Automated digital histopathology image segmentation is an important task to help pathologists diagnose tumors and cancer subtypes. For pathological diagnosis of cancer subtypes, pathologists usually change the magnification of whole-slide images (WSI) viewers. A key assumption is that the importance of the magnifications depends on the characteristics of the input image, such as cancer subtypes. In this paper, we propose a novel semantic segmentation method, called Adaptive-Weighting-Multi-Field-of-View-CNN (AWMF-CNN), that can adaptively use image features from images with different magnifications to segment multiple cancer subtype regions in the input image. The proposed method aggregates several expert CNNs for images of different magnifications by adaptively changing the weight of each expert depending on the input image. It leverages information in the images with different magnifications that might be useful for identifying the subtypes. It outperformed other state-of-the-art methods in experiments.
Kyushu University（九州大学）；Kyoto University Hospital（京都大学医院）；National Institute of Informatics（国立信息学研究所）
We propose a weakly-supervised cell tracking method that can train a convolutional neural network (CNN) by using only the annotation of "cell detection" (i.e., the coordinates of cell positions) without association information, in which cell positions can be easily obtained by nuclear staining. First, we train a co-detection CNN that detects cells in successive frames by using weak-labels. Our key assumption is that the co-detection CNN implicitly learns association in addition to detection. To obtain the association information, we propose a backward-and-forward propagation method that analyz…
University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；University of Kansas Medical Center（堪萨斯大学医学中心）；UCLA David Geffen School of Medicine（加州大学洛杉矶分校大卫·格芬医学院）；Baylor College of Medicine（贝勒医学院）
This work presents a mitosis detection method with only one vanilla Convolutional Neural Network (CNN). Our method consists of two steps: given an image, we first apply a CNN using a sliding window technique to extract patches that have mitoses; we then calculate each extracted patch's class activation map to obtain the mitosis's precise location. To increase the model performance on high-domain-variance pathology images, we train the CNN with a data augmentation pipeline, a noise-tolerant loss that copes with unlabeled images, and a multi-rounded active learning strategy. In the MIDOG 2022 ch…
Multi-Source and Multi-Sequence Myocardial Pathology Segmentation Using a Cascading Refinement CNN
Institute of Computer Graphics and Vision, Graz University of Technology（格拉茨工业大学计算机图形学与视觉研究所）；AVL List GmbH（AVL List 有限公司）；Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz（格拉茨医科大学医学信息学、统计学与文献学研究所）
Recent breakthroughs in object detection and image classification using Convolutional Neural Networks (CNNs) are revolutionizing the state of the art in medical imaging, and microscopy in particular presents abundant opportunities for computer vision algorithms to assist medical professionals in diagnosis of diseases ranging from malaria to cancer. High resolution scans of microscopy slides called Whole Slide Images (WSIs) offer enough information for a cancer pathologist to come to a conclusion regarding cancer presence, subtype, and severity based on measurements of features within the slide…
Norwegian Computing Center（挪威计算中心）；UiT the Arctic University of Norway（挪威北极大学）
We propose a novel architecture called the Multi-view Self-Constructing Graph Convolutional Networks (MSCG-Net) for semantic segmentation. Building on the recently proposed Self-Constructing Graph (SCG) module, which makes use of learnable latent variables to self-construct the underlying graphs directly from the input features without relying on manually built prior knowledge graphs, we leverage multiple views in order to explicitly exploit the rotational invariance in airborne images. We further develop an adaptive class weighting loss to address the class imbalance. We demonstrate the effec…
Beijing University of Posts and Telecommunications（北京邮电大学）；Chinese Academy of Sciences（中国科学院）
