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arXiv 2107.12357eess.IVcs.CV
Structure-Preserving Multi-Domain Stain Color Augmentation using Style-Transfer with Disentangled Representations
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）
Sophia J. Wagner, Nadieh Khalili, Raghav Sharma, Melanie Boxberg, Carsten Marr, Walter de Back, Tingying Peng
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 a novel color augmentation technique, HistAuGAN, that can simulate a wide variety of realistic histology stain colors, thus making neural networks stain-invariant when applied during training. Based on a generative adversarial network (GAN) for image-to-image translation, our model disentangles the content of the image, i.e., the morphological tissue structure, from the stain color attributes. It can be trained on multiple domains and, therefore, learns to cover different stain colors as well as other domain-specific variations introduced in the slide preparation and imaging process. We demonstrate that HistAuGAN outperforms conventional color augmentation techniques on a classification task on the publicly available dataset Camelyon17 and show that it is able to mitigate present batch effects.
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…
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 …
University of Houston（休斯顿大学）；University Hospital of Cologne（科隆大学医院）
The classification of Antibody Mediated Rejection (AMR) in kidney transplant remains challenging even for experienced nephropathologists; this is partly because histological tissue stain analysis is often characterized by low inter-observer agreement and poor reproducibility. One of the implicated causes for inter-observer disagreement is the variability of tissue stain quality between (and within) pathology labs, coupled with the gradual fading of archival sections. Variations in stain colors and intensities can make tissue evaluation difficult for pathologists, ultimately affecting their abi…
Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）；Stony Brook University（石溪大学）
Variations in hematoxylin and eosin (H&E) stained images (due to clinical lab protocols, scanners, etc) directly impact the quality and accuracy of clinical diagnosis, and hence it is important to control for these variations for a reliable diagnosis. In this work, we present a new approach based on the multimarginal Wasserstein barycenter to normalize and augment H&E stained images given one or more references. Specifically, we provide a mathematically robust way of naturally incorporating additional images as intermediate references to drive stain normalization and augmentation simultaneousl…
TUV SUD Singapore（新加坡TUV南德意志集团）；Nanyang Technological University（南洋理工大学）
Autonomous vehicles (AV) have progressed rapidly with the advancements in computer vision algorithms. The deep convolutional neural network as the main contributor to this advancement has boosted the classification accuracy dramatically. However, the discovery of adversarial examples reveals the generalization gap between dataset and the real world. Furthermore, affine transformations may also confuse computer vision based object detectors. The degradation of the perception system is undesirable for safety critical systems such as autonomous vehicles. In this paper, a deep learning system is p…
Histopathology whole slide images (WSIs) can reveal significant inter-hospital variability such as illumination, color or optical artifacts. These variations, caused by the use of different scanning protocols across medical centers (staining, scanner), can strongly harm algorithms generalization on unseen protocols. This motivates development of new methods to limit such drop of performances. In this paper, to enhance robustness on unseen target protocols, we propose a new test-time data augmentation based on multi domain image-to-image translation. It allows to project images from unseen prot…
We propose a method to disentangle linear-encoded facial semantics from StyleGAN without external supervision. The method derives from linear regression and sparse representation learning concepts to make the disentangled latent representations easily interpreted as well. We start by coupling StyleGAN with a stabilized 3D deformable facial reconstruction method to decompose single-view GAN generations into multiple semantics. Latent representations are then extracted to capture interpretable facial semantics. In this work, we make it possible to get rid of labels for disentangling meaningful f…
School of Engineering, University of Edinburgh（爱丁堡大学工程学院）；Canon Medical Research Europe Ltd.（佳能医疗欧洲研究有限公司）；The Alan Turing Institute（艾伦·图灵研究所）
