Data augmentation is of paramount importance in biomedical image processing tasks, characterized by inadequate amounts of labelled data, to best use all of the data that is present. In-use techniques range from intensity transformations and elastic deformations, to linearly combining existing data points to make new ones. In this work, we propose the use of spectral techniques for data augmentation, using the discrete cosine and wavelet transforms. We empirically evaluate our approaches on a CT texture analysis task to detect abnormal lung-tissue in patients with cystic fibrosis. Empirical experiments show that the proposed spectral methods perform favourably as compared to the existing methods. When used in combination with existing methods, our proposed approach can increase the relative minor class segmentation performance by 44.1% over a simple replication baseline.
Recent works show that Generative Adversarial Networks (GANs) can be successfully applied to chest X-ray data augmentation for lung disease recognition. However, the implausible and distorted pathology features generated from the less than perfect generator may lead to wrong clinical decisions. Why not keep the original pathology region? We proposed a novel approach that allows our generative model to generate high quality plausible images that contain undistorted pathology areas. The main idea is to design a training scheme based on an image-to-image translation network to introduce variation…
Pathology slides of lung malignancies are classified using resource-frugal convolution neural networks (CNNs) that may be deployed on mobile devices. In particular, the challenging task of distinguishing adenocarcinoma (LUAD) and squamous-cell carcinoma (LUSC) lung cancer subtypes is approached in two stages. First, whole-slide histopathology images are downsampled to a size too large for CNN analysis but large enough to retain key anatomic detail. The downsampled images are decomposed into smaller square tiles, which are sifted based on their image entropies. A lightweight CNN produces tile-l…
A Clinically Validated Foundation Model for Comprehensive Lung Pathology Interpretation
Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China（南方医科大学南芳医院病理科，广州，中国）；Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China（南方医科大学基础医学学院病理科，广州，中国）；Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Hong Kong, China（香港科技大学计算机科学与工程系，香港，中国）；Guangdong Provincial Key Laboratory of Molecular Tumor Pathology, Guangzhou, China（广东省分子肿瘤病理重点实验室，广州，中国）；Department of Pathology, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China（山东省青岛坊山医院病理科，济南，山东，中国）
Shanghai Jiao Tong University（上海交通大学）；Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能医疗科技有限公司）；ShanghaiTech University（上海科技大学）
Lung nodule detection in chest X-ray (CXR) images is common to early screening of lung cancers. Deep-learning-based Computer-Assisted Diagnosis (CAD) systems can support radiologists for nodule screening in CXR. However, it requires large-scale and diverse medical data with high-quality annotations to train such robust and accurate CADs. To alleviate the limited availability of such datasets, lung nodule synthesis methods are proposed for the sake of data augmentation. Nevertheless, previous methods lack the ability to generate nodules that are realistic with the size attribute desired by the …
Suboptimal generalization of machine learning models on unseen data is a key challenge which hampers the clinical applicability of such models to medical imaging. Although various methods such as domain adaptation and domain generalization have evolved to combat this challenge, learning robust and generalizable representations is core to medical image understanding, and continues to be a problem. Here, we propose STRAP (Style TRansfer Augmentation for histoPathology), a form of data augmentation based on random style transfer from non-medical style source such as artistic paintings, for learni…
Lung and Colon cancer are one of the leading causes of mortality and morbidity in adults. Histopathological diagnosis is one of the key components to discern cancer type. The aim of the present research is to propose a computer aided diagnosis system for diagnosing squamous cell carcinomas and adenocarcinomas of lung as well as adenocarcinomas of colon using convolutional neural networks by evaluating the digital pathology images for these cancers. Hereby, rendering artificial intelligence as useful technology in the near future. A total of 2500 digital images were acquired from LC25000 datase…
