Microscopic examination of tissues or histopathology is one of the diagnostic procedures for detecting colorectal cancer. The pathologist involved in such an examination usually identifies tissue type based on texture analysis, especially focusing on tumour-stroma ratio. In this work, we automate the task of tissue classification within colorectal cancer histology samples using deep transfer learning. We use discriminative fine-tuning with one-cycle-policy and apply structure-preserving colour normalization to boost our results. We also provide visual explanations of the deep neural network's decision on texture classification. With achieving state-of-the-art test accuracy of 96.2% we also embark on using deployment friendly architecture called SqueezeNet for memory-limited hardware.
Qatar University(卡塔尔大学);Izmir University of Economics(伊兹密尔经济大学);Tampere University of Technology(坦佩雷理工大学)
Computer-aided diagnosis (CAD) based on histopathological imaging has progressed rapidly in recent years with the rise of machine learning based methodologies. Traditional approaches consist of training a classification model using features extracted from the images, based on textures or morphological properties. Recently, deep-learning based methods have been applied directly to the raw (unprocessed) data. However, their usability is impacted by the paucity of annotated data in the biomedical sector. In order to leverage the learning capabilities of deep Convolutional Neural Nets (CNNs) withi…
University of Warwick(华威大学);University Hospital Coventry and Warwickshire(考文垂和沃里克郡大学医院)
To train a robust deep learning model, one usually needs a balanced set of categories in the training data. The data acquired in a medical domain, however, frequently contains an abundance of healthy patients, versus a small variety of positive, abnormal cases. Moreover, the annotation of a positive sample requires time consuming input from medical domain experts. This scenario would suggest a promise for one-class classification type approaches. In this work we propose a general one-class classification model for histology, that is meta-trained on multiple histology datasets simultaneously, a…
Microsatellite instability (MSI) is a tumor phenotype whose diagnosis largely impacts patient care in colorectal cancers (CRC), and is associated with response to immunotherapy in all solid tumors. Deep learning models detecting MSI tumors directly from H&E stained slides have shown promise in improving diagnosis of MSI patients. Prior deep learning models for MSI detection have relied on neural networks pretrained on ImageNet dataset, which does not contain any medical image. In this study, we leverage recent advances in self-supervised learning by training neural networks on histology images…
School of Computer Science(计算机科学学院);School of Medicine(医学院);University of St Andrews(圣安德鲁斯大学)
Digital pathology (DP) is a new research area which falls under the broad umbrella of health informatics. Owing to its potential for major public health impact, in recent years DP has been attracting much research attention. Nevertheless, a wide breadth of significant conceptual and technical challenges remain, few of them greater than those encountered in the field of oncology. The automatic analysis of digital pathology slides of cancerous tissues is particularly problematic due to the inherent heterogeneity of the disease, extremely large images, amongst numerous others. In this paper we in…
Expanding the Medical Decathlon dataset: segmentation of colon and colorectal cancer from computed tomography images
Neural Network Technologies Center(神经网络技术中心);Institute of Urology and Human Reproductive Health(泌尿学与人类生殖健康研究所);N.E. Bauman Moscow State Technical University(鲍曼莫斯科国立技术大学);I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University)(俄罗斯联邦卫生部I.M.谢切诺夫第一莫斯科国立医科大学(谢切诺夫大学));Hospital of Faculty Surgery No. 2, UKB No. 4(第4大学临床医院第二外科教学医院);University Clinical Hospital No. 2(第二大学临床医院)
本文通过为 Medical Decathlon 数据集增加经放射科医生验证的结直肠癌 CT 分割标记,并训练 UNet 模型进行 5 折交叉验证,以提升结直肠癌自动分割与早期检测能力。
Dealing with the application of grading colorectal cancer images, this work proposes a 3 step pipeline for prediction of cancer levels from a histopathology image. The overall model performs better compared to other state of the art methods on the colorectal cancer grading data set and shows excellent performance for the extended colorectal cancer grading set. The performance improvements can be attributed to two main factors: The feature selection and graph augmentation method described here are spatially aware, but overall pixel position independent. Further, the graph size in terms of nodes…
