In this article we investigate the efficiency of deep learning algorithms in solving the task of detecting anatomical reference points on radiological images of the head in lateral projection using a fully convolutional neural network and a fully convolutional neural network with an extended architecture for biomedical image segmentation - U-Net. A comparison is made for the results of detection anatomical reference points for each of the selected neural network architectures and their comparison with the results obtained when orthodontists detected anatomical reference points. Based on the obtained results, it was concluded that a U-Net neural network allows performing the detection of anatomical reference points more accurately than a fully convolutional neural network. The results of the detection of anatomical reference points by the U-Net neural network are closer to the average results of the detection of reference points by a group of orthodontists.
Deep Anatomical Federated Network (Dafne): An open client-server framework for the continuous, collaborative improvement of deep learning-based medical image segmentation
University of Basel（巴塞尔大学）；University Hospital Basel（巴塞尔大学医院）；University of Pavia（帕维亚大学）；Leiden University Medical Center（莱顿大学医学中心）；Siemens Healthineers International AG（西门子医疗国际股份公司）；Balgrist Campus（巴尔格里斯特校区）；Peking Union Medical College Hospital（北京协和医院）；Istituti Clinici Scientifici Maugeri IRCCS（莫杰里科学临床研究所）；IRCCS Mondino Foundation（蒙迪诺基金会国立卫生研究院）；NYU Grossman School of Medicine（纽约大学格罗斯曼医学院）；Stanford University（斯坦福大学）
University of Basel（巴塞尔大学）；University Hospital Basel（巴塞尔大学医院）；MIAC AG
We present an automated method for localizing an anatomical landmark in three-dimensional medical images. The method combines two recurrent neural networks in a coarse-to-fine approach: The first network determines a candidate neighborhood by analyzing the complete given image volume. The second network localizes the actual landmark precisely and accurately in the candidate neighborhood. Both networks take advantage of multi-dimensional gated recurrent units in their main layers, which allow for high model complexity with a comparatively small set of parameters. We localize the medullopontine …
University of Oxford（牛津大学）；Plexalis Ltd（Plexalis有限公司）
This paper proposes a novel transformer-based model architecture for medical imaging problems involving analysis of vertebrae. It considers two applications of such models in MR images: (a) detection of spinal metastases and the related conditions of vertebral fractures and metastatic cord compression, (b) radiological grading of common degenerative changes in intervertebral discs. Our contributions are as follows: (i) We propose a Spinal Context Transformer (SCT), a deep-learning architecture suited for the analysis of repeated anatomical structures in medical imaging such as vertebral bodies…
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…
Imperial College London（帝国理工学院）；ETH Zurich（苏黎世联邦理工学院）；Guy’s and St Thomas’ NHS Foundation（盖伊和圣托马斯国民保健服务基金会）
Measurement of head biometrics from fetal ultrasonography images is of key importance in monitoring the healthy development of fetuses. However, the accurate measurement of relevant anatomical structures is subject to large inter-observer variability in the clinic. To address this issue, an automated method utilizing Fully Convolutional Networks (FCN) is proposed to determine measurements of fetal head circumference (HC) and biparietal diameter (BPD). An FCN was trained on approximately 2000 2D ultrasound images of the head with annotations provided by 45 different sonographers during routine …
National Institute of Dental and Craniofacial Research (NIDCR), National Institutes of Health (NIH)（美国国立卫生研究院（NIH）国立牙科与颅面研究所（NIDCR））；University of South Dakota Sanford School of Medicine（南达科他大学桑福德医学院）；University of Central Florida（中佛罗里达大学）
In this paper, we propose a novel deep learning framework for anatomy segmentation and automatic landmark- ing. Specifically, we focus on the challenging problem of mandible segmentation from cone-beam computed tomography (CBCT) scans and identification of 9 anatomical landmarks of the mandible on the geodesic space. The overall approach employs three inter-related steps. In step 1, we propose a deep neu- ral network architecture with carefully designed regularization, and network hyper-parameters to perform image segmentation without the need for data augmentation and complex post- processing…
