Automatic segmentation of vertebral bodies (VBs) and intervertebral discs (IVDs) in 3D magnetic resonance (MR) images is vital in diagnosing and treating spinal diseases. However, segmenting the VBs and IVDs simultaneously is not trivial. Moreover, problems exist, including blurry segmentation caused by anisotropy resolution, high computational cost, inter-class similarity and intra-class variability, and data imbalances. We proposed a two-stage algorithm, named semi-supervised hybrid spine network (SSHSNet), to address these problems by achieving accurate simultaneous VB and IVD segmentation. In the first stage, we constructed a 2D semi-supervised DeepLabv3+ by using cross pseudo supervision to obtain intra-slice features and coarse segmentation. In the second stage, a 3D full-resolution patch-based DeepLabv3+ was built. This model can be used to extract inter-slice information and combine the coarse segmentation and intra-slice features provided from the first stage. Moreover, a cross tri-attention module was applied to compensate for the loss of inter-slice and intra-slice information separately generated from 2D and 3D networks, thereby improving feature representation ability and achieving satisfactory segmentation results. The proposed SSHSNet was validated on a publicly available spine MR image dataset, and remarkable segmentation performance was achieved. Moreover, results show that the proposed method has great potential in dealing with the data imbalance problem. Based on previous reports, few studies have incorporated a semi-supervised learning strategy with a cross attention mechanism for spine segmentation. Therefore, the proposed method may provide a useful tool for spine segmentation and aid clinically in spinal disease diagnoses and treatments. Codes are publicly available at: https://github.com/Meiyan88/SSHSNet.
Adaptive Transformer Attention and Multi-Scale Fusion for Spine 3D Segmentation
University of Houston（休斯顿大学）；New York University（纽约大学）；University of Massachusetts Boston（马萨诸塞大学波士顿分校）；University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）；Tulane University（杜兰大学）
SPINEPS -- Automatic Whole Spine Segmentation of T2-weighted MR images using a Two-Phase Approach to Multi-class Semantic and Instance Segmentation
Technical University of Munich（慕尼黑工业大学）；Klinikum rechts der Isar（伊萨尔河右岸医院）；University of Zurich（苏黎世大学）；Imperial College London（帝国理工学院）；Helmholtz Munich（亥姆霍兹慕尼黑中心）；University Medical Center Rostock（罗斯托克大学医学中心）；University of Freiburg（弗赖堡大学）；University Hospital Augsburg（奥格斯堡大学医院）；Augsburg University（奥格斯堡大学）
University of Oxford（牛津大学）；Beihang University（北京航空航天大学）
Segmentation algorithms for medical images are widely studied for various clinical and research purposes. In this paper, we propose a new and efficient method for medical image segmentation under noisy labels. The method operates under a deep learning paradigm, incorporating four novel contributions. Firstly, a residual interconnection is explored in different scale encoders to transfer gradient information efficiently. Secondly, four copy-and-crop connections are replaced by residual-block-based concatenation to alleviate the disparity between encoders and decoders. Thirdly, convolutional att…
Fundaciò per al Foment de la Investigaciò Sanitària i Biomèdica (FISABIO)（瓦伦西亚卫生与生物医学研究促进基金会（FISABIO））；Hospital Arnau de Vilanova（阿尔瑙·德·比拉诺瓦医院）；Universitat Politècnica de València（瓦伦西亚理工大学）；Regional ministry of Universal Health and Public Health in Valencia（瓦伦西亚全民健康与公共卫生部）
One of the major difficulties in medical image segmentation is the high variability of these images, which is caused by their origin (multi-centre), the acquisition protocols (multi-parametric), as well as the variability of human anatomy, the severity of the illness, the effect of age and gender, among others. The problem addressed in this work is the automatic semantic segmentation of lumbar spine Magnetic Resonance images using convolutional neural networks. The purpose is to assign a class label to each pixel of an image. Classes were defined by radiologists and correspond to different str…
Lumbar Spine Tumor Segmentation and Localization in T2 MRI Images Using AI
A. K. Choudhury School of Information Technology, University of Calcutta（加尔各答大学A.K.乔杜里信息技术学院）；Rammohan College, University of Calcutta（加尔各答大学拉莫汉学院）；Indian Statistical Institute（印度统计研究院）
SpineMamba: Enhancing 3D Spinal Segmentation in Clinical Imaging through Residual Visual Mamba Layers and Shape Priors
Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）；University of Chinese Academy of Sciences（中国科学院大学）；Northeast Petroleum University（东北石油大学）；Northeastern University（东北大学）；Southern Medical University（南方医科大学）