Neuromation;Massachusetts Institute of Technology(麻省理工学院);Lyft Inc.(Lyft公司);University of Michigan(密歇根大学)
Breast cancer is one of the main causes of cancer death worldwide. Early diagnostics significantly increases the chances of correct treatment and survival, but this process is tedious and often leads to a disagreement between pathologists. Computer-aided diagnosis systems showed potential for improving the diagnostic accuracy. In this work, we develop the computational approach based on deep convolution neural networks for breast cancer histology image classification. Hematoxylin and eosin stained breast histology microscopy image dataset is provided as a part of the ICIAR 2018 Grand Challenge…
University of Warwick(华威大学);Tissue Image Analytics (TIA) Centre, University of Warwick(华威大学组织图像分析中心)
The problem of recognizing various types of tissues present in multi-gigapixel histology images is an important fundamental pre-requisite for downstream analysis of the tumor microenvironment in a bottom-up analysis paradigm for computational pathology. In this paper, we propose a deep dictionary learning approach to solve the problem of tissue phenotyping in histology images. We propose deep Multi-Resolution Dictionary Learning (deepMRDL) in order to benefit from deep texture descriptors at multiple different spatial resolutions. We show the efficacy of the proposed approach through extensive…
Domain-specific transfer learning in the automated scoring of tumor-stroma ratio from histopathological images of colorectal cancer
University of Jyväskylä(于韦斯屈莱大学);Oulu University Hospital(奥卢大学医院);University of Oulu(奥卢大学);Tampere University(坦佩雷大学);University of Turku(图尔库大学);Turku University Hospital(图尔库大学医院);Hospital Nova of Central Finland(中芬兰新星医院)
本文提出基于卷积神经网络的结直肠癌组织病理图像 TSR 自动估算方法,评估领域特定迁移学习,最高三类分类准确率达 96.1%,与病理学家评估相关性为 0.57。
Radboud University Medical Center(拉德堡德大学医学中心);Laboratorium Pathologie Oost Nederland(东荷兰病理学实验室)
The development of reliable imaging biomarkers for the analysis of colorectal cancer (CRC) in hematoxylin and eosin (H&E) stained histopathology images requires an accurate and reproducible classification of the main tissue components in the image. In this paper, we propose a system for CRC tissue classification based on convolutional networks (ConvNets). We investigate the importance of stain normalization in tissue classification of CRC tissue samples in H&E-stained images. Furthermore, we report the performance of ConvNets on a cohort of rectal cancer samples and on an independent publicly …
Breast cancer is one of the leading causes of mortality in women. Early detection and treatment are imperative for improving survival rates, which have steadily increased in recent years as a result of more sophisticated computer-aided-diagnosis (CAD) systems. A critical component of breast cancer diagnosis relies on histopathology, a laborious and highly subjective process. Consequently, CAD systems are essential to reduce inter-rater variability and supplement the analyses conducted by specialists. In this paper, a transfer-learning based approach is proposed, for the task of breast histolog…
Improving Colorectal Cancer Screening and Risk Assessment through Predictive Modeling on Medical Images and Records
Geisel School of Medicine at Dartmouth(达特茅斯盖泽尔医学院);Dartmouth-Hitchcock Medical Center(达特茅斯-希区柯克医学中心);New Hampshire Colonoscopy Registry(新罕布什尔结肠镜检查登记处);White River Junction VA Medical Center(怀特河交界处退伍军人事务医疗中心);Dartmouth College(达特茅斯学院)
Cancer is the uncontrollable cell division of abnormal cells inside the human body, which can spread to other body organs. It is one of the non-communicable diseases (NCDs) and NCDs accounts for 71% of total deaths worldwide whereas lung cancer is the second most diagnosed cancer after female breast cancer. Cancer survival rate of lung cancer is only 19%. There are various methods for the diagnosis of lung cancer, such as X-ray, CT scan, PET-CT scan, bronchoscopy and biopsy. However, to know the subtype of lung cancer based on the tissue type H and E staining is widely used, where the staining…
MedBravo;Alicante University General Hospital(阿利坎特大学综合医院);Alicante Institute for Health and Biomedical Research(阿利坎特健康与生物医学研究所);Yale University(耶鲁大学);Hospital del Mar(马尔医院);Hospital del Mar Medical Research Institute(马尔医院医学研究所);Hospital Clínic(医院诊所医院);University of Barcelona(巴塞罗那大学)