Dense pose estimation is a dense 3D prediction task for instance-level human analysis, aiming to map human pixels from an RGB image to a 3D surface of the human body. Due to a large amount of surface point regression, the training process appears to be easy to collapse compared to other region-based human instance analyzing tasks. By analyzing the loss formulation of the existing dense pose estimation model, we introduce a novel point regression loss function, named Dense Points} loss to stable the training progress, and a new balanced loss weighting strategy to handle the multi-task losses. W…
Symbiosis International University（symbiosis国际大学）；National Institute of Mental Health and Neurosciences（国家精神卫生与神经科学研究院）
We propose a CNN based technique that aggregates feature maps from its multiple layers that can localize abnormalities with greater details as well as predict pathology under consideration. Existing class activation mapping (CAM) techniques extract feature maps from either the final layer or a single intermediate layer to create the discriminative maps and then interpolate to upsample to the original image resolution. In this case, the subject specific localization is coarse and is unable to capture subtle abnormalities. To mitigate this, our method builds a novel CNN based discriminative loca…
Radboud University Medical Center（拉德堡德大学医学中心）；Linköping University（林雪平大学）
Stain variation is a phenomenon observed when distinct pathology laboratories stain tissue slides that exhibit similar but not identical color appearance. Due to this color shift between laboratories, convolutional neural networks (CNNs) trained with images from one lab often underperform on unseen images from the other lab. Several techniques have been proposed to reduce the generalization error, mainly grouped into two categories: stain color augmentation and stain color normalization. The former simulates a wide variety of realistic stain variations during training, producing stain-invarian…
Beyond Classification: Pathology Foundation Models as Detection Encoders for Mitotic Figures
Flensburg University of Applied Sciences（弗伦斯堡应用科学大学）；University of Veterinary Medicine, Vienna（维也纳兽医大学）；Freie Universität Berlin（柏林自由大学）；Technische Hochschule Ingolstadt（英戈尔施塔特应用技术大学）；Medical University of Vienna（维也纳医科大学）；Julius-Maximilians-Universität Würzburg（维尔zburg大学）；Friedrich-Alexander-Universität Erlangen-Nürnberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学）
Fraunhofer Institute for Digital Medicine MEVIS（弗劳恩霍夫数字医学研究所MEVIS）；Technische Universität Berlin（柏林工业大学）
Image analysis tasks in computational pathology are commonly solved using convolutional neural networks (CNNs). The selection of a suitable CNN architecture and hyperparameters is usually done through exploratory iterative optimization, which is computationally expensive and requires substantial manual work. The goal of this article is to evaluate how generic tools for neural network architecture search and hyperparameter optimization perform for common use cases in computational pathology. For this purpose, we evaluated one on-premises and one cloud-based tool for three different classificati…
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…
University of Waterloo（滑铁卢大学）；Amirkabir University（阿米尔卡比尔理工大学）；Nanjing University of Science & Technology（南京理工大学）；Deakin University（迪肯大学）；University of Ontario Institute of Technology（安大略理工大学）
In this paper, we introduce a new dataset, \textbf{Kimia Path24}, for image classification and retrieval in digital pathology. We use the whole scan images of 24 different tissue textures to generate 1,325 test patches of size 1000$\times$1000 (0.5mm$\times$0.5mm). Training data can be generated according to preferences of algorithm designer and can range from approximately 27,000 to over 50,000 patches if the preset parameters are adopted. We propose a compound patch-and-scan accuracy measurement that makes achieving high accuracies quite challenging. In addition, we set the benchmarking line…
Institute of Biophysics, Center for Physiological Medicine, Medical University of Graz（格拉茨医科大学医学生物物理研究所）；Institute of Neuroinformatics, University of Zurich and ETH Zurich（苏黎世大学与苏黎世联邦理工学院神经信息学研究所）；Institute for Computer Graphics and Vision, Graz University of Technology（格拉茨技术大学计算机图形与视觉研究所）；Ludwig Boltzmann Institute for Clinical Forensic Imaging（路德维希·玻尔兹曼临床法医影像研究所）；BioTechMed-Graz（格拉茨生物技术医学联盟）
