Automatic instance segmentation of glomeruli within kidney Whole Slide Imaging (WSI) is essential for clinical research in renal pathology. In computer vision, the end-to-end instance segmentation methods (e.g., Mask-RCNN) have shown their advantages relative to detect-then-segment approaches by performing complementary detection and segmentation tasks simultaneously. As a result, the end-to-end Mask-RCNN approach has been the de facto standard method in recent glomerular segmentation studies, where downsampling and patch-based techniques are used to properly evaluate the high resolution images from WSI (e.g., >10,000x10,000 pixels on 40x). However, in high resolution WSI, a single glomerulus itself can be more than 1,000x1,000 pixels in original resolution which yields significant information loss when the corresponding features maps are downsampled via the Mask-RCNN pipeline. In this paper, we assess if the end-to-end instance segmentation framework is optimal for high-resolution WSI objects by comparing Mask-RCNN with our proposed detect-then-segment framework. Beyond such a comparison, we also comprehensively evaluate the performance of our detect-then-segment pipeline through: 1) two of the most prevalent segmentation backbones (U-Net and DeepLab_v3); 2) six different image resolutions (from 512x512 to 28x28); and 3) two different color spaces (RGB and LAB). Our detect-then-segment pipeline, with the DeepLab_v3 segmentation framework operating on previously detected glomeruli of 512x512 resolution, achieved a 0.953 dice similarity coefficient (DSC), compared with a 0.902 DSC from the end-to-end Mask-RCNN pipeline. Further, we found that neither RGB nor LAB color spaces yield better performance when compared against each other in the context of a detect-then-segment framework. Detect-then-segment pipeline achieved better segmentation performance compared with End-to-end method.
University of Science and Technology of China（中国科学技术大学）；Hefei University of Technology（合肥工业大学）
Automatic medical image segmentation has wide applications for disease diagnosing. However, it is much more challenging than natural optical image segmentation due to the high-resolution of medical images and the corresponding huge computation cost. The sliding window is a commonly used technique for whole slide image (WSI) segmentation, however, for these methods based on the sliding window, the main drawback is lacking global contextual information for supervision. In this paper, we propose a dual-inputs attention network (denoted as DA-RefineNet) for WSI segmentation, where both local fine-…
Khalifa University（哈利法大学）；Beihang University（北京航空航天大学）；University of Louisville（路易斯维尔大学）
Prostate cancer (PCa) is the second deadliest form of cancer in males, and it can be clinically graded by examining the structural representations of Gleason tissues. This paper proposes \RV{a new method} for segmenting the Gleason tissues \RV{(patch-wise) in order to grade PCa from the whole slide images (WSI).} Also, the proposed approach encompasses two main contributions: 1) A synergy of hybrid dilation factors and hierarchical decomposition of latent space representation for effective Gleason tissues extraction, and 2) A three-tiered loss function which can penalize different semantic seg…
Digital pathology provides an excellent opportunity for applying fully convolutional networks (FCNs) to tasks, such as semantic segmentation of whole slide images (WSIs). However, standard FCNs face challenges with respect to multi-resolution, inherited from the pyramid arrangement of WSIs. As a result, networks specifically designed to learn and aggregate information at different levels are desired. In this paper, we propose two novel multi-resolution networks based on the popular `U-Net' architecture, which are evaluated on a benchmark dataset for binary semantic segmentation in WSIs. The pr…
Tissue segmentation is an important pre-requisite for efficient and accurate diagnostics in digital pathology. However, it is well known that whole-slide scanners can fail in detecting all tissue regions, for example due to the tissue type, or due to weak staining because their tissue detection algorithms are not robust enough. In this paper, we introduce two different convolutional neural network architectures for whole slide image segmentation to accurately identify the tissue sections. We also compare the algorithms to a published traditional method. We collected 54 whole slide images with …