We present a system for the prediction of microsatellite instability (MSI) from H&E images of colorectal cancer using deep learning (DL) techniques customized for tissue microarrays (TMAs). The system incorporates an end-to-end image preprocessing module that produces tiles at multiple magnifications in the regions of interest as guided by a tissue classifier module, and a multiple-bias rejecting module. The training and validation TMA samples were obtained from the EPICOLON project and further enriched with samples from a single institution. A systematic study of biases at tile level identifi…
The University of Texas at Austin(德克萨斯大学奥斯汀分校);New York University(纽约大学)
In this study, with the goal of reducing the early detection miss rate of colorectal cancer (CRC) polyps, we propose utilizing a novel hyper-sensitive vision-based tactile sensor called HySenSe and a complementary and novel machine learning (ML) architecture that explores the potentials of utilizing dilated convolutions, the beneficial features of the ResNet architecture, and the transfer learning concept applied on a small dataset with the scale of hundreds of images. The proposed tactile sensor provides high-resolution 3D textural images of CRC polyps that will be used for their accurate cla…
Google Health(谷歌健康);Medical University of Graz(格拉茨医科大学);Tempus Labs Inc(Tempus Labs公司)
Deriving interpretable prognostic features from deep-learning-based prognostic histopathology models remains a challenge. In this study, we developed a deep learning system (DLS) for predicting disease specific survival for stage II and III colorectal cancer using 3,652 cases (27,300 slides). When evaluated on two validation datasets containing 1,239 cases (9,340 slides) and 738 cases (7,140 slides) respectively, the DLS achieved a 5-year disease-specific survival AUC of 0.70 (95%CI 0.66-0.73) and 0.69 (95%CI 0.64-0.72), and added significant predictive value to a set of 9 clinicopathologic fe…
AG-CRC: Anatomy-Guided Colorectal Cancer Segmentation in CT with Imperfect Anatomical Knowledge
Shanghai Artificial Intelligence Laboratory(上海人工智能实验室);Shanghai Digital Medicine Innovation Center(上海数字医学创新中心);Ruijin Hospital(瑞金医院);Shanghai Jiao Tong University School of Medicine(上海交通大学医学院)
Dartmouth College(达特茅斯学院);Dartmouth-Hitchcock Medical Center(达特茅斯-希区柯克医疗中心);Minnesota Gastroenterology PA(明尼苏达胃肠病学协会);Fairview Southdale Hospital(费尔维尤索斯代尔医院);University of North Carolina(北卡罗来纳大学)
Histological classification of colorectal polyps plays a critical role in both screening for colorectal cancer and care of affected patients. An accurate and automated algorithm for the classification of colorectal polyps on digitized histopathology slides could benefit clinicians and patients. Evaluate the performance and assess the generalizability of a deep neural network for colorectal polyp classification on histopathology slide images using a multi-institutional dataset. In this study, we developed a deep neural network for classification of four major colorectal polyp types, tubular ade…
INESC TEC - Institute for Systems and Computer Engineering, Technology and Science(系统与计算机工程、技术与科学研究所);Faculty of Engineering of University of Porto(波尔图大学工程学院);Seek AI Limited(Seek AI有限公司);Icahn School of Medicine at Mount Sinai(西奈山伊坎医学院);The Mount Sinai Hospital(西奈山医院)
Breast cancer is the most common invasive cancer in women, affecting more than 10% of women worldwide. Microscopic analysis of a biopsy remains one of the most important methods to diagnose the type of breast cancer. This requires specialized analysis by pathologists, in a task that i) is highly time- and cost-consuming and ii) often leads to nonconsensual results. The relevance and potential of automatic classification algorithms using hematoxylin-eosin stained histopathological images has already been demonstrated, but the reported results are still sub-optimal for clinical use. With the goa…
University of Warwick(华威大学);National University of Sciences and Technology(国立科技大学);University Hospitals Coventry(考文垂大学医院);The Alan Turing Institute(艾伦·图灵研究所)
Digital histology images are amenable to the application of convolutional neural network (CNN) for analysis due to the sheer size of pixel data present in them. CNNs are generally used for representation learning from small image patches (e.g. 224x224) extracted from digital histology images due to computational and memory constraints. However, this approach does not incorporate high-resolution contextual information in histology images. We propose a novel way to incorporate larger context by a context-aware neural network based on images with a dimension of 1,792x1,792 pixels. The proposed fr…
University of Warwick(华威大学);University Hospitals Coventry and Warwickshire(考文垂和沃里克大学医院);The Alan Turing Institute(艾伦·图灵研究所)