Segmentation of histopathology sections is an ubiquitous requirement in digital pathology and due to the large variability of biological tissue, machine learning techniques have shown superior performance over standard image processing methods. As part of the GlaS@MICCAI2015 colon gland segmentation challenge, we present a learning-based algorithm to segment glands in tissue of benign and malignant colorectal cancer. Images are preprocessed according to the Hematoxylin-Eosin staining protocol and two deep convolutional neural networks (CNN) are trained as pixel classifiers. The CNN predictions…
Université de Sherbrooke（舍布鲁克大学）；Imagia cybernetics（Imagia cybernetics公司）；Google（谷歌）；Imeka Inc.（Imeka公司）
Segmentation of focal (localized) brain pathologies such as brain tumors and brain lesions caused by multiple sclerosis and ischemic strokes are necessary for medical diagnosis, surgical planning and disease development as well as other applications such as tractography. Over the years, attempts have been made to automate this process for both clinical and research reasons. In this regard, machine learning methods have long been a focus of attention. Over the past two years, the medical imaging field has seen a rise in the use of a particular branch of machine learning commonly known as deep l…
Hamburg University of Technology（汉堡工业大学）；University Medical Center Hamburg-Eppendorf（汉堡-埃彭多夫大学医学中心）；DAISYlabs, Forschungszentrum Medizintechnik Hamburg（汉堡医疗技术研究中心DAISYlabs）
Objective: This work addresses two key problems of skin lesion classification. The first problem is the effective use of high-resolution images with pretrained standard architectures for image classification. The second problem is the high class imbalance encountered in real-world multi-class datasets. Methods: To use high-resolution images, we propose a novel patch-based attention architecture that provides global context between small, high-resolution patches. We modify three pretrained architectures and study the performance of patch-based attention. To counter class imbalance problems, we …
University of Science and Technology of China（中国科学技术大学）；UNSW Sydney（新南威尔士大学）；Genmab Inc.（Genmab公司）
NLP-based computer vision models, particularly vision transformers, have been shown to outperform CNN models in many imaging tasks. However, most digital pathology artificial-intelligence models are based on CNN architectures, probably owing to a lack of data regarding NLP models for pathology images. In this study, we developed digital pathology pipelines to benchmark the five most recently proposed NLP models (vision transformer (ViT), Swin Transformer, MobileViT, CMT, and Sequencer2D) and four popular CNN models (ResNet18, ResNet50, MobileNetV2, and EfficientNet) to predict biomarkers in co…
Kharkevich Institute for Information Transmission Problems（信息传输问题研究所（Kharkevich研究所））；Moscow Institute of Physics and Technology（莫斯科物理技术学院）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）
In the last years, neural networks have proven to be a powerful framework for various image analysis problems. However, some application domains have specific limitations. Notably, digital pathology is an example of such fields due to tremendous image sizes and quite limited number of training examples available. In this paper, we adopt state-of-the-art convolutional neural networks (CNN) architectures for digital pathology images analysis. We propose to classify image patches to increase effective sample size and then to apply an ensembling technique to build prediction for the original image…
Eltwise layer is a commonly used structure in the multi-branch deep learning network. In a filter-wise pruning procedure, due to the specific operation of the eltwise layer, all its previous convolutional layers should vote for which filters by index should be pruned. Since only an intersection of the voted filters is pruned, the compression rate is limited. This work proposes a method called Directed-Weighting Group Lasso (DWGL), which enforces an index-wise incremental (directed) coefficient on the filterlevel group lasso items, so that the low index filters getting high activation tend to b…
The field of computational pathology presents many challenges for computer vision algorithms due to the sheer size of pathology images. Histopathology images are large and need to be split up into image tiles or patches so modern convolutional neural networks (CNNs) can process them. In this work, we present a method to generate an interpretable image representation of computational pathology images using quadtrees and a pipeline to use these representations for highly accurate downstream classification. To the best of our knowledge, this is the first attempt to use quadtrees for pathology ima…