Background and Purpose: Radiomics features are used to identify disease types and predict therapy outcomes. However, how the radiomics features are different among different anatomical structures has never been investigated. Hence, we analyzed the radiomics features of 22 anatomical structures in the head and neck area in CT images. Furthermore, we studied whether CT radiomics can classify anatomical structures of the head and neck using unsupervised machine-learning techniques. Materials and methods: We obtained IMRT/VMAT treatment planning data from 36 patients treated for head and neck canc…
In medical imaging, radiological scans of different modalities serve to enhance different sets of features for clinical diagnosis and treatment planning. This variety enriches the source information that could be used for outcome prediction. Deep learning methods are particularly well-suited for feature extraction from high-dimensional inputs such as images. In this work, we apply a CNN classification network augmented with a FCN preprocessor sub-network to a public TCIA head and neck cancer dataset. The training goal is survival prediction of radiotherapy cases based on pre-treatment FDG PET-…
Sequential Spatial-Temporal Network for Interpretable Automatic Ultrasonic Assessment of Fetal Head during labor
School of Computer Science, The University of Sydney（悉尼大学计算机科学学院）；Sydney School of Health Sciences, The University of Sydney（悉尼大学悉尼健康科学学院）；School of Science, Edith Cowan University（伊迪丝·考恩大学理学院）；Orange Hospital（奥兰治医院）
Segmentation is one of the most important tasks in MRI medical image analysis and is often the first and the most critical step in many clinical applications. In brain MRI analysis, head segmentation is commonly used for measuring and visualizing the brain's anatomical structures and is also a necessary step for other applications such as current-source reconstruction in electroencephalography and magnetoencephalography (EEG/MEG). Here we propose a deep learning framework that can segment brain, skull, and extra-cranial tissue using only T1-weighted MRI as input. In addition, we describe a rob…
CDPDNet: Integrating Text Guidance with Hybrid Vision Encoders for Medical Image Segmentation
J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida（J. Crayton Pruitt家庭生物医学工程系，佛罗里达大学）；Department of Medicine, University of Florida（医学系，佛罗里达大学）
Unidad Mixta de Imagen Biomédica FISABIO-CIPF（FISABIO-CIPF生物医学成像联合单元）；Universidad de Alicante（阿利坎特大学）；Medbravo；Hospital San Juan de Alicante（阿利坎特圣胡安医院）；Universidad Miguel Hernández（米格尔·埃尔南德斯大学）；Sierra Research SL（Sierra Research有限公司）；Bioinformatics & Biostatistics Unit, Principe Felipe Research Center（费利佩王子研究中心生物信息学与生物统计学单元）
This paper describes BIMCV COVID-19+, a large dataset from the Valencian Region Medical ImageBank (BIMCV) containing chest X-ray images CXR (CR, DX) and computed tomography (CT) imaging of COVID-19+ patients along with their radiological findings and locations, pathologies, radiological reports (in Spanish), DICOM metadata, Polymerase chain reaction (PCR), Immunoglobulin G (IgG) and Immunoglobulin M (IgM) diagnostic antibody tests. The findings have been mapped onto standard Unified Medical Language System (UMLS) terminology and cover a wide spectrum of thoracic entities, unlike the considerab…
University College London（伦敦大学学院）；University of Sheffield（谢菲尔德大学）
A chest X-ray is one of the most widely available radiological examinations for diagnosing and detecting various lung illnesses. The National Institutes of Health (NIH) provides an extensive database, ChestX-ray8 and ChestXray14, to help establish a deep learning community for analysing and predicting lung diseases. ChestX-ray14 consists of 112,120 frontal-view X-ray images of 30,805 distinct patients with text-mined fourteen disease image labels, where each image has multiple labels and has been utilised in numerous research in the past. To our current knowledge, no previous study has investi…
Purpose: CBCT-based adaptive radiotherapy requires daily images for accurate dose calculations. This study investigates the feasibility of applying a single convolutional network to facilitate CBCT-to-CT synthesis for head-and-neck, lung, and breast cancer patients. Methods: Ninety-nine patients diagnosed with head-and-neck, lung or breast cancer undergoing radiotherapy with CBCT-based position verification were included in this study. CBCTs were registered to planning CTs according to clinical procedures. Three cycle-consistent generative adversarial networks (cycle-GANs) were trained in an u…
Anatomical landmarks are a crucial prerequisite for many medical imaging tasks. Usually, the set of landmarks for a given task is predefined by experts. The landmark locations for a given image are then annotated manually or via machine learning methods trained on manual annotations. In this paper, in contrast, we present a method to automatically discover and localize anatomical landmarks in medical images. Specifically, we consider landmarks that attract the visual attention of humans, which we term visually salient landmarks. We illustrate the method for fetal neurosonographic images. First…