Radboud University Medical Center（拉德堡德大学医学中心）；Institute of Experimental Immunology, University of Zurich（苏黎世大学实验免疫学研究所）；Center for Medical Image Science and Visualization, Linköping University（林雪平大学医学影像科学与可视化中心）
We propose HookNet, a semantic segmentation model for histopathology whole-slide images, which combines context and details via multiple branches of encoder-decoder convolutional neural networks. Concentricpatches at multiple resolutions with different fields of view are used to feed different branches of HookNet, and intermediate representations are combined via a hooking mechanism. We describe a framework to design and train HookNet for achieving high-resolution semantic segmentation and introduce constraints to guarantee pixel-wise alignment in feature maps during hooking. We show the advan…
Hazara University（哈扎拉大学）；National University of Sciences & Technology (NUST)（国家科技大学）
Previous works on segmentation of SEM (scanning electron microscope) blood cell image ignore the semantic segmentation approach of whole-slide blood cell segmentation. In the proposed work, we address the problem of whole-slide blood cell segmentation using the semantic segmentation approach. We design a novel convolutional encoder-decoder framework along with VGG-16 as the pixel-level feature extraction model. -e proposed framework comprises 3 main steps: First, all the original images along with manually generated ground truth masks of each blood cell type are passed through the preprocessin…
IBM Zurich Research Lab（IBM苏黎世研究实验室）；EPFL（洛桑联邦理工学院）；APHP. Centre（巴黎公立医院中心）；Cochin hospital（科钦医院）；Université de Paris（巴黎大学）；ETH Zurich（苏黎世联邦理工学院）；Uppsala University（乌普萨拉大学）
Segmenting histology images into diagnostically relevant regions is imperative to support timely and reliable decisions by pathologists. To this end, computer-aided techniques have been proposed to delineate relevant regions in scanned histology slides. However, the techniques necessitate task-specific large datasets of annotated pixels, which is tedious, time-consuming, expensive, and infeasible to acquire for many histology tasks. Thus, weakly-supervised semantic segmentation techniques are proposed to utilize weak supervision that is cheaper and quicker to acquire. In this paper, we propose…
Slide presentations are an effective and efficient tool used by the teaching community for classroom communication. However, this teaching model can be challenging for blind and visually impaired (VI) students. The VI student required personal human assistance for understand the presented slide. This shortcoming motivates us to design a Classroom Slide Narration System (CSNS) that generates audio descriptions corresponding to the slide content. This problem poses as an image-to-markup language generation task. The initial step is to extract logical regions such as title, text, equation, figure…
Uppsala University（乌普萨拉大学）；Karolinska Universitetsjukhuset（卡罗林斯卡大学医院）
Oral cancer incidence is rapidly increasing worldwide. The most important determinant factor in cancer survival is early diagnosis. To facilitate large scale screening, we propose a fully automated pipeline for oral cancer detection on whole slide cytology images. The pipeline consists of fully convolutional regression-based nucleus detection, followed by per-cell focus selection, and CNN based classification. Our novel focus selection step provides fast per-cell focus decisions at human-level accuracy. We demonstrate that the pipeline provides efficient cancer classification of whole slide cy…
Deep learning methods are widely applied in digital pathology to address clinical challenges such as prognosis and diagnosis. As one of the most recent applications, deep models have also been used to extract molecular features from whole slide images. Although molecular tests carry rich information, they are often expensive, time-consuming, and require additional tissue to sample. In this paper, we propose tRNAsfomer, an attention-based topology that can learn both to predict the bulk RNA-seq from an image and represent the whole slide image of a glass slide simultaneously. The tRNAsfomer use…