Combining nonparametric spatial context priors with nonparametric shape priors for dendritic spine segmentation in 2-photon microscopy images
Sabanci University（萨班哲大学）；ARM Ltd.（ARM有限公司）；University of Zurich（苏黎世大学）；University of Utah（犹他大学）；Izmir University of Economics（伊兹密尔经济大学）；University of Rochester（罗切斯特大学）
Reconstruction of 3D lumbar spine models from incomplete segmentations using landmark detection
University of Koblenz（科布伦茨大学）；Institute for Computational Visualistics（计算视觉研究所）；Institute for Medical Technology and Information Processing（医学技术与信息处理研究所）
CTSpine1K: A Large-Scale Dataset for Spinal Vertebrae Segmentation in Computed Tomography
Key Lab of Intelligent Information Processing of Chinese Academy of Sciences, Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所智能信息处理重点实验室）；Suzhou Institute of Intelligent Computing Technology, Chinese Academy of Sciences（中国科学院苏州智能计算技术研究院）；Beijing Jishuitan Hospital（北京积水潭医院）；School of Medicine, South China University of Technology（华南理工大学医学院）
ShanghaiTech University（上海科技大学）；University of Chinese Academy of Sciences（中国科学院大学）；University of Alberta（阿尔伯塔大学）
Objective: The spinous process angle (SPA) is one of the essential parameters to denote three-dimensional (3-D) deformity of spine. We propose an automatic segmentation method based on Stacked Hourglass Network (SHN) to detect the spinous processes (SP) on ultrasound (US) spine images and to measure the SPAs of clinical scoliotic subjects. Methods: The network was trained to detect vertebral SP and laminae as five landmarks on 1200 ultrasound transverse images and validated on 100 images. All the processed transverse images with highlighted SP and laminae were reconstructed into a 3D image vol…
R2MF-Net: A Recurrent Residual Multi-Path Fusion Network for Robust Multi-directional Spine X-ray Segmentation
School of Information Science & Engineering, Shandong Normal University（信息科学与工程学院，山东师范大学）；Tajik State University of Law, Business and Politics（塔吉克国立法律、商业与政治大学）
École de Technologie Supérieure（高等技术学院）；CHU Sainte-Justine Research Center（圣茹斯特医院研究中心）；Polytechnique Montréal（蒙特利尔理工学院）
Vertebral bone segmentation from magnetic resonance (MR) images is a challenging task. Due to the inherent nature of the modality to emphasize soft tissues of the body, common thresholding algorithms are ineffective in detecting bones in MR images. On the other hand, it is relatively easier to segment bones from CT images because of the high contrast between bones and the surrounding regions. For this reason, we perform a cross-modality synthesis between MR and CT domains for simple thresholding-based segmentation of the vertebral bones. However, this implicitly assumes the availability of pai…
The Hong Kong Polytechnic University（香港理工大学）；University of Technology Sydney（悉尼科技大学）；Harbin Engineering University（哈尔滨工程大学）；Department of Electronic and Information Engineering, The Hong Kong Polytechnic University（电子与信息工程系，香港理工大学）；School of Biomedical Engineering, University of Technology Sydney（生物医学工程学院，悉尼科技大学）；Department of Biomedical Engineering, The Hong Kong Polytechnic University（生物医学工程系，香港理工大学）；College of Information and Communication Engineering, Harbin Engineering University（信息与通信工程学院，哈尔滨工程大学）
3D ultrasound imaging shows great promise for scoliosis diagnosis thanks to its low-costing, radiation-free and real-time characteristics. The key to accessing scoliosis by ultrasound imaging is to accurately segment the bone area and measure the scoliosis degree based on the symmetry of the bone features. The ultrasound images tend to contain many speckles and regular occlusion noise which is difficult, tedious and time-consuming for experts to find out the bony feature. In this paper, we propose a robust bone feature segmentation method based on the U-net structure for ultrasound spine Volum…
Technische Universität München（慕尼黑工业大学）；ScintHealth GmbH（ScintHealth有限公司）；Reply SpA（Reply股份公司）；Helmholtz Zentrum München（慕尼黑亥姆霍兹中心）；Helmholtz AI（亥姆霍兹人工智能研究所）
CT and MRI are two of the most informative modalities in spinal diagnostics and treatment planning. CT is useful when analysing bony structures, while MRI gives information about the soft tissue. Thus, fusing the information of both modalities can be very beneficial. Registration is the first step for this fusion. While the soft tissues around the vertebra are deformable, each vertebral body is constrained to move rigidly. We propose a weakly-supervised deep learning framework that preserves the rigidity and the volume of each vertebra while maximizing the accuracy of the registration. To achi…
University of California, Los Angeles（加州大学洛杉矶分校）；Tencent Hippocrates Research Lab（腾讯希波克拉底研究实验室）；The University of Hong Kong（香港大学）；VoxelCloud, Inc.（VoxelCloud公司）