We hypothesize that anatomical priors can be viable mediums to infuse domain-specific clinical knowledge into state-of-the-art convolutional neural networks (CNN) based on the U-Net architecture. We introduce a probabilistic population prior which captures the spatial prevalence and zonal distinction of clinically significant prostate cancer (csPCa), in order to improve its computer-aided detection (CAD) in bi-parametric MR imaging (bpMRI). To evaluate performance, we train 3D adaptations of the U-Net, U-SEResNet, UNet++ and Attention U-Net using 800 institutional training-validation scans, pa…
Medical University of Vienna（维也纳医科大学）；Carl Zeiss Meditec, Inc.（卡尔蔡司医疗技术公司）
The automatic detection and localization of anatomical features in retinal imaging data are relevant for many aspects. In this work, we follow a data-centric approach to optimize classifier training for optic nerve head detection and localization in optical coherence tomography en face images of the retina. We examine the effect of domain knowledge driven spatial complexity reduction on the resulting optic nerve head segmentation and localization performance. We present a machine learning approach for segmenting optic nerve head in 2D en face projections of 3D widefield swept source optical co…
Shanghai Jiaotong University（上海交通大学）；Shanghai AI Lab（上海人工智能实验室）；University of Electronic Science and Technology of China（电子科技大学）；Sensetime Research（商汤科技研究院）
Deep neural networks usually require accurate and a large number of annotations to achieve outstanding performance in medical image segmentation. One-shot segmentation and weakly-supervised learning are promising research directions that lower labeling effort by learning a new class from only one annotated image and utilizing coarse labels instead, respectively. Previous works usually fail to leverage the anatomical structure and suffer from class imbalance and low contrast problems. Hence, we present an innovative framework for 3D medical image segmentation with one-shot and weakly-supervised…
Cancer Hospital of University of the Chinese Academy of Sciences (Zhejiang Cancer Hospital)（中国科学院大学附属肿瘤医院（浙江省肿瘤医院））；Rutgers University（罗格斯大学）；The Chinese University of Hong Kong（香港中文大学）；SenseTime Research（商汤科技研究院）
Radiotherapy is a treatment where radiation is used to eliminate cancer cells. The delineation of organs-at-risk (OARs) is a vital step in radiotherapy treatment planning to avoid damage to healthy organs. For nasopharyngeal cancer, more than 20 OARs are needed to be precisely segmented in advance. The challenge of this task lies in complex anatomical structure, low-contrast organ contours, and the extremely imbalanced size between large and small organs. Common segmentation methods that treat them equally would generally lead to inaccurate small-organ labeling. We propose a novel two-stage de…
UMIT – Private University for Health Sciences, Medical Informatics and Technology（UMIT——健康科学、医学信息学与技术私立大学）
The segmentation of organs at risk (OAR) is a required precondition for the cancer treatment with image guided radiation therapy. The automation of the segmentation task is therefore of high clinical relevance. Deep Learning (DL) based medical image segmentation is currently the most successful approach, but suffers from the over-presence of the background class and the anatomically given organ size difference, which is most severe in the head and neck (HAN) area. To tackle the HAN area specific class imbalance problem we first optimize the patch-size of the currently best performing general p…
Ping An Technology（平安科技）；Changhai Hospital（长海医院）；PAII Inc.（PAII公司）；Shengjing Hospital of China Medical University（中国医科大学附属盛京医院）；Tianjin Medical University Cancer Institute and Hospital（天津医科大学肿瘤医院）
Lymph node (LN) metastasis status is one of the most critical prognostic and cancer staging factors for patients with resectable pancreatic ductal adenocarcinoma (PDAC), or in general, for any types of solid malignant tumors. Preoperative prediction of LN metastasis from non-invasive CT imaging is highly desired, as it might be straightforwardly used to guide the following neoadjuvant treatment decision and surgical planning. Most studies only capture the tumor characteristics in CT imaging to implicitly infer LN metastasis and very few work exploit direct LN's CT imaging information. To the b…
Pitfalls of defacing whole-head MRI: re-identification risk with diffusion models and compromised research potential