Recently, various deep learning methods have shown significant successes in medical image analysis, especially in the detection of cancer metastases in hematoxylin and eosin (H&E) stained whole-slide images (WSIs). However, in order to obtain good performance, these research achievements rely on hundreds of well-annotated WSIs. In this study, we tackle the tumor localization and detection problem under the setting of few labeled whole slide images and introduce a patch-based analysis pipeline based on the latest reverse knowledge distillation architecture. To address the extremely unbalanced n…
Muroran Institute of Technology（室兰工业大学）；Niigata University of Health and Welfare（新潟医疗福祉大学）；Konica Minolta, Inc.（柯尼卡美能达公司）
Multi-stain whole-slide-image (WSI) registration is an active field of research. It is unclear, however, how the current WSI registration methods would perform on a real-world data set. AutomatiC Registration Of Breast cAncer Tissue (ACROBAT) challenge is held to verify the performance of the current WSI registration methods by using a new dataset that originates from routine diagnostics to assess real-world applicability. In this report, we present our solution for the ACROBAT challenge. We employ a two-step approach including rigid and non-rigid transforms. The experimental results show that…
The application of deep learning to pathology assumes the existence of digital whole slide images of pathology slides. However, slide digitization is bottlenecked by the high cost of precise motor stages in slide scanners that are needed for position information used for slide stitching. We propose GloFlow, a two-stage method for creating a whole slide image using optical flow-based image registration with global alignment using a computationally tractable graph-pruning approach. In the first stage, we train an optical flow predictor to predict pairwise translations between successive video fr…
The widespread adoption of whole slide imaging has increased the demand for effective and efficient gigapixel image analysis. Deep learning is at the forefront of computer vision, showcasing significant improvements over previous methodologies on visual understanding. However, whole slide images have billions of pixels and suffer from high morphological heterogeneity as well as from different types of artefacts. Collectively, these impede the conventional use of deep learning. For the clinical translation of deep learning solutions to become a reality, these challenges need to be addressed. In…
Northwestern Polytechnical University（西北工业大学）；Tianjin Medical University（天津医科大学）
Goal: Squamous cell carcinoma of cervix is one of the most prevalent cancer worldwide in females. Traditionally, the most indispensable diagnosis of cervix squamous carcinoma is histopathological assessment which is achieved under microscope by pathologist. However, human evaluation of pathology slide is highly depending on the experience of pathologist, thus big inter- and intra-observer variability exists. Digital pathology, in combination with deep learning provides an opportunity to improve the objectivity and efficiency of histopathologic slide analysis. Methods: In this study, we obtaine…
University of California, Los Angeles（加州大学洛杉矶分校）；Cedars-Sinai Medical Center（西达赛奈医疗中心）
Histology review is often used as the `gold standard' for disease diagnosis. Computer aided diagnosis tools can potentially help improve current pathology workflows by reducing examination time and interobserver variability. Previous work in cancer grading has focused mainly on classifying pre-defined regions of interest (ROIs), or relied on large amounts of fine-grained labels. In this paper, we propose a two-stage attention-based multiple instance learning model for slide-level cancer grading and weakly-supervised ROI detection and demonstrate its use in prostate cancer. Compared with existi…
University of British Columbia（不列颠哥伦比亚大学）；Vancouver General Hospital（温哥华综合医院）；BC Cancer Research Center（不列颠哥伦比亚癌症研究中心）