The Norwegian University of Science and Technology（挪威科技大学）；St. Olavs Hospital, Trondheim University Hospital（圣奥拉夫斯医院，特隆赫姆大学医院）；SINTEF
Deep convolutional neural networks (CNNs) are the current state-of-the-art for digital analysis of histopathological images. The large size of whole-slide microscopy images (WSIs) requires advanced memory handling to read, display and process these images. There are several open-source platforms for working with WSIs, but few support deployment of CNN models. These applications use third-party solutions for inference, making them less user-friendly and unsuitable for high-performance image analysis. To make deployment of CNNs user-friendly and feasible on low-end machines, we have developed a …
University of Waterloo（滑铁卢大学）；University of Toronto（多伦多大学）；Huron Digital Pathology（休伦数字病理公司）
Out-of-focus microscopy lens in digital pathology is a critical bottleneck in high-throughput Whole Slide Image (WSI) scanning platforms, for which pixel-level automated Focus Quality Assessment (FQA) methods are highly desirable to help significantly accelerate the clinical workflows. Existing FQA methods include both knowledge-driven and data-driven approaches. While data-driven approaches such as Convolutional Neural Network (CNN) based methods have shown great promises, they are difficult to use in practice due to their high computational complexity and lack of transferability. Here, we pr…
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…
University of Sydney（悉尼大学）；University of New South Wales（新南威尔士大学）；Brigham and Women’s Hospital（布莱根妇女医院）；Harvard Medical School（哈佛医学院）；University of Pittsburgh（匹兹堡大学）；Microsoft Corporation（微软公司）
Unsupervised domain adaptation (UDA) for nuclei instance segmentation is important for digital pathology, as it alleviates the burden of labor-intensive annotation and domain shift across datasets. In this work, we propose a Cycle Consistency Panoptic Domain Adaptive Mask R-CNN (CyC-PDAM) architecture for unsupervised nuclei segmentation in histopathology images, by learning from fluorescence microscopy images. More specifically, we first propose a nuclei inpainting mechanism to remove the auxiliary generated objects in the synthesized images. Secondly, a semantic branch with a domain discrimi…
This paper is about few-shot segmentation of foreground objects in images. We train a CNN on small subsets of training images, each mimicking the few-shot setting. In each subset, one image serves as the query and the other(s) as support image(s) with ground-truth segmentation. The CNN first extracts feature maps from the query and support images. Then, a class feature vector is computed as an average of the support's feature maps over the known foreground. Finally, the target object is segmented in the query image by using a cosine similarity between the class feature vector and the query's f…
Large amounts of unlabelled data are commonplace for many applications in computational pathology, whereas labelled data is often expensive, both in time and cost, to acquire. We investigate the performance of unsupervised and supervised deep learning methods when few labelled data are available. Three methods are compared: clustering autoencoder latent vectors (unsupervised), a single layer classifier combined with a pre-trained autoencoder (semi-supervised), and a supervised CNN. We apply these methods on hematoxylin and eosin (H&E) stained prostatectomy images to classify tumour versus non-…
University of Warwick（华威大学）；The Alan Turing Institute（艾伦·图灵研究所）；University Hospitals Coventry & Warwickshire（考文垂与沃里克郡大学医院）
Convolutional neural networks (CNNs) have been recently used for a variety of histology image analysis. However, availability of a large dataset is a major prerequisite for training a CNN which limits its use by the computational pathology community. In previous studies, CNNs have demonstrated their potential in terms of feature generalizability and transferability accompanied with better performance. Considering these traits of CNN, we propose a simple yet effective method which leverages the strengths of CNN combined with the advantages of including contextual information, particularly desig…
DPSeq: A Novel and Efficient Digital Pathology Classifier for Predicting Cancer Biomarkers using Sequencer Architecture