Chest X-ray (CXR) is the most common examination for fast detection of pulmonary abnormalities. Recently, automated algorithms have been developed to classify multiple diseases and abnormalities in CXR scans. However, because of the limited availability of scans containing nodules and the subtle properties of nodules in CXRs, state-of-the-art methods do not perform well on nodule classification. To create additional data for the training process, standard augmentation techniques are applied. However, the variance introduced by these methods are limited as the images are typically modified glob…
The University of Tokyo（东京大学）；University of Cambridge（剑桥大学）；Fujifilm Corporation（富士胶片公司）；Jikei University School of Medicine（慈惠会医科大学）；Juntendo University School of Medicine（顺天堂大学医学部）
Accurate Computer-Assisted Diagnosis, relying on large-scale annotated pathological images, can alleviate the risk of overlooking the diagnosis. Unfortunately, in medical imaging, most available datasets are small/fragmented. To tackle this, as a Data Augmentation (DA) method, 3D conditional Generative Adversarial Networks (GANs) can synthesize desired realistic/diverse 3D images as additional training data. However, no 3D conditional GAN-based DA approach exists for general bounding box-based 3D object detection, while it can locate disease areas with physicians' minimum annotation cost, unli…
LinkSprite Technologies（LinkSprite科技公司）；Shenzhen Deepcam Information Technologies（深圳深视信息科技公司）
We present an automatic COVID1-19 diagnosis framework from lung CT images. The focus is on signal processing and classification on small datasets with efforts putting into exploring data preparation and augmentation to improve the generalization capability of the 2D CNN classification models. We propose a unique and effective data augmentation method using multiple Hounsfield Unit (HU) normalization windows. In addition, the original slice image is cropped to exclude background, and a filter is applied to filter out closed-lung images. For the classification network, we choose to use 2D Densen…
James A. Haley Veterans’ Hospital（詹姆斯·A·黑利退伍军人医院）；University of South Florida（南佛罗里达大学）；Moffitt Cancer Center（莫菲特癌症中心）
The field of Machine Learning, a subset of Artificial Intelligence, has led to remarkable advancements in many areas, including medicine. Machine Learning algorithms require large datasets to train computer models successfully. Although there are medical image datasets available, more image datasets are needed from a variety of medical entities, especially cancer pathology. Even more scarce are ML-ready image datasets. To address this need, we created an image dataset (LC25000) with 25,000 color images in 5 classes. Each class contains 5,000 images of the following histologic entities: colon a…
The University of Tokyo（东京大学）；National Center for Global Health and Medicine（国立国际医疗研究中心）；Kyushu Medical Center（九州医疗中心）
Convolutional Neural Networks (CNNs) can play a key role in Medical Image Analysis under large-scale annotated datasets. However, preparing such massive dataset is demanding. In this context, Generative Adversarial Networks (GANs) can generate realistic but novel samples, and thus effectively cover the real image distribution. In terms of interpolation, the GAN-based medical image augmentation is reliable because medical modalities can display the human body's strong anatomical consistency at fixed position while clearly reflecting inter-subject variability; thus, we propose to use noise-to-im…
College of Aerospace Science and Engineering, National University of Defense Technology（国防科技大学航空航天科学与工程学院）；Eindhoven University of Technology（埃因霍温理工大学）；ScreenPoint Medical（ScreenPoint Medical 公司）；Pingan Technology（平安科技）；Lunit Inc.（Lunit 公司）；Queen Mary University of London（伦敦玛丽女王大学）；Beihang University（北京航空航天大学）；Beijing Advanced Innovation Center for Biomedical Engineering（北京生物医学工程高精尖创新中心）
Accurate segmentation of lung cancer in pathology slides is a critical step in improving patient care. We proposed the ACDC@LungHP (Automatic Cancer Detection and Classification in Whole-slide Lung Histopathology) challenge for evaluating different computer-aided diagnosis (CADs) methods on the automatic diagnosis of lung cancer. The ACDC@LungHP 2019 focused on segmentation (pixel-wise detection) of cancer tissue in whole slide imaging (WSI), using an annotated dataset of 150 training images and 50 test images from 200 patients. This paper reviews this challenge and summarizes the top 10 submi…
The abundance of overlapping anatomical structures appearing in chest radiographs can reduce the performance of lung pathology detection by automated algorithms (CAD) as well as the human reader. In this paper, we present a deep learning based image processing technique for enhancing the contrast of soft lung structures in chest radiographs using Fully Convolutional Neural Networks (FCNN). Two 2D FCNN architectures were trained to accomplish the task: The first performs 2D lung segmentation which is used for normalization of the lung area. The second FCNN is trained to extract lung structures.…