Ovarian cancer is the most lethal cancer of the female reproductive organs. There are $5$ major histological subtypes of epithelial ovarian cancer, each with distinct morphological, genetic, and clinical features. Currently, these histotypes are determined by a pathologist's microscopic examination of tumor whole-slide images (WSI). This process has been hampered by poor inter-observer agreement (Cohen's kappa $0.54$-$0.67$). We utilized a \textit{two}-stage deep transfer learning algorithm based on convolutional neural networks (CNN) and progressive resizing for automatic classification of ep…
Faculty of Sciences（理学院）；Mohammed V University（穆罕默德五世大学）；École Normale Supérieure（高等师范学院）
Cervical cancer will cause 460 000 deaths per year by 2040, approximately 90% are Sub-Saharan African women. A constantly increasing incidence in Africa making cervical cancer a priority by the World Health Organization (WHO) in terms of screening, diagnosis, and treatment. Conventionally, cancer diagnosis relies primarily on histopathological assessment, a deeply error-prone procedure requiring intelligent computer-aided systems as low-cost patient safety mechanisms but lack of labeled data in digital pathology limits their applicability. In this study, few cervical tissue digital slides from…
FedWSIDD: Federated Whole Slide Image Classification via Dataset Distillation
Union Hospital, Tongji Medical College, Huazhong University of Science and Technology（华中科技大学同济医学院附属同济医院）；Centre for Health Informatics, Australian Institute of Health Innovation, Macquarie University（澳大利亚健康创新研究所健康信息中心，麦觉大学）
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…
University of Oxford（牛津大学）；Oxford NIHR Biomedical Research Centre（牛津NIHR生物医学研究中心）；John Radcliffe Hospital（约翰·拉德克利夫医院）
Histopathology slides are routinely marked by pathologists using permanent ink markers that should not be removed as they form part of the medical record. Often tumour regions are marked up for the purpose of highlighting features or other downstream processing such an gene sequencing. Once digitised there is no established method for removing this information from the whole slide images limiting its usability in research and study. Removal of marker ink from these high-resolution whole slide images is non-trivial and complex problem as they contaminate different regions and in an inconsistent…
Joint analysis of multiple biomarker images and tissue morphology is important for disease diagnosis, treatment planning and drug development. It requires cross-staining comparison among Whole Slide Images (WSIs) of immuno-histochemical and hematoxylin and eosin (H&E) microscopic slides. However, automatic, and fast cross-staining alignment of enormous gigapixel WSIs at single-cell precision is challenging. In addition to morphological deformations introduced during slide preparation, there are large variations in cell appearance and tissue morphology across different staining. In this paper, …
University of Leeds（利兹大学）；Leeds Teaching Hospitals NHS Trust（利兹教学医院NHS信托基金会）
Weakly-supervised classification of histopathology slides is a computationally intensive task, with a typical whole slide image (WSI) containing billions of pixels to process. We propose Discriminative Region Active Sampling for Multiple Instance Learning (DRAS-MIL), a computationally efficient slide classification method using attention scores to focus sampling on highly discriminative regions. We apply this to the diagnosis of ovarian cancer histological subtypes, which is an essential part of the patient care pathway as different subtypes have different genetic and molecular profiles, treat…
Medmain Inc.（Medmain公司）；Sapporo Kosei General Hospital（札幌厚生综合医院）；Hiroshima University Hospital（广岛大学医院）
Signet ring cell carcinoma (SRCC) of the stomach is a rare type of cancer with a slowly rising incidence. It tends to be more difficult to detect by pathologists mainly due to its cellular morphology and diffuse invasion manner, and it has poor prognosis when detected at an advanced stage. Computational pathology tools that can assist pathologists in detecting SRCC would be of a massive benefit. In this paper, we trained deep learning models using transfer learning, fully-supervised learning, and weakly-supervised learning to predict SRCC in Whole Slide Images (WSIs) using a training set of 1,…