Synthetic images can be used for the development and evaluation of deep learning algorithms in the context of limited availability of data. In the field of computational pathology, where histology images are large in size and visual context is crucial, synthesis of large high resolution images via generative modeling is a challenging task. This is due to memory and computational constraints hindering the generation of large images. To address this challenge, we propose a novel SAFRON (Stitching Across the FRONtiers) framework to construct realistic, large high resolution tissue image tiles fro…
Broad Institute of Harvard and MIT(哈佛大学与麻省理工学院博德研究所);Dana-Farber Cancer Institute(丹娜法伯癌症研究院);Department of Biomedical Informatics, Harvard Medical School(哈佛医学院生物医学信息学系)
Cancer diagnosis, prognosis, and therapeutic response predictions are based on morphological information from histology slides and molecular profiles from genomic data. However, most deep learning-based objective outcome prediction and grading paradigms are based on histology or genomics alone and do not make use of the complementary information in an intuitive manner. In this work, we propose Pathomic Fusion, an interpretable strategy for end-to-end multimodal fusion of histology image and genomic (mutations, CNV, RNA-Seq) features for survival outcome prediction. Our approach models pairwise…
The Chinese University of Hong Kong(香港中文大学);University of Warwick(华威大学)
Colorectal cancer (CRC) grading is typically carried out by assessing the degree of gland formation within histology images. To do this, it is important to consider the overall tissue micro-environment by assessing the cell-level information along with the morphology of the gland. However, current automated methods for CRC grading typically utilise small image patches and therefore fail to incorporate the entire tissue micro-architecture for grading purposes. To overcome the challenges of CRC grading, we present a novel cell-graph convolutional neural network (CGC-Net) that converts each large…
Indian Institute of Technology Jodhpur(印度理工学院焦特布尔分校);Shri Guruji Gobind Singhji Institute of Engineering and Technology(什里古鲁吉·戈宾德·辛格吉工程技术学院)
Colorectal cancer is a leading cause of death worldwide. However, early diagnosis dramatically increases the chances of survival, for which it is crucial to identify the tumor in the body. Since its imaging uses high-resolution techniques, annotating the tumor is time-consuming and requires particular expertise. Lately, methods built upon Convolutional Neural Networks(CNNs) have proven to be at par, if not better in many biomedical segmentation tasks. For the task at hand, we propose another CNN-based approach, which uses atrous convolutions and residual connections besides the conventional fi…
Colorectal cancer is a leading cause of cancer death for both men and women. For this reason, histopathological characterization of colorectal polyps is the major instrument for the pathologist in order to infer the actual risk for cancer and to guide further follow-up. Colorectal polyps diagnosis includes the evaluation of the polyp type, and more importantly, the grade of dysplasia. This latter evaluation represents a critical step for the clinical follow-up. The proposed deep learning-based classification pipeline is based on state-of-the-art convolutional neural network, trained using prop…
This paper presents results of applying Inception v4 deep convolutional neural network to ICIAR-2018 Breast Cancer Classification Grand Challenge, part a. The Challenge task is to classify breast cancer biopsy results, presented in form of hematoxylin and eosin stained images. Breast cancer classification is of primary interest to the medical practitioners and thus binary classification of breast cancer images have been under investigation by many researchers, but multi-class categorization of histology breast images have been challenging due to the subtle differences among the categories. In …
Multi-Scale Hybrid Vision Transformer for Learning Gastric Histology: AI-Based Decision Support System for Gastric Cancer Treatment
KAIST(韩国科学技术院);Chungnam National University School of Medicine(忠南大学医学院);Chungnam National University Hospital(忠南大学医院);Chungnam National University Sejong Hospital(忠南大学世宗医院)
本文提出基于两阶段混合 ViT 与多尺度自注意力的 AI 系统,实现胃癌病理五分类并匹配治疗指南,在多中心切片中验证可提升灵敏度并缩短筛查时间。
EPFL(洛桑联邦理工学院);Bern(伯尔尼大学);Lausanne University Hospital(洛桑大学医院);Center of Biomedical Imaging(生物医学成像中心)