University of Waterloo（滑铁卢大学）；Vector Institute（向量研究所）
Representation learning for Whole Slide Images (WSIs) is pivotal in developing image-based systems to achieve higher precision in diagnostic pathology. We propose a two-stage framework for WSI representation learning. We sample relevant patches using a color-based method and use graph neural networks to learn relations among sampled patches to aggregate the image information into a single vector representation. We introduce attention via graph pooling to automatically infer patches with higher relevance. We demonstrate the performance of our approach for discriminating two sub-types of lung ca…
Hunan University（湖南大学）；Central South University（中南大学）；Third Xiangya Hospital（湘雅三医院）
Computational pathology is part of precision oncology medicine. The integration of high-throughput data including genomics, transcriptomics, proteomics, metabolomics, pathomics, and radiomics into clinical practice improves cancer treatment plans, treatment cycles, and cure rates, and helps doctors open up innovative approaches to patient prognosis. In the past decade, rapid advances in artificial intelligence, chip design and manufacturing, and mobile computing have facilitated research in computational pathology and have the potential to provide better-integrated solutions for whole-slide im…
Technical University Munich（慕尼黑工业大学）；Helmholtz AI（亥姆霍兹人工智能研究所）；Munich School of Data Science (MuDS)（慕尼黑数据科学学院）；ContextVision AB（ContextVision公司）；Institute for Computational Biology, HelmholtzZentrum Munich（慕尼黑亥姆霍兹中心计算生物学研究所）
In digital pathology, different staining procedures and scanners cause substantial color variations in whole-slide images (WSIs), especially across different laboratories. These color shifts result in a poor generalization of deep learning-based methods from the training domain to external pathology data. To increase test performance, stain normalization techniques are used to reduce the variance between training and test domain. Alternatively, color augmentation can be applied during training leading to a more robust model without the extra step of color normalization at test time. We propose…
University of Technology Sydney（悉尼科技大学）；IBM Australia Limited（IBM澳大利亚有限公司）；Sejong University（世宗大学）；Universiti Kebangsaan Malaysia（马来西亚国民大学）；Charles Sturt University（查尔斯特大学）
Lung cancer is the leading cause of cancer death and morbidity worldwide. Many studies have shown machine learning models to be effective at detecting lung nodules from chest X-ray images. However, these techniques have yet to be embraced by the medical community due to several practical, ethical, and regulatory constraints stemming from the black-box nature of deep learning models. Additionally, most lung nodules visible on chest X-ray are benign; therefore, the narrow task of computer vision-based lung nodule detection cannot be equated to automated lung cancer detection. Addressing both con…
The paper presents and comparatively analyses several deep learning approaches to automatically detect tuberculosis related lesions in lung CTs, in the context of the ImageClef 2020 Tuberculosis task. Three classes of methods, different with respect to the way the volumetric data is given as input to neural network-based classifiers are discussed and evaluated. All these come with a rich experimental analysis comprising a variety of neural network architectures, various segmentation algorithms and data augmentation schemes. The reported work belongs to the SenticLab.UAIC team, which obtained t…
Automatic segmentation of infected regions in computed tomography (CT) images is necessary for the initial diagnosis of COVID-19. Deep-learning-based methods have the potential to automate this task but require a large amount of data with pixel-level annotations. Training a deep network with annotated lung cancer CT images, which are easier to obtain, can alleviate this problem to some extent. However, this approach may suffer from a reduction in performance when applied to unseen COVID-19 images during the testing phase due to the domain shift. In this paper, we propose a novel unsupervised m…
Sejong University（世宗大学）；Kangbuk Samsung Hospital（江北三星医院）；Sungkyunkwan University School of Medicine（成均馆大学医学院）；Korea University（高丽大学）
An automated segmentation and classification of nuclei is an essential task in digital pathology. The current deep learning-based approaches require a vast amount of annotated datasets by pathologists. However, the existing datasets are imbalanced among different types of nuclei in general, leading to a substantial performance degradation. In this paper, we propose a simple but effective data augmentation technique, termed GradMix, that is specifically designed for nuclei segmentation and classification. GradMix takes a pair of a major-class nucleus and a rare-class nucleus, creates a customiz…
