore content relevance an…
University of Science and Technology Beijing（北京科技大学）；University of Central Florida（中佛罗里达大学）
Transformer, benefiting from global (long-range) information modeling using self-attention mechanism, has been successful in natural language processing and computer vision recently. Convolutional Neural Networks, capable of capturing local features, are difficult to model explicit long-distance dependencies from global feature space. However, both local and global features are crucial for dense prediction tasks, especially for 3D medical image segmentation. In this paper, we present the further attempt to exploit Transformer in 3D CNN for 3D medical image volumetric segmentation and propose a…
In the isointense stage, the accurate volumetric image segmentation is a challenging task due to the low contrast between tissues. In this paper, we propose a novel very deep network architecture based on a densely convolutional network for volumetric brain segmentation. The proposed network architecture provides a dense connection between layers that aims to improve the information flow in the network. By concatenating features map of fine and coarse dense blocks, it allows capturing multi-scale contextual information. Experimental results demonstrate significant advantages of the proposed me…
Recently deep residual learning with residual units for training very deep neural networks advanced the state-of-the-art performance on 2D image recognition tasks, e.g., object detection and segmentation. However, how to fully leverage contextual representations for recognition tasks from volumetric data has not been well studied, especially in the field of medical image computing, where a majority of image modalities are in volumetric format. In this paper we explore the deep residual learning on the task of volumetric brain segmentation. There are at least two main contributions in our work.…
University of Freiburg（弗莱堡大学）；BIOSS Centre for Biological Signalling Studies（BIOSS生物信号研究中心）；University Medical Center Freiburg（弗莱堡大学医学中心）；University Hospital Freiburg（弗莱堡大学医院）；Google DeepMind（谷歌DeepMind）
This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from Ronn…
NYU Multimedia and Visual Computing Lab（纽约大学多媒体与视觉计算实验室）；NYU Abu Dhabi（纽约大学阿布扎比分校）；New York University（纽约大学）
Recently researchers have been shifting their focus towards learned 3D shape descriptors from hand-craft ones to better address challenging issues of the deformation and structural variation inherently present in 3D objects. 3D geometric data are often transformed to 3D Voxel grids with regular format in order to be better fed to a deep neural net architecture. However, the computational intractability of direct application of 3D convolutional nets to 3D volumetric data severely limits the efficiency (i.e. slow processing) and effectiveness (i.e. unsatisfied accuracy) in processing 3D geometri…
We propose an attention mechanism for 3D medical image segmentation. The method, named segmentation-by-detection, is a cascade of a detection module followed by a segmentation module. The detection module enables a region of interest to come to attention and produces a set of object region candidates which are further used as an attention model. Rather than dealing with the entire volume, the segmentation module distills the information from the potential region. This scheme is an efficient solution for volumetric data as it reduces the influence of the surrounding noise which is especially im…
The design, analysis and application of a volumetric convolutional neural network (VCNN) are studied in this work. Although many CNNs have been proposed in the literature, their design is empirical. In the design of the VCNN, we propose a feed-forward K-means clustering algorithm to determine the filter number and size at each convolutional layer systematically. For the analysis of the VCNN, the cause of confusing classes in the output of the VCNN is explained by analyzing the relationship between the filter weights (also known as anchor vectors) from the last fully-connected layer to the outp…
We present 3DVNet, a novel multi-view stereo (MVS) depth-prediction method that combines the advantages of previous depth-based and volumetric MVS approaches. Our key idea is the use of a 3D scene-modeling network that iteratively updates a set of coarse depth predictions, resulting in highly accurate predictions which agree on the underlying scene geometry. Unlike existing depth-prediction techniques, our method uses a volumetric 3D convolutional neural network (CNN) that operates in world space on all depth maps jointly. The network can therefore learn meaningful scene-level priors. Furtherm…
We introduce a convolutional neural network for inferring a compact disentangled graphical description of objects from 2D images that can be used for volumetric reconstruction. The network comprises an encoder and a twin-tailed decoder. The encoder generates a disentangled graphics code. The first decoder generates a volume, and the second decoder reconstructs the input image using a novel training regime that allows the graphics code to learn a separate representation of the 3D object and a description of its lighting and pose conditions. We demonstrate this method by generating volumes and d…
MISCGrasp: Leveraging Multiple Integrated Scales and Contrastive Learning for Enhanced Volumetric Grasping
State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences（多模态人工智能系统国家重点实验室，自动化研究所，中国科学院）；School of Artificial Intelligence, University of Chinese Academy of Sciences（中国科学院大学人工智能学院）；Qiyuan Lab（启元实验室）
ASRI, Seoul National University（首尔国立大学自动化与系统研究所）；Kwangwoon University（光云大学）