With the long-term rapid increase in incidences of colorectal cancer (CRC), there is an urgent clinical need to improve risk stratification. The conventional pathology report is usually limited to only a few histopathological features. However, most of the tumor microenvironments used to describe patterns of aggressive tumor behavior are ignored. In this work, we aim to learn histopathological patterns within cancerous tissue regions that can be used to improve prognostic stratification for colorectal cancer. To do so, we propose a self-supervised learning method that jointly learns a represen…
University of Science and Technology of China(中国科学技术大学);UNSW Sydney(悉尼新南威尔士大学);Genmab Inc.(Genmab公司)
Several deep learning algorithms have been developed to predict survival of cancer patients using whole slide images (WSIs).However, identification of image phenotypes within the WSIs that are relevant to patient survival and disease progression is difficult for both clinicians, and deep learning algorithms. Most deep learning based Multiple Instance Learning (MIL) algorithms for survival prediction use either top instances (e.g., maxpooling) or top/bottom instances (e.g., MesoNet) to identify image phenotypes. In this study, we hypothesize that wholistic information of the distribution of the…
Worldwide, prostate cancer is one of the main cancers affecting men. The final diagnosis of prostate cancer is based on the visual detection of Gleason patterns in prostate biopsy by pathologists. Computer-aided-diagnosis systems allow to delineate and classify the cancerous patterns in the tissue via computer-vision algorithms in order to support the physicians' task. The methodological core of this work is a U-Net convolutional neural network for image segmentation modified with residual blocks able to segment cancerous tissue according to the full Gleason system. This model outperforms othe…
Northumbria University at Newcastle(纽卡斯尔诺森比亚大学);College of Computer and Information Sciences, King Saud University(沙特国王大学计算机与信息科学学院)
Colorectal and prostate cancers are the most common types of cancer in men worldwide. To diagnose colorectal and prostate cancer, a pathologist performs a histological analysis on needle biopsy samples. This manual process is time-consuming and error-prone, resulting in high intra and interobserver variability, which affects diagnosis reliability. This study aims to develop an automatic computerized system for diagnosing colorectal and prostate tumors by using images of biopsy samples to reduce time and diagnosis error rates associated with human analysis. We propose a CNN model for classifyin…
University of Oxford(牛津大学);University Hospitals Coventry and Warwickshire(考文垂与沃里克郡大学医院);University of Warwick(华威大学);Hamad Medical Corporation(哈马德医疗公司);International Association for Cancer Research(国际癌症研究协会)
Distant metastasis is the major cause of death in colorectal cancer (CRC). Patients at high risk of developing distant metastasis could benefit from appropriate adjuvant and follow-up treatments if stratified accurately at an early stage of the disease. Studies have increasingly recognized the role of diverse cellular components within the tumor microenvironment in the development and progression of CRC tumors. In this paper, we show that a new method of automated analysis of digitized images from colorectal cancer tissue slides can provide important estimates of distant metastasis-free surviv…
Towards a Benchmark for Colorectal Cancer Segmentation in Endorectal Ultrasound Videos: Dataset and Model Development
The Chinese University of Hong Kong, Shenzhen(香港中文大学(深圳));Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore(新加坡科技研究局高性能计算研究所);Affiliated Hospital of North Sichuan Medical College(川北医学院附属医院);Shenzhen Research Institute of Big Data(深圳大数据研究院)
Department Of Computer Science University of Massachusetts Lowell(马萨诸塞大学洛厄尔分校计算机科学系)
Colorectal cancer (CRC) is a common and lethal disease. Globally, CRC is the third most commonly diagnosed cancer in males and the second in females. For colorectal cancer, the best screening test available is the colonoscopy. During a colonoscopic procedure, a tiny camera at the tip of the endoscope generates a video of the internal mucosa of the colon. The video data are displayed on a monitor for the physician to examine the lining of the entire colon and check for colorectal polyps. Detection and removal of colorectal polyps are associated with a reduction in mortality from colorectal canc…
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers and a leading cause of cancer deaths in the United States. Colorectal polyps that grow on the intima of the colon or rectum is an important precursor for CRC. Currently, the most common way for colorectal polyp detection and precancerous pathology is the colonoscopy. Therefore, accurate colorectal polyp segmentation during the colonoscopy procedure has great clinical significance in CRC early detection and prevention. In this paper, we propose a novel end-to-end deep learning framework for the colorectal polyp segmentation. …