Siemens Healthineers（西门子医疗）；University Medical Center Goettingen（哥廷根大学医学中心）
Current approaches for classification of whole slide images (WSI) in digital pathology predominantly utilize a two-stage learning pipeline. The first stage identifies areas of interest (e.g. tumor tissue), while the second stage processes cropped tiles from these areas in a supervised fashion. During inference, a large number of tiles are combined into a unified prediction for the entire slide. A major drawback of such approaches is the requirement for task-specific auxiliary labels which are not acquired in clinical routine. We propose a novel learning pipeline for WSI classification that is …
University College London（伦敦大学学院）；Frimley Health NHS Foundation Trust（弗林姆利健康国民医疗服务基金会信托）；Royal Berkshire NHS Foundation Trust（皇家伯克郡国民医疗服务基金会信托）；Hospital de La Santa Creu I Sant Pau（圣克鲁和圣保罗医院）；West Suffolk NHS Foundation Trust（西萨福克国民医疗服务基金会信托）；Cambridge University Hospital（剑桥大学医院）；University of Cambridge（剑桥大学）；Great Ormond Street Children's Hospital NHS Foundation Trust（大奥蒙德街儿童医院国民医疗服务基金会信托）；Institute of Child Health, University College London（伦敦大学学院儿童健康研究所）；UCL Queen Square Institute of Neurology（伦敦大学学院皇后广场神经病学研究所）；University of Pavia（帕维亚大学）
Lung ultrasound imaging has been shown effective in detecting typical patterns for interstitial pneumonia, as a point-of-care tool for both patients with COVID-19 and other community-acquired pneumonia (CAP). In this work, we focus on the hyperechoic B-line segmentation task. Using deep neural networks, we automatically outline the regions that are indicative of pathology-sensitive artifacts and their associated sonographic patterns. With a real-world data-scarce scenario, we investigate approaches to utilize both COVID-19 and CAP lung ultrasound data to train the networks; comparing fine-tuni…
We propose a novel framework for controllable pathological image synthesis for data augmentation. Inspired by CycleGAN, we perform cycle-consistent image-to-image translation between two domains: healthy and pathological. Guided by a semantic mask, an adversarially trained generator synthesizes pathology on a healthy image in the specified location. We demonstrate our approach on an institutional dataset of cerebral microbleeds in traumatic brain injury patients. We utilize synthetic images generated with our method for data augmentation in cerebral microbleeds detection. Enriching the trainin…
CC-DCNet: Dynamic Convolutional Neural Network with Contrastive Constraints for Identifying Lung Cancer Subtypes on Multi-modality Images
Zhejiang Lab（之江实验室）；Institute of Computer Graphics and Vision（计算机图形与视觉研究所）；Graz University of Technology（格拉茨工业大学）；School of Computer Science and Engineering（计算机科学与工程学院）；Northwestern Polytechnical University（西北工业大学）；Zhejiang University School of Medicine（浙江大学医学院）；Sir Run Run Shaw Hospital（邵逸夫医院）；Shanghai Artificial Intelligence Laboratory（上海人工智能实验室）
Implementing Trust in Non-Small Cell Lung Cancer Diagnosis with a Conformalized Uncertainty-Aware AI Framework in Whole-Slide Images
The Hong Kong Polytechnic University（香港理工大学）；Vanderbilt University Medical Center（范德堡大学医学中心）；Hong Kong Baptist University（香港浸会大学）；Vanderbilt University（范德堡大学）
University of Strasbourg（斯特拉斯堡大学）；University of Belgrade（贝尔格莱德大学）；University of Kragujevac（克拉古耶瓦茨大学）；Hannover Medical School（汉诺威医学院）；University Clinic, Freiburg（弗赖堡大学诊所）
The application of supervised deep learning methods in digital pathology is limited due to their sensitivity to domain shift. Digital Pathology is an area prone to high variability due to many sources, including the common practice of evaluating several consecutive tissue sections stained with different staining protocols. Obtaining labels for each stain is very expensive and time consuming as it requires a high level of domain knowledge. In this article, we propose an unsupervised augmentation approach based on adversarial image-to-image translation, which facilitates the training of stain in…
In medical image diagnosis, pathology image analysis using semantic segmentation becomes important for efficient screening as a field of digital pathology. The spatial augmentation is ordinary used for semantic segmentation. Tumor images under malignant are rare and to annotate the labels of nuclei region takes much time-consuming. We require an effective use of dataset to maximize the segmentation accuracy. It is expected that some augmentation to transform generalized images influence the segmentation performance. We propose a synthetic augmentation using label-to-image translation, mapping …
Detection of pulmonary pathologies using convolutional neural networks, Data Augmentation, ResNet50 and Vision Transformers