University of Waterloo（滑铁卢大学）；Vector Institute（向量研究所）；Ontario Tech University（安大略理工大学）
Deep learning methods such as convolutional neural networks (CNNs) are difficult to directly utilize to analyze whole slide images (WSIs) due to the large image dimensions. We overcome this limitation by proposing a novel two-stage approach. First, we extract a set of representative patches (called mosaic) from a WSI. Each patch of a mosaic is encoded to a feature vector using a deep network. The feature extractor model is fine-tuned using hierarchical target labels of WSIs, i.e., anatomic site and primary diagnosis. In the second stage, a set of encoded patch-level features from a WSI is used…
Harbin Institute of Technology（哈尔滨工业大学）；Peng Cheng Laboratory（鹏城实验室）；Tsinghua University（清华大学）；McMaster University（麦克马斯特大学）；Shanghai Jiao Tong University（上海交通大学）
Whole slide imaging (WSI) is an emerging technology for digital pathology. The process of autofocusing is the main influence of the performance of WSI. Traditional autofocusing methods either are time-consuming due to repetitive mechanical motions, or require additional hardware and thus are not compatible to current WSI systems. In this paper, we propose the concept of \textit{virtual autofocusing}, which does not rely on mechanical adjustment to conduct refocusing but instead recovers in-focus images in an offline learning-based manner. With the initial focal position, we only perform two-sh…
University of Texas at Arlington（得克萨斯大学阿灵顿分校）；University of New South Wales（新南威尔士大学）；UNSW Sydney（新南威尔士大学悉尼分校）
Traditional image-based survival prediction models rely on discriminative patch labeling which make those methods not scalable to extend to large datasets. Recent studies have shown Multiple Instance Learning (MIL) framework is useful for histopathological images when no annotations are available in classification task. Different to the current image-based survival models that limit to key patches or clusters derived from Whole Slide Images (WSIs), we propose Deep Attention Multiple Instance Survival Learning (DeepAttnMISL) by introducing both siamese MI-FCN and attention-based MIL pooling to …
Comparing ImageNet Pre-training with Digital Pathology Foundation Models for Whole Slide Image-Based Survival Analysis
Imperial College London, Department of Electrical and Electronic Engineering, London, UK（帝国理工学院伦敦分校，电子与电气工程系）；Department of Pathology, Institut de Pathologie Multisite, Groupement Hospitalier Sud, Lyon University Hospital, Pierre-Bénite, France（病理学系，多站点病理研究所，南部医院集团，里昂大学医院，皮埃尔-贝内蒂，法国）；University of Lyon, Université Claude Bernard Lyon 1, Lyon, France（里昂大学， Claude Bernard 里昂第一大学，里昂，法国）
CentraleSupélec, Université Paris-Saclay（巴黎萨克雷大学中央高等电力学院）；Gustave Roussy Cancer Campus（古斯塔夫·鲁西癌症校区）；Therapanacea（Therapanacea公司）
In whole slide imaging, commonly used staining techniques based on hematoxylin and eosin (H&E) and immunohistochemistry (IHC) stains accentuate different aspects of the tissue landscape. In the case of detecting metastases, IHC provides a distinct readout that is readily interpretable by pathologists. IHC, however, is a more expensive approach and not available at all medical centers. Virtually generating IHC images from H&E using deep neural networks thus becomes an attractive alternative. Deep generative models such as CycleGANs learn a semantically-consistent mapping between two image domai…
Weisberg Division of Computer Science, Marshall University（马歇尔大学魏斯伯格计算机科学分部）；Kitware, Inc.（Kitware公司）；Emory University School of Medicine（埃默里大学医学院）；National Cancer Institute（美国国家癌症研究所）；Cairo University（开罗大学）；Northwestern University Feinberg School of Medicine（西北大学费恩伯格医学院）
Extracting quantitative phenotypic information from whole-slide images presents significant challenges for investigators who are not experienced in developing image analysis algorithms. We present new software that enables rapid learn-by-example training of machine learning classifiers for detection of histologic patterns in whole-slide imaging datasets. HistomicsML2.0 uses convolutional networks to be readily adaptable to a variety of applications, provides a web-based user interface, and is available as a software container to simplify deployment.