Robust cardiac image segmentation is still an open challenge due to the inability of the existing methods to achieve satisfactory performance on unseen data of different domains. Since the acquisition and annotation of medical data are costly and time-consuming, recent work focuses on domain adaptation and generalization to bridge the gap between data from different populations and scanners. In this paper, we propose two data augmentation methods that focus on improving the domain adaptation and generalization abilities of state-to-the-art cardiac segmentation models. In particular, our "Resol…
Definiens（Definiens公司）；School Of Medicine, University of St Andrews（圣安德鲁斯大学医学院）
The detection of nuclei is one of the most fundamental components of computational pathology. Current state-of-the-art methods are based on deep learning, with the prerequisite that extensive labeled datasets are available. The increasing number of patient cohorts to be analyzed, the diversity of tissue stains and indications, as well as the cost of dataset labeling motivates the development of novel methods to reduce labeling effort across domains. We introduce in this work a weakly supervised 'inter-domain' approach that (i) performs stain normalization and unpaired image-to-image translatio…
Shiraz University of Technology（设拉子理工大学）；National Brain Mapping Laboratory（国家脑图谱实验室）
We propose a two-step domain shift-invariant mitosis cell detection method based on Faster RCNN and a convolutional neural network (CNN). We generate various domain-shifted versions of existing histopathology images using a stain augmentation technique, enabling our method to effectively learn various stain domains and achieve better generalization. The performance of our method is evaluated on the preliminary test data set of the MIDOG-2021 challenge. The experimental results demonstrate that the proposed mitosis detection method can achieve promising performance for domain-shifted histopatho…
CSIRO（澳大利亚联邦科学与工业研究组织）；National University of Singapore（新加坡国立大学）
Previous robustness approaches for deep learning models such as data augmentation techniques via data transformation or adversarial training cannot capture real-world variations that preserve the semantics of the input, such as a change in lighting conditions. To bridge this gap, we present NaTra, an adversarial training scheme that is designed to improve the robustness of image classification algorithms. We target attributes of the input images that are independent of the class identification, and manipulate those attributes to mimic real-world natural transformations (NaTra) of the inputs, w…
Tsinghua Shenzhen International Graduate School, Tsinghua University（清华大学深圳国际研究生院，清华大学）；University of Manchester（曼彻斯特大学）
Deep learning-based melanoma classification with dermoscopic images has recently shown great potential in automatic early-stage melanoma diagnosis. However, limited by the significant data imbalance and obvious extraneous artifacts, i.e., the hair and ruler markings, discriminative feature extraction from dermoscopic images is very challenging. In this study, we seek to resolve these problems respectively towards better representation learning for lesion features. Specifically, a GAN-based data augmentation (GDA) strategy is adapted to generate synthetic melanoma-positive images, in conjunctio…
SiliCoN: Simultaneous Nuclei Segmentation and Color Normalization of Histological Images
Biomedical Imaging and Bioinformatics Lab, Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India（生物医学影像与生物信息学实验室，人工智能单元，印度统计研究所，科拉卡特，印度）
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 …
Imagia（Imagia公司）；Montréal Institute for Learning Algorithms (MILA)（蒙特利尔学习算法研究所）；Université de Montréal（蒙特利尔大学）；University of Victoria（维多利亚大学）；West China Hospital of Sichuan University（四川大学华西医院）
Synthetic medical image generation has a huge potential for improving healthcare through many applications, from data augmentation for training machine learning systems to preserving patient privacy. Conditional Adversarial Generative Networks (cGANs) use a conditioning factor to generate images and have shown great success in recent years. Intuitively, the information in an image can be divided into two parts: 1) content which is presented through the conditioning vector and 2) style which is the undiscovered information missing from the conditioning vector. Current practices in using cGANs f…
Futurewei Technologies（未来技术公司）；University of Rochester（罗切斯特大学）
Representation learning with small labeled data have emerged in many problems, since the success of deep neural networks often relies on the availability of a huge amount of labeled data that is expensive to collect. To address it, many efforts have been made on training sophisticated models with few labeled data in an unsupervised and semi-supervised fashion. In this paper, we will review the recent progresses on these two major categories of methods. A wide spectrum of models will be categorized in a big picture, where we will show how they interplay with each other to motivate explorations …