Universidad Abierta Interamericana（泛美开放大学）；Faculty of Information Technology（信息技术学院）；Center for Advanced Studies in Information Technology（信息技术高级研究中心）；Interamerican Open University（泛美开放大学）
The University of Tokyo（东京大学）；LPIXEL Inc.（LPIXEL公司）；National Institute of Informatics（国立信息学研究所）；University of Cambridge（剑桥大学）；Keio University（庆应义塾大学）
Despite the success of Convolutional Neural Network-based Computer-Aided Diagnosis research, its clinical applications remain challenging. Accordingly, developing medical Artificial Intelligence (AI) fitting into a clinical environment requires identifying/bridging the gap between AI and Healthcare sides. Since the biggest problem in Medical Imaging lies in data paucity, confirming the clinical relevance for diagnosis of research-proven image augmentation techniques is essential. Therefore, we hold a clinically valuable AI-envisioning workshop among Japanese Medical Imaging experts, physicians…
Georgia Institute of Technology（佐治亚理工学院）；Memorial Sloan-Kettering Cancer Center（纪念斯隆-凯特琳癌症中心）；Peking University Cancer Hospital（北京大学肿瘤医院）
In current clinical practice, noisy and artifact-ridden weekly cone-beam computed tomography (CBCT) images are only used for patient setup during radiotherapy. Treatment planning is done once at the beginning of the treatment using high-quality planning CT (pCT) images and manual contours for organs-at-risk (OARs) structures. If the quality of the weekly CBCT images can be improved while simultaneously segmenting OAR structures, this can provide critical information for adapting radiotherapy mid-treatment as well as for deriving biomarkers for treatment response. Using a novel physics-based da…
Segmentation of Non-Small Cell Lung Carcinomas: Introducing DRU-Net and Multi-Lens Distortion
Norwegian University of Science and Technology (NTNU)（挪威科技大学）；Levanger hospital, Nord-Trøndelag Health Trust（北特伦德拉格健康信托利旺格医院）；St. Olavs hospital, Trondheim University Hospital（特隆赫姆大学医院圣奥拉夫斯医院）；Sopra Steria（索拉斯特里亚）；SINTEF Digital（辛特夫数字研究院）
Dali University（大理大学）；Liuzhou Vocational & Technical College（柳州职业技术学院）；The Second Xiangya Hospital of Central South University（中南大学湘雅二医院）；Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer（湖南省肺癌早期诊断与精准治疗重点实验室）；Early-Stage Lung Cancer Center（早期肺癌中心）
Detection of pulmonary nodules by CT is used for screening lung cancer in early stages.omputer aided diagnosis (CAD) based on deep-learning method can identify the suspected areas of pulmonary nodules in CT images, thus improving the accuracy and efficiency of CT diagnosis. The accuracy and robustness of deep learning models. Method:In this paper, we explore (1) the data augmentation method based on the generation model and (2) the model structure improvement method based on the embedding mechanism. Two strategies have been introduced in this study: a new data augmentation method and a embeddi…
Isfahan University of Technology（伊斯法罕理工大学）；Seattle University（西雅图大学）；McMaster University（麦克马斯特大学）
Coronavirus has caused hundreds of thousands of deaths. Fatalities could decrease if every patient could get suitable treatment by the healthcare system. Machine learning, especially computer vision methods based on deep learning, can help healthcare professionals diagnose and treat COVID-19 infected cases more efficiently. Hence, infected patients can get better service from the healthcare system and decrease the number of deaths caused by the coronavirus. This research proposes a method for segmenting infected lung regions in a CT image. For this purpose, a convolutional neural network with …
University of Copenhagen（哥本哈根大学）；Cerebriu AS（Cerebriu公司）；Technical University of Denmark（丹麦技术大学）
Pulmonary opacification is the inflammation in the lungs caused by many respiratory ailments, including the novel corona virus disease 2019 (COVID-19). Chest X-rays (CXRs) with such opacifications render regions of lungs imperceptible, making it difficult to perform automated image analysis on them. In this work, we focus on segmenting lungs from such abnormal CXRs as part of a pipeline aimed at automated risk scoring of COVID-19 from CXRs. We treat the high opacity regions as missing data and present a modified CNN-based image segmentation network that utilizes a deep generative model for dat…
LeFusion: Controllable Pathology Synthesis via Lesion-Focused Diffusion Models
University of Science and Technology of China (USTC)（中国科学技术大学）；Beihang University（北京航空航天大学）；Swiss Federal Institute of Technology Lausanne (EPFL)（洛桑联邦理工学院）；Stanford University（斯坦福大学）
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 …
Tissue Concepts: supervised foundation models in computational pathology
Fraunhofer Institute for Digital Medicine MEVIS（弗劳恩霍夫数字医学研究所MEVIS）；Institute for Pathology, Hannover Medical School（汉诺威医学院病理学研究所）；University of Regensburg（雷根斯堡大学）；RWTH Aachen University（亚琛工业大学）