University of Toronto（多伦多大学）；University of British Columbia（不列颠哥伦比亚大学）；Sunnybrook Health Science Center（森尼布鲁克健康科学中心）；Sunnybrook Research Institute（森尼布鲁克研究所）
Whole slide images (WSIs) pose unique challenges when training deep learning models. They are very large which makes it necessary to break each image down into smaller patches for analysis, image features have to be extracted at multiple scales in order to capture both detail and context, and extreme class imbalances may exist. Significant progress has been made in the analysis of these images, thanks largely due to the availability of public annotated datasets. We postulate, however, that even if a method scores well on a challenge task, this success may not translate to good performance in a…
University of Toronto（多伦多大学）；Huron Digital Pathology Inc.（休伦数字病理公司）
One of the challenges facing the adoption of digital pathology workflows for clinical use is the need for automated quality control. As the scanners sometimes determine focus inaccurately, the resultant image blur deteriorates the scanned slide to the point of being unusable. Also, the scanned slide images tend to be extremely large when scanned at greater or equal 20X image resolution. Hence, for digital pathology to be clinically useful, it is necessary to use computational tools to quickly and accurately quantify the image focus quality and determine whether an image needs to be re-scanned.…
Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）；University of Ulsan College of Medicine（蔚山大学医学院）；Asan Medical Center（峨山医学中心）；Ajou University School of Medicine（亚洲大学医学院）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）
Deep learning has been widely used to analyze digitized hematoxylin and eosin (H&E)-stained histopathology whole slide images. Automated cancer segmentation using deep learning can be used to diagnose malignancy and to find novel morphological patterns to predict molecular subtypes. To train pixel-wise cancer segmentation models, manual annotation from pathologists is generally a bottleneck due to its time-consuming nature. In this paper, we propose Deep Interactive Learning with a pretrained segmentation model from a different cancer type to reduce manual annotation time. Instead of annotatin…
Geisel School of Medicine at Dartmouth（达特茅斯盖泽尔医学院）；Dartmouth-Hitchcock Medical Center（达特茅斯-希区柯克医疗中心）；Dartmouth College（达特茅斯学院）
In pathology, whole-slide images (WSI) based survival prediction has attracted increasing interest. However, given the large size of WSIs and the lack of pathologist annotations, extracting the prognostic information from WSIs remains a challenging task. Previous studies have used multiple instance learning approaches to combine the information from multiple randomly sampled patches, but different visual patterns may contribute differently to prognosis prediction. In this study, we developed a multi-head attention approach to focus on various parts of a tumor slide, for more comprehensive info…
DPsurv: Dual-Prototype Evidential Fusion for Uncertainty-Aware and Interpretable Whole-Slide Image Survival Prediction
National University of Singapore；National University of Singapore Guangzhou Research Translation；Innovation Institute；Imperial College London；Peking Union Medical College Hospital, Chinese Academy of Medical Sciences \& Peking Union Medical College；Hunan University；Institute of High Performance Computing, Agency for Science, Technology；Research (A STAR)
Information Systems Institute, University of Applied Sciences Western Switzerland（西瑞士应用科学大学信息系统学院）；AGH University of Kraków（克拉科夫AGH大学）；University of Padova（帕多瓦大学）；University of Geneva（日内瓦大学）
Image Data Analytics, Informatics IT, Merck \& Co., Inc., West Point, PA 19486, USA Image Data Analytics, Informatics IT, Merck \& Co., Inc., Rahway, NJ 07065, USA
It is common for pathologists to annotate specific regions of the tissue, such as tumor, directly on the glass slide with markers. Although this practice was helpful prior to the advent of histology whole slide digitization, it often occludes important details which are increasingly relevant to immuno-oncology due to recent advancements in digital pathology imaging techniques. The current work uses a generative adversarial network with cycle loss to remove these annotations while still maintaining the underlying structure of the tissue by solving an image-to-image translation problem. We train…
INSA Centre Val de Loire（卢瓦尔河谷国立应用科学学院）；PRISME（PRISME实验室）
This paper addresses the problem of liver cancer segmentation in Whole Slide Image (WSI). We propose a multi-scale image processing method based on automatic end-to-end deep neural network algorithm for segmentation of cancer area. A seven-levels gaussian pyramid representation of the histopathological image was built to provide the texture information in different scales. In this work, several neural architectures were compared using the original image level for the training procedure. The proposed method is based on U-Net applied to seven levels of various resolutions (pyramidal subsumpling)…
SUNY Buffalo（纽约州立大学布法罗分校）；Johns Hopkins University School of Medicine（约翰斯·霍普金斯大学医学院）
We created a custom pipeline (histo-fetch) to efficiently extract random patches and labels from pathology whole slide images (WSIs) for input to a neural network on-the-fly. We prefetch these patches as needed during network training, avoiding the need for WSI preparation such as chopping/tiling. We demonstrate the utility of this pipeline to perform artificial stain transfer and image generation using the popular networks CycleGAN and ProGAN, respectively.