University of Texas at Austin(德克萨斯大学奥斯汀分校);MD Anderson Cancer Center(MD安德森癌症中心)
In this study, to address the current high earlydetection miss rate of colorectal cancer (CRC) polyps, we explore the potentials of utilizing transfer learning and machine learning (ML) classifiers to precisely and sensitively classify the type of CRC polyps. Instead of using the common colonoscopic images, we applied three different ML algorithms on the 3D textural image outputs of a unique vision-based surface tactile sensor (VS-TS). To collect realistic textural images of CRC polyps for training the utilized ML classifiers and evaluating their performance, we first designed and additively m…
Northeastern University(东北大学);Cancer Hospital, China Medical University(中国医科大学肿瘤医院);Liaoning Cancer Hospital and Institute(辽宁省肿瘤医院暨研究所);University of New South Wales(新南威尔士大学);Stevens Institute of Technology(史蒂文斯理工学院);Shengjing Hospital, China Medical University(中国医科大学附属盛京医院);Liaoning Shihua University(辽宁石油化工大学);University of Luebeck(吕贝克大学)
Background and purpose: Colorectal cancer has become the third most common cancer worldwide, accounting for approximately 10% of cancer patients. Early detection of the disease is important for the treatment of colorectal cancer patients. Histopathological examination is the gold standard for screening colorectal cancer. However, the current lack of histopathological image datasets of colorectal cancer, especially enteroscope biopsies, hinders the accurate evaluation of computer-aided diagnosis techniques. Methods: A new publicly available Enteroscope Biopsy Histopathological H&E Image Dataset…
University of Central Florida(中佛罗里达大学);Mayo Clinic(妙佑医疗国际(梅奥诊所));University of Catania(卡塔尼亚大学)
Colorectal cancer, largely arising from precursor lesions called polyps, remains one of the leading causes of cancer-related death worldwide. Current clinical standards require the resection and histopathological analysis of polyps due to test accuracy and sensitivity of optical biopsy methods falling substantially below recommended levels. In this study, we design a novel capsule network architecture (D-Caps) to improve the viability of optical biopsy of colorectal polyps. Our proposed method introduces several technical novelties including a novel capsule architecture with a capsule-average …
University of Chicago Medicine(芝加哥大学医学中心);Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai(西奈山伊坎医学院蒂施癌症研究所);Ghost Autonomy, Inc.(Ghost Autonomy 公司);University of Wisconsin at Madison(威斯康星大学麦迪逊分校);University of Chicago(芝加哥大学)
Artificial intelligence methods including deep neural networks (DNN) can provide rapid molecular classification of tumors from routine histology with accuracy that matches or exceeds human pathologists. Discerning how neural networks make their predictions remains a significant challenge, but explainability tools help provide insights into what models have learned when corresponding histologic features are poorly defined. Here, we present a method for improving explainability of DNN models using synthetic histology generated by a conditional generative adversarial network (cGAN). We show that …
Prostate cancer is one of the most prevalent cancers worldwide. One of the key factors in reducing its mortality is based on early detection. The computer-aided diagnosis systems for this task are based on the glandular structural analysis in histology images. Hence, accurate gland detection and segmentation is crucial for a successful prediction. The methodological basis of this work is a prostate gland segmentation based on U-Net convolutional neural network architectures modified with residual and multi-resolution blocks, trained using data augmentation techniques. The residual configuratio…
Identification and quantification of nuclei in colorectal cancer haematoxylin \& eosin (H\&E) stained histology images is crucial to prognosis and patient management. In computational pathology these tasks are referred to as nuclear segmentation, classification and composition and are used to extract meaningful interpretable cytological and architectural features for downstream analysis. The CoNIC challenge poses the task of automated nuclei segmentation, classification and composition into six different types of nuclei from the largest publicly known nuclei dataset - Lizard. In this regard, w…