We propose a novel approach to 3D human pose estimation from a single depth map. Recently, convolutional neural network (CNN) has become a powerful paradigm in computer vision. Many of computer vision tasks have benefited from CNNs, however, the conventional approach to directly regress 3D body joint locations from an image does not yield a noticeably improved performance. In contrast, we formulate the problem as estimating per-voxel likelihood of key body joints from a 3D occupancy grid. We argue that learning a mapping from volumetric input to volumetric output with 3D convolution consistent…
The Johns Hopkins University（约翰斯·霍普金斯大学）；The Johns Hopkins University School of Medicine（约翰斯·霍普金斯大学医学院）
There has been a debate on whether to use 2D or 3D deep neural networks for volumetric organ segmentation. Both 2D and 3D models have their advantages and disadvantages. In this paper, we present an alternative framework, which trains 2D networks on different viewpoints for segmentation, and builds a 3D Volumetric Fusion Net (VFN) to fuse the 2D segmentation results. VFN is relatively shallow and contains much fewer parameters than most 3D networks, making our framework more efficient at integrating 3D information for segmentation. We train and test the segmentation and fusion modules individu…
Human shape estimation is an important task for video editing, animation and fashion industry. Predicting 3D human body shape from natural images, however, is highly challenging due to factors such as variation in human bodies, clothing and viewpoint. Prior methods addressing this problem typically attempt to fit parametric body models with certain priors on pose and shape. In this work we argue for an alternative representation and propose BodyNet, a neural network for direct inference of volumetric body shape from a single image. BodyNet is an end-to-end trainable network that benefits from …
Technische Universität München（慕尼黑工业大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；Klinikum Grosshadern（大哈登医院）；Ludwig-Maximilians-Universität München（慕尼黑大学）
Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most medical data used in clinical practice consists of 3D volumes. In this work we propose an approach to 3D image segmentation based on a volumetric, fully convolutional, neural network. Our CNN is trained end-to-end on MRI volumes depicting prostate, and learns to predict segmentation for the whole volume at once. We introduce a novel objective function, that we o…
Deep convolutional neural networks are powerful tools for learning visual representations from images. However, designing efficient deep architectures to analyse volumetric medical images remains challenging. This work investigates efficient and flexible elements of modern convolutional networks such as dilated convolution and residual connection. With these essential building blocks, we propose a high-resolution, compact convolutional network for volumetric image segmentation. To illustrate its efficiency of learning 3D representation from large-scale image data, the proposed network is valid…
Anhui University（安徽大学）；China University of Mining and Technology（中国矿业大学）
With the thriving of deep learning, 3D Convolutional Neural Networks have become a popular choice in volumetric image analysis due to their impressive 3D contexts mining ability. However, the 3D convolutional kernels will introduce a significant increase in the amount of trainable parameters. Considering the training data is often limited in biomedical tasks, a tradeoff has to be made between model size and its representational power. To address this concern, in this paper, we propose a novel 3D Dense Separated Convolution (3D-DSC) module to replace the original 3D convolutional kernels. The 3…
Stereo-LiDAR fusion is a promising task in that we can utilize two different types of 3D perceptions for practical usage -- dense 3D information (stereo cameras) and highly-accurate sparse point clouds (LiDAR). However, due to their different modalities and structures, the method of aligning sensor data is the key for successful sensor fusion. To this end, we propose a geometry-aware stereo-LiDAR fusion network for long-range depth estimation, called volumetric propagation network. The key idea of our network is to exploit sparse and accurate point clouds as a cue for guiding correspondences o…
Shanghai Jiao Tong University（上海交通大学）；University of Sydney（悉尼大学）
Dynamic medical imaging is usually limited in application due to the large radiation doses and longer image scanning and reconstruction times. Existing methods attempt to reduce the dynamic sequence by interpolating the volumes between the acquired image volumes. However, these methods are limited to either 2D images and/or are unable to support large variations in the motion between the image volume sequences. In this paper, we present a spatiotemporal volumetric interpolation network (SVIN) designed for 4D dynamic medical images. SVIN introduces dual networks: first is the spatiotemporal mot…
Contextual Embedding Learning to Enhance 2D Networks for Volumetric Image Segmentation
Shenzhen University（深圳大学）；Shenzhen University Medical School（深圳大学医学院）；School of Biomedical Engineering（生物医学工程学院）；Huawei Cloud Computing Technologies Company Limited（华为云计算技术有限公司）；Shenzhen University General Hospital（深圳大学总医院）
There are many approaches to weakly-supervised training of networks to segment 2D images. By contrast, existing approaches to segmenting volumetric images rely on full-supervision of a subset of 2D slices of the 3D volume. We propose an approach to volume segmentation that is truly weakly-supervised in the sense that we only need to provide a sparse set of 3D points on the surface of target objects instead of detailed 2D masks. We use the 3D points to deform a 3D template so that it roughly matches the target object outlines and we introduce an architecture that exploits the supervision it pro…