School of Data Science, University of Science and Technology of China（中国科学技术大学数据科学学院）；School of Management, University of Science and Technology of China（中国科学技术大学管理学院）；School of Population Health, UNSW Sydney（新南威尔士大学悉尼分校人口健康学院）；Genmab Inc.（杰特贝公司）
University of Dayton（代顿大学）；Deep Lens Inc（Deep Lens公司）
Deep Learning (DL) approaches have been providing state-of-the-art performance in different modalities in the field of medical imagining including Digital Pathology Image Analysis (DPIA). Out of many different DL approaches, Deep Convolutional Neural Network (DCNN) technique provides superior performance for classification, segmentation, and detection tasks. Most of the task in DPIA problems are somehow possible to solve with classification, segmentation, and detection approaches. In addition, sometimes pre and post-processing methods are applied for solving some specific type of problems. Rec…
University of Warwick（华威大学）；Alan Turing Institute（艾伦·图灵研究所）；Institute for Infocomm Research（资讯通信研究院）；University of Sheffield（谢菲尔德大学）
While high-resolution pathology images lend themselves well to `data hungry' deep learning algorithms, obtaining exhaustive annotations on these images is a major challenge. In this paper, we propose a self-supervised CNN approach to leverage unlabeled data for learning generalizable and domain invariant representations in pathology images. The proposed approach, which we term as Self-Path, is a multi-task learning approach where the main task is tissue classification and pretext tasks are a variety of self-supervised tasks with labels inherent to the input data. We introduce novel domain spec…
Lexington High School（列克星敦高中）；Stony Brook University（石溪大学）；Ecole Centrale Paris（巴黎中央理工学院）；Oak Ridge National Laboratory（橡树岭国家实验室）；Stony Brook University Hospital（石溪大学医院）
Classifying the various shapes and attributes of a glioma cell nucleus is crucial for diagnosis and understanding the disease. We investigate automated classification of glioma nuclear shapes and visual attributes using Convolutional Neural Networks (CNNs) on pathology images of automatically segmented nuclei. We propose three methods that improve the performance of a previously-developed semi-supervised CNN. First, we propose a method that allows the CNN to focus on the most important part of an image- the image's center containing the nucleus. Second, we inject (concatenate) pre-extracted VG…
IBM Research Africa（IBM非洲研究院）；National Cancer Registry（国家癌症登记处）
Like most global cancer registries, the National Cancer Registry in South Africa employs expert human coders to label pathology reports using appropriate International Classification of Disease for Oncology (ICD-O) codes spanning 42 different cancer types. The annotation is extensive for the large volume of cancer pathology reports the registry receives annually from public and private sector institutions. This manual process, coupled with other challenges results in a significant 4-year lag in reporting of annual cancer statistics in South Africa. We present a hierarchical deep learning ensem…
In pathology, tissue samples are assessed using multiple staining techniques to enhance contrast in unique histologic features. In this paper, we introduce a multimodal CNN-GNN based graph fusion approach that leverages complementary information from multiple non-registered histopathology images to predict pathologic scores. We demonstrate this approach in nonalcoholic steatohepatitis (NASH) by predicting CRN fibrosis stage and NAFLD Activity Score (NAS). Primary assessment of NASH typically requires liver biopsy evaluation on two histological stains: Trichrome (TC) and hematoxylin and eosin (…
Conventional 2D Convolutional Neural Networks (CNN) extract features from an input image by applying linear filters. These filters compute the spatial coherence by weighting the photometric information on a fixed neighborhood without taking into account the geometric information. We tackle the problem of improving the classical RGB CNN methods by using the depth information provided by the RGB-D cameras. State-of-the-art approaches use depth as an additional channel or image (HHA) or pass from 2D CNN to 3D CNN. This paper proposes a novel and generic procedure to articulate both photometric an…
Google Brain（谷歌大脑）；Google Inc（谷歌公司）；Verily Life Sciences（Verily生命科学）