Imaging Informatics Division（成像信息学部门）；Bioinformatics Institute（生物信息学研究所）；A*STAR（新加坡科技研究局）；Lucence Diagnostics（Lucence诊断公司）；Institute of Bioengineering and Nanotechnology（生物工程与纳米技术研究所）；Singapore General Hospital（新加坡综合医院）；National Cancer Centre Singapore（新加坡国家癌症中心）；Institute of Molecular and Cell Biology（分子与细胞生物学研究所）；National University of Singapore（新加坡国立大学）；Singapore Eye Research Institute（新加坡眼科研究所）；Image and Pervasive Access Lab（图像与普适访问实验室）
Motivation: High resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, however, requires accurate reconstruction of the tissue volume from the 2D image stack. This task is not trivial due to the distortions that each individual tissue slice experiences while cutting and mounting the tissue on the glass slide. Performing registration for the whole tissue slices may be adversely affected by the deformed tissue regions. Consequently, regional registratio…
We present a novel approach to train pixel resolution segmentation models on whole slide images in a weakly supervised setup. The model is trained to classify patches extracted from slides. This leads the training to be made under noisy labeled data. We solve the problem with two complementary strategies. First, the patches are sampled online using the model's knowledge by focusing on regions where the model's confidence is higher. Second, we propose an extension of the KL divergence that is robust to noisy labels. Our preliminary experiment on CAMELYON 16 data set show promising results. The …
How similar are two images? In computational pathology, where Whole Slide Images (WSIs) of digitally scanned tissue samples from patients can be multi-gigapixels in size, determination of degree of similarity between two WSIs is a challenging task with a number of practical applications. In this work, we explore a novel strategy based on kernelized Maximum Mean Discrepancy (MMD) analysis for determination of pairwise similarity between WSIs. The proposed approach works by calculating MMD between two WSIs using kernels over deep features of image patches. This allows representation of an entire…
In recent years, the availability of digitized Whole Slide Images (WSIs) has enabled the use of deep learning-based computer vision techniques for automated disease diagnosis. However, WSIs present unique computational and algorithmic challenges. WSIs are gigapixel-sized ($\sim$100K pixels), making them infeasible to be used directly for training deep neural networks. Also, often only slide-level labels are available for training as detailed annotations are tedious and can be time-consuming for experts. Approaches using multiple-instance learning (MIL) frameworks have been shown to overcome th…
Brigham and Women’s Hospital（布里格姆妇女医院）；Harvard Medical School（哈佛医学院）；Broad Institute of Harvard and MIT（哈佛-麻省理工学院布罗德研究所）；Department of Pathology（病理系）；Northwell Health（诺斯韦尔健康）；Department of Biomedical Informatics（生物医学信息学系）；Dana-Farber Cancer Institute（达纳-法伯癌症研究所）；Cancer Program（癌症项目）；Cancer Data Science（癌症数据科学）
Deep Learning-based computational pathology algorithms have demonstrated profound ability to excel in a wide array of tasks that range from characterization of well known morphological phenotypes to predicting non-human-identifiable features from histology such as molecular alterations. However, the development of robust, adaptable, and accurate deep learning-based models often rely on the collection and time-costly curation large high-quality annotated training data that should ideally come from diverse sources and patient populations to cater for the heterogeneity that exists in such dataset…
Duke University（杜克大学）；Duke University Medical Center（杜克大学医学中心）
We consider preoperative prediction of thyroid cancer based on ultra-high-resolution whole-slide cytopathology images. Inspired by how human experts perform diagnosis, our approach first identifies and classifies diagnostic image regions containing informative thyroid cells, which only comprise a tiny fraction of the entire image. These local estimates are then aggregated into a single prediction of thyroid malignancy. Several unique characteristics of thyroid cytopathology guide our deep-learning-based approach. While our method is closely related to multiple-instance learning, it deviates fr…