Vanderbilt University（范德堡大学）；Vanderbilt University Medical Center（范德堡大学医学中心）；National Institute on Aging, National Institutes of Health（美国国立卫生研究院国家老龄化研究所）；University of Pennsylvania（宾夕法尼亚大学）；Johns Hopkins University（约翰斯·霍普金斯大学）
Department of Radiology, Massachusetts General Hospital（麻省总医院放射科）；Radiology, Perelman School of Medicine, University of Pennsylvania（宾夕法尼亚大学佩雷尔曼医学院放射科）
In fetal-brain MRI, head-pose changes between prescription and acquisition present a challenge to obtaining the standard sagittal, coronal and axial views essential to clinical assessment. As motion limits acquisitions to thick slices that preclude retrospective resampling, technologists repeat ~55-second stack-of-slices scans (HASTE) with incrementally reoriented field of view numerous times, deducing the head pose from previous stacks. To address this inefficient workflow, we propose a robust head-pose detection algorithm using full-uterus scout scans (EPI) which take ~5 seconds to acquire. …
Deep Learning-Based Cross-Anatomy CT Synthesis Using Adapted nnResU-Net with Anatomical Feature Prioritized Loss
Univ. Bordeaux, CNRS, LaBRI, UMR 5800, F-33400 Talence, France（波尔多大学，法国国家科学研究中心，LaBRI研究院，UMR 5800）；Universidad Autónoma de Madrid, Madrid, 28049, Spain（马德里自治大学，西班牙）；Pazmany Peter Catholic University, Budapest, 1083, Hungary（佩斯大学，匈牙利）；RIKEN Center for Integrative Medical Sciences, Medical Data Deep Learning Team, Tokyo, Japan（日本再生医学科学中心，医学数据深度学习团队）
Nagoya Institute of Technology（名古屋工业大学）；The British University in Egypt（埃及英国大学）；Suez Canal University（苏伊士运河大学）
The development of personalized human head models from medical images has become an important topic in the electromagnetic dosimetry field, including the optimization of electrostimulation, safety assessments, etc. Human head models are commonly generated via the segmentation of magnetic resonance images into different anatomical tissues. This process is time consuming and requires special experience for segmenting a relatively large number of tissues. Thus, it is challenging to accurately compute the electric field in different specific brain regions. Recently, deep learning has been applied …
Yale University（耶鲁大学）；New York University（纽约大学）；Hyperfine Research（Hyperfine研究公司）
Multi-contrast MRI (MC-MRI) captures multiple complementary imaging modalities to aid in radiological decision-making. Given the need for lowering the time cost of multiple acquisitions, current deep accelerated MRI reconstruction networks focus on exploiting the redundancy between multiple contrasts. However, existing works are largely supervised with paired data and/or prohibitively expensive fully-sampled MRI sequences. Further, reconstruction networks typically rely on convolutional architectures which are limited in their capacity to model long-range interactions and may lead to suboptima…
Femoroacetabular impingement (FAI) cam morphology is routinely assessed using two-dimensional alpha angles which do not provide specific data on cam size characteristics. The purpose of this study is to implement a novel, automated three-dimensional (3D) pipeline, CamMorph, for segmentation and measurement of cam volume, surface area and height from magnetic resonance (MR) images in patients with FAI. The CamMorph pipeline involves two processes: i) proximal femur segmentation using an approach integrating 3D U-net with focused shape modelling (FSM); ii) use of patient-specific anatomical info…
Computer vision and image processing techniques provide important assistance to physicians and relieve their workload in different tasks. In particular, identifying objects of interest such as lesions and anatomical structures from the image is a challenging and iterative process that can be done by using computer vision and image processing approaches in a successful manner. Optic Nerve Head (ONH) detection is a crucial step in retinal image analysis algorithms. The goal of ONH detection is to find and detect other retinal landmarks and lesions and their corresponding diameters, to use as a l…
Medical imaging phantoms are widely used for validation and verification of imaging systems and algorithms in surgical guidance and radiation oncology procedures. Especially, for the performance evaluation of new algorithms in the field of medical imaging, manufactured phantoms need to replicate specific properties of the human body, e.g., tissue morphology and radiological properties. Additive manufacturing (AM) technology provides an inexpensive opportunity for accurate anatomical replication with customization capabilities. In this study, we proposed a simple and cheap protocol to manufactu…