University of Innsbruck（因斯布鲁克大学）；Medizinische Universität Innsbruck（因斯布鲁克医科大学）
Convolutional neural networks are state-of-the-art for various segmentation tasks. While for 2D images these networks are also computationally efficient, 3D convolutions have huge storage requirements and require long training time. To overcome this issue, we introduce a network structure for volumetric data without 3D convolutional layers. The main idea is to include maximum intensity projections from different directions to transform the volumetric data to a sequence of images, where each image contains information of the full data. We then apply 2D convolutions to these projection images an…
We introduce a novel cost aggregation network, dubbed Volumetric Aggregation with Transformers (VAT), to tackle the few-shot segmentation task by using both convolutions and transformers to efficiently handle high dimensional correlation maps between query and support. In specific, we propose our encoder consisting of volume embedding module to not only transform the correlation maps into more tractable size but also inject some convolutional inductive bias and volumetric transformer module for the cost aggregation. Our encoder has a pyramidal structure to let the coarser level aggregation to …
3DQ: Compact Quantized Neural Networks for Volumetric Whole Brain Segmentation
Technical University of Munich（慕尼黑工业大学）；Ludwig Maximilian University（路德维希-马克西米利安大学）；University of California Berkeley（加州大学伯克利分校）；Johns Hopkins University（约翰斯·霍普金斯大学）
本文提出三值量化方法 3DQ，首次用于三维 F-CNN，在全脑分割任务及 3D U-Net、V-Net 上实现 16 倍压缩并保持全精度性能。
The goal of our work is to perform pixel label semantic segmentation on 3D biomedical volumetric data. Manual annotation is always difficult for a large bio-medical dataset. So, we consider two cases where one dataset is fully labeled and the other dataset is assumed to be fully unlabelled. We first perform Semantic Segmentation on the fully labeled isotropic biomedical source data (FIBSEM) and try to incorporate the the trained model for segmenting the target unlabelled dataset(SNEMI3D)which shares some similarities with the source dataset in the context of different types of cellular bodies …
This paper proposes the use of an end-to-end Convolutional Neural Network for direct reconstruction of the 3D geometry of humans via volumetric regression. The proposed method does not require the fitting of a shape model and can be trained to work from a variety of input types, whether it be landmarks, images or segmentation masks. Additionally, non-visible parts, either self-occluded or otherwise, are still reconstructed, which is not the case with depth map regression. We present results that show that our method can handle both pose variation and detailed reconstruction given appropriate d…
The high incidence rate of prostate disease poses a requirement in early detection for diagnosis. As one of the main imaging methods used for prostate cancer detection, Magnetic Resonance Imaging (MRI) has wide range of appearance and imbalance problems, making automated prostate segmentation fundamental but challenging. Here we propose a novel Densely Dilated Spatial Pooling Convolutional Network (DDSP ConNet) in encoder-decoder structure. It employs dense structure to combine dilated convolution and global pooling, thus supplies coarse segmentation results from encoder and decoder subnet and…
ETH Zurich（苏黎世联邦理工学院）；Beijing Institute of Technology（北京理工大学）
Despite recent progress of automatic medical image segmentation techniques, fully automatic results usually fail to meet the clinical use and typically require further refinement. In this work, we propose a quality-aware memory network for interactive segmentation of 3D medical images. Provided by user guidance on an arbitrary slice, an interaction network is firstly employed to obtain an initial 2D segmentation. The quality-aware memory network subsequently propagates the initial segmentation estimation bidirectionally over the entire volume. Subsequent refinement based on additional user gui…
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 …
Graduate School of Informatics, Nagoya University（名古屋大学信息学院研究生院）；Graduate School of Information Science, Nagoya University（名古屋大学信息科学研究生院）；Faculty of Information Science, Aichi Institute of Technology（爱知工业大学信息科学学院）；Nagoya University Graduate School of Medicine（名古屋大学医学院研究生院）；Department of Gastroenterological Surgery, Aichi Cancer Center Hospital（爱知癌症中心医院胃肠外科）；Information & Communications, Nagoya University（名古屋大学信息与通信学院）
Pancreas segmentation in computed tomography imaging has been historically difficult for automated methods because of the large shape and size variations between patients. In this work, we describe a custom-build 3D fully convolutional network (FCN) that can process a 3D image including the whole pancreas and produce an automatic segmentation. We investigate two variations of the 3D FCN architecture; one with concatenation and one with summation skip connections to the decoder part of the network. We evaluate our methods on a dataset from a clinical trial with gastric cancer patients, includin…
Ubisoft（育碧）；The European Institute for Molecular Imaging（欧洲分子影像研究所）
Recent advances in 3D imaging technologies provide novel insights to researchers and reveal finer and more detail of examined specimen, especially in the biomedical domain, but also impose huge challenges regarding scalability for automated analysis algorithms due to rapidly increasing dataset sizes. In particular, existing research towards automated vessel network analysis does not consider memory requirements of proposed algorithms and often generates a large number of spurious branches for structures consisting of many voxels. Additionally, very often these algorithms have further restricti…
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…