University of New South Wales（新南威尔士大学）；Prince of Wales Hospital（威尔士亲王医院）
Computer aided diagnostics often requires analysis of a region of interest (ROI) within a radiology scan, and the ROI may be an organ or a suborgan. Although deep learning algorithms have the ability to outperform other methods, they rely on the availability of a large amount of annotated data. Motivated by the need to address this limitation, an approach to localisation and detection of multiple organs based on supervised and semi-supervised learning is presented here. It draws upon previous work by the authors on localising the thoracic and lumbar spine region in CT images. The method genera…
Technical University of Munich（慕尼黑工业大学）；Klinikum Rechts der Isar（伊萨尔河右岸医院）；Helmholtz Zentrum München（亥姆霍兹慕尼黑中心）；Graz University of Technology（格拉茨工业大学）；Medical University of Graz（格拉茨医科大学）；The University of Auckland（奥克兰大学）；iFLYTEK Research（科大讯飞研究院）
Vertebral labelling and segmentation are two fundamental tasks in an automated spine processing pipeline. Reliable and accurate processing of spine images is expected to benefit clinical decision-support systems for diagnosis, surgery planning, and population-based analysis on spine and bone health. However, designing automated algorithms for spine processing is challenging predominantly due to considerable variations in anatomy and acquisition protocols and due to a severe shortage of publicly available data. Addressing these limitations, the Large Scale Vertebrae Segmentation Challenge (VerS…
Technical University of Munich（慕尼黑工业大学）；University Medical Center Freiburg（弗莱堡大学医学中心）
With the advent of deep learning algorithms, fully automated radiological image analysis is within reach. In spine imaging, several atlas- and shape-based as well as deep learning segmentation algorithms have been proposed, allowing for subsequent automated analysis of morphology and pathology. The first Large Scale Vertebrae Segmentation Challenge (VerSe 2019) showed that these perform well on normal anatomy, but fail in variants not frequently present in the training dataset. Building on that experience, we report on the largely increased VerSe 2020 dataset and results from the second iterat…
University of Oxford（牛津大学）；UiT The Arctic University of Norway（挪威北极大学）；Sun Yat-sen University（中山大学）；Carnegie Mellon University（卡内基梅隆大学）；Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
The data-driven nature of deep learning (DL) models for semantic segmentation requires a large number of pixel-level annotations. However, large-scale and fully labeled medical datasets are often unavailable for practical tasks. Recently, partially supervised methods have been proposed to utilize images with incomplete labels in the medical domain. To bridge the methodological gaps in partially supervised learning (PSL) under data scarcity, we propose Vicinal Labels Under Uncertainty (VLUU), a simple yet efficient framework utilizing the human structure similarity for partially supervised medi…
Korea Advanced Institute of Science and Technology (KAIST)（韩国高等科学技术研究院（KAIST））
Vessel segmentation in medical images is one of the important tasks in the diagnosis of vascular diseases and therapy planning. Although learning-based segmentation approaches have been extensively studied, a large amount of ground-truth labels are required in supervised methods and confusing background structures make neural networks hard to segment vessels in an unsupervised manner. To address this, here we introduce a novel diffusion adversarial representation learning (DARL) model that leverages a denoising diffusion probabilistic model with adversarial learning, and apply it to vessel seg…
Lesion segmentation is a core task for quantitative analysis of MRI scans of Multiple Sclerosis patients. The recent success of deep learning techniques in a variety of medical image analysis applications has renewed community interest in this challenging problem and led to a burst of activity for new algorithm development. In this survey, we investigate the supervised CNN-based methods for MS lesion segmentation. We decouple these reviewed works into their algorithmic components and discuss each separately. For methods that provide evaluations on public benchmark datasets, we report compariso…
Frenet-Serret Frame-based Decomposition for Part Segmentation of 3D Curvilinear Structures
John A. Paulson School of Engineering and Applied Sciences, Harvard University（哈佛大学约翰·A·保罗森工程与应用科学学院）；Boston College（波士顿学院）；Université de Montréal（蒙特利尔大学）；Swiss Federal Institute of Technology Lausanne（瑞士洛桑联邦理工学院）；Carnegie Mellon University（卡内基梅隆大学）；Department of Molecular and Cellular Biology, Harvard University（哈佛大学分子与细胞生物学系）