Each year, the treatment decisions for more than 230,000 breast cancer patients in the U.S. hinge on whether the cancer has metastasized away from the breast. Metastasis detection is currently performed by pathologists reviewing large expanses of biological tissues. This process is labor intensive and error-prone. We present a framework to automatically detect and localize tumors as small as 100 x 100 pixels in gigapixel microscopy images sized 100,000 x 100,000 pixels. Our method leverages a convolutional neural network (CNN) architecture and obtains state-of-the-art results on the Camelyon16…
DeepRadiology, INC.（DeepRadiology 公司）；University of California, Los Angeles（加州大学洛杉矶分校）；University of California, San Diego（加州大学圣迭戈分校）；University of Oxford（牛津大学）
We describe a system to automatically filter clinically significant findings from computerized tomography (CT) head scans, operating at performance levels exceeding that of practicing radiologists. Our system, named DeepRadiologyNet, builds on top of deep convolutional neural networks (CNNs) trained using approximately 3.5 million CT head images gathered from over 24,000 studies taken from January 1, 2015 to August 31, 2015 and January 1, 2016 to April 30 2016 in over 80 clinical sites. For our initial system, we identified 30 phenomenological traits to be recognized in the CT scans. To test t…
Institute of Information Systems, HES-SO (University of Applied Sciences and Arts Western Switzerland)（瑞士西部应用科学与艺术大学 信息系统研究所）；Department of Computer Science, University of Geneva（日内瓦大学 计算机科学系）；Department of Neurosciences, University of Padua（帕多瓦大学 神经科学系）；Inselspital, Bern Hospital（伯尔尼大学医院）；Medical Faculty, University of Geneva（日内瓦大学 医学院）
Computational pathology is a domain that aims to develop algorithms to automatically analyze large digitized histopathology images, called whole slide images (WSI). WSIs are produced scanning thin tissue samples that are stained to make specific structures visible. They show stain colour heterogeneity due to different preparation and scanning settings applied across medical centers. Stain colour heterogeneity is a problem to train convolutional neural networks (CNN), the state-of-the-art algorithms for most computational pathology tasks, since CNNs usually underperform when tested on images in…
Nanjing University of Posts and Telecommunications（南京邮电大学）；Nanjing University of Science and Technology（南京理工大学）；Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information of Ministry of Education（高维信息智能感知与系统教育部重点实验室）
In this paper, we propose an easily trained yet powerful representation learning approach with performance highly competitive to deep neural networks in a digital pathology image segmentation task. The method, called sparse coding driven deep decision tree ensembles that we abbreviate as ScD2TE, provides a new perspective on representation learning. We explore the possibility of stacking several layers based on non-differentiable pairwise modules and generate a densely concatenated architecture holding the characteristics of feature map reuse and end-to-end dense learning. Under this architect…
Xiamen University（厦门大学）；University College London（伦敦大学学院）
Facial Attribute Classification (FAC) has attracted increasing attention in computer vision and pattern recognition. However, state-of-the-art FAC methods perform face detection/alignment and FAC independently. The inherent dependencies between these tasks are not fully exploited. In addition, most methods predict all facial attributes using the same CNN network architecture, which ignores the different learning complexities of facial attributes. To address the above problems, we propose a novel deep multi-task multi-label CNN, termed DMM-CNN, for effective FAC. Specifically, DMM-CNN jointly o…
Visual place recognition (VPR) is usually considered as a specific image retrieval problem. Limited by existing training frameworks, most deep learning-based works cannot extract sufficiently stable global features from RGB images and rely on a time-consuming re-ranking step to exploit spatial structural information for better performance. In this paper, we propose StructVPR, a novel training architecture for VPR, to enhance structural knowledge in RGB global features and thus improve feature stability in a constantly changing environment. Specifically, StructVPR uses segmentation images as a …
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…