Hebei University of Technology（河北工业大学）；University of Oxford（牛津大学）
Deep learning based semi-supervised learning (SSL) methods have achieved strong performance in medical image segmentation, which can alleviate doctors' expensive annotation by utilizing a large amount of unlabeled data. Unlike most existing semi-supervised learning methods, adversarial training based methods distinguish samples from different sources by learning the data distribution of the segmentation map, leading the segmenter to generate more accurate predictions. We argue that the current performance restrictions for such approaches are the problems of feature extraction and learning pref…
Southwestern Hospital（西南医院）；Army Medical University（陆军军医大学）
Intervertebral discs (IVDs), as small joints lying between adjacent vertebrae, have played an important role in pressure buffering and tissue protection. The fully-automatic localization and segmentation of IVDs have been discussed in the literature for many years since they are crucial to spine disease diagnosis and provide quantitative parameters in the treatment. Traditionally hand-crafted features are derived based on image intensities and shape priors to localize and segment IVDs. With the advance of deep learning, various neural network models have gained great success in image analysis …
Deakin University（迪肯大学）；Lancaster University（兰卡斯特大学）；The University of Warwick（华威大学）；South China University of Technology（华南理工大学）；Medigrowth Australia Pty Ltd（澳大利亚Medigrowth私人有限公司）
As an essential prerequisite task in image-based plant phenotyping, leaf segmentation has garnered increasing attention in recent years. While self-supervised learning is emerging as an effective alternative to various computer vision tasks, its adaptation for image-based plant phenotyping remains rather unexplored. In this work, we present a self-supervised leaf segmentation framework consisting of a self-supervised semantic segmentation model, a color-based leaf segmentation algorithm, and a self-supervised color correction model. The self-supervised semantic segmentation model groups the se…
In this work, we used a semi-supervised learning method to train deep learning model that can segment the brain MRI images. The semi-supervised model uses less labeled data, and the performance is competitive with the supervised model with full labeled data. This framework could reduce the cost of labeling MRI images. We also introduced robust loss to reduce the noise effects of inaccurate labels generated in semi-supervised learning.
University of Science and Technology of China（中国科学技术大学）；Guangzhou First People’s Hospital（广州市第一人民医院）；South China University of Technology（华南理工大学）
In the paper, we present an approach for learning a single model that universally segments 33 anatomical structures, including vertebrae, pelvic bones, and abdominal organs. Our model building has to address the following challenges. Firstly, while it is ideal to learn such a model from a large-scale, fully-annotated dataset, it is practically hard to curate such a dataset. Thus, we resort to learn from a union of multiple datasets, with each dataset containing the images that are partially labeled. Secondly, along the line of partial labelling, we contribute an open-source, large-scale verteb…
Inception Institute of Artificial Intelligence（人工智能初创研究院）
Segmentation of Prostate Cancer (PCa) tissues from Gleason graded histopathology images is vital for accurate diagnosis. Although deep learning (DL) based segmentation methods achieve state-of-the-art accuracy, they rely on large datasets with manual annotations. We propose a method to synthesize for PCa histopathology images by learning the geometrical relationship between different disease labels using self-supervised learning. We use a weakly supervised segmentation approach that uses Gleason score to segment the diseased regions and the resulting segmentation map is used to train a Shape R…
Muroran Institute of Technology（室兰工业大学）；Niigata University of Health and Welfare（新潟医疗福祉大学）
To promote the development of medical image segmentation technology, AMOS, a large-scale abdominal multi-organ dataset for versatile medical image segmentation, is provided and AMOS 2022 challenge is held by using the dataset. In this report, we present our solution for the AMOS 2022 challenge. We employ residual U-Net with deep super vision as our base model. The experimental results show that the mean scores of Dice similarity coefficient and normalized surface dice are 0.8504 and 0.8476 for CT only task and CT/MRI task, respectively.
Stanford University（斯坦福大学）；Wake Forest School of Medicine（维克森林医学院）
Although supervised learning has enabled high performance for image segmentation, it requires a large amount of labeled training data, which can be difficult to obtain in the medical imaging field. Self-supervised learning (SSL) methods involving pretext tasks have shown promise in overcoming this requirement by first pretraining models using unlabeled data. In this work, we evaluate the efficacy of two SSL methods (inpainting-based pretext tasks of context prediction and context restoration) for CT and MRI image segmentation in label-limited scenarios, and investigate the effect of implementa…
University of Adelaide（阿德莱德大学）；Queensland University of Technology（昆士兰科技大学）
Intra-operative automatic semantic segmentation of knee joint structures can assist surgeons during knee arthroscopy in terms of situational awareness. However, due to poor imaging conditions (e.g., low texture, overexposure, etc.), automatic semantic segmentation is a challenging scenario, which justifies the scarce literature on this topic. In this paper, we propose a novel self-supervised monocular depth estimation to regularise the training of the semantic segmentation in knee arthroscopy. To further regularise the depth estimation, we propose the use of clean training images captured by t…
This paper presents the preliminary findings of a semi-supervised segmentation method for extracting roads from sattelite images. Artificial Neural Networks and image segmentation methods are among the most successful methods for extracting road data from satellite images. However, these models require large amounts of training data from different regions to achieve high accuracy rates. In cases where this data needs to be of more quantity or quality, it is a standard method to train deep neural networks by transferring knowledge from annotated data obtained from different sources. This study …
University of Arkansas（阿肯色大学）；Cyberlogitec Vietnam（越南赛博罗吉泰克公司）；VinAI（越南人工智能研究院）
Capsule network is a recent new deep network architecture that has been applied successfully for medical image segmentation tasks. This work extends capsule networks for volumetric medical image segmentation with self-supervised learning. To improve on the problem of weight initialization compared to previous capsule networks, we leverage self-supervised learning for capsule networks pre-training, where our pretext-task is optimized by self-reconstruction. Our capsule network, SS-3DCapsNet, has a UNet-based architecture with a 3D Capsule encoder and 3D CNNs decoder. Our experiments on multiple…
University of Electronic Science and Technology of China（电子科技大学）；Shanghai AI Lab（上海人工智能实验室）；SenseTime Research（商汤科技研究院）
Medical image segmentation plays an irreplaceable role in computer-assisted diagnosis, treatment planning, and following-up. Collecting and annotating a large-scale dataset is crucial to training a powerful segmentation model, but producing high-quality segmentation masks is an expensive and time-consuming procedure. Recently, weakly-supervised learning that uses sparse annotations (points, scribbles, bounding boxes) for network training has achieved encouraging performance and shown the potential for annotation cost reduction. However, due to the limited supervision signal of sparse annotatio…
Armed Forces Yangju Hospital（杨州武装部队医院）；Seoul National University（首尔国立大学）
For more clinical applications of deep learning models for medical image segmentation, high demands on labeled data and computational resources must be addressed. This study proposes a coarse-to-fine framework with two teacher models and a student model that combines knowledge distillation and cross teaching, a consistency regularization based on pseudo-labels, for efficient semi-supervised learning. The proposed method is demonstrated on the abdominal multi-organ segmentation task in CT images under the MICCAI FLARE 2022 challenge, with mean Dice scores of 0.8429 and 0.8520 in the validation …
The scarcity of pixel-level annotation is a prevalent problem in medical image segmentation tasks. In this paper, we introduce a novel regularization strategy involving interpolation-based mixing for semi-supervised medical image segmentation. The proposed method is a new consistency regularization strategy that encourages segmentation of interpolation of two unlabelled data to be consistent with the interpolation of segmentation maps of those data. This method represents a specific type of data-adaptive regularization paradigm which aids to minimize the overfitting of labelled data under high…
Analysis of supervised and semi-supervised GrowCut applied to segmentation of masses in mammography images
Center for Informatics, Federal University of Pernambuco（伯南布哥联邦大学信息学中心）；Department of Biomedical Engineering, Federal University of Pernambuco（伯南布哥联邦大学生物医学工程系）