University of Saskatchewan（萨斯喀彻温大学）；University of Tulane（杜兰大学）
Breast cancer is one of the most common causes of cancer-related death in women worldwide. Early and accurate diagnosis of breast cancer may significantly increase the survival rate of patients. In this study, we aim to develop a fully automatic, deep learning-based, method using descriptor features extracted by Deep Convolutional Neural Network (DCNN) models and pooling operation for the classification of hematoxylin and eosin stain (H&E) histological breast cancer images provided as a part of the International Conference on Image Analysis and Recognition (ICIAR) 2018 Grand Challenge on BreAs…
École de Technologie Superiéure, Université du Québec（魁北克大学高等技术学院）；State University of Ponta Grossa (UEPG)（蓬塔格罗萨州立大学）；Pontifical Catholic University of Paraná（巴拉那天主教大学）；Federal University of Paraná（巴拉那联邦大学）
Data imbalance is a major problem that affects several machine learning (ML) algorithms. Such a problem is troublesome because most of the ML algorithms attempt to optimize a loss function that does not take into account the data imbalance. Accordingly, the ML algorithm simply generates a trivial model that is biased toward predicting the most frequent class in the training data. In the case of histopathologic images (HIs), both low-level and high-level data augmentation (DA) techniques still present performance issues when applied in the presence of inter-patient variability; whence the model…
Stony Brook University（石溪大学）；Newark Beth Israel Medical Center（纽瓦克贝斯以色列医疗中心）；University Hospitals Cleveland Medical Center（克利夫兰大学医院医疗中心）
Well-labeled datasets of chest radiographs (CXRs) are difficult to acquire due to the high cost of annotation. Thus, it is desirable to learn a robust and transferable representation in an unsupervised manner to benefit tasks that lack labeled data. Unlike natural images, medical images have their own domain prior; e.g., we observe that many pulmonary diseases, such as the COVID-19, manifest as changes in the lung tissue texture rather than the anatomical structure. Therefore, we hypothesize that studying only the texture without the influence of structure variations would be advantageous for …
Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences（广东省人民医院、广东省医学科学院）；Guilin University of Electronic Technology（桂林电子科技大学）
Nuclear segmentation and classification is an essential step for computational pathology. TIA lab from Warwick University organized a nuclear segmentation and classification challenge (CoNIC) for H&E stained histopathology images in colorectal cancer with two highly correlated tasks, nuclei segmentation and classification task and cellular composition task. There are a few obstacles we have to address in this challenge, 1) limited training samples, 2) color variation, 3) imbalanced annotations, 4) similar morphological appearance among classes. To deal with these challenges, we proposed a stan…
Helmholtz AI（亥姆霍兹AI）；Helmholtz Center Munich（慕尼黑亥姆霍兹中心）；Klinikum Rechts der Isar（右岸医院）；Technical University of Munich (TUM)（慕尼黑工业大学）
In recent years, data-driven machine learning (ML) methods have revolutionized the computer vision community by providing novel efficient solutions to many unsolved (medical) image analysis problems. However, due to the increasing privacy concerns and data fragmentation on many different sites, existing medical data are not fully utilized, thus limiting the potential of ML. Federated learning (FL) enables multiple parties to collaboratively train a ML model without exchanging local data. However, data heterogeneity (non-IID) among the distributed clients is yet a challenge. To this end, we pro…
University Hospital and University of Zurich（苏黎世大学医院和苏黎世大学）
Making histopathology image classifiers robust to a wide range of real-world variability is a challenging task. Here, we describe a candidate deep learning solution for the Mitosis Domain Generalization Challenge 2022 (MIDOG) to address the problem of generalization for mitosis detection in images of hematoxylin-eosin-stained histology slides under high variability (scanner, tissue type and species variability). Our approach consists in training a rotation-invariant deep learning model using aggressive data augmentation with a training set enriched with hard negative examples and automatically…
Are nuclear masks all you need for improved out-of-domain generalisation? A closer look at cancer classification in histopathology
University of Oslo（奥斯陆大学）；Otto-von-Guericke University Magdeburg（马格德堡奥托·冯·格里克大学）；Singapore Institute of Technology（新加坡科技学院）；Oslo University Hospital（奥斯陆大学医院）；UiT The Arctic University of Norway（挪威北极大学）
NEC Laboratories America（NEC美国实验室）；NEC Corporation（NEC公司）；Hokkaido University Hospital（北海道大学医院）
We propose a method to accurately obtain the ratio of tumor cells over an entire histological slide. We use deep fully convolutional neural network models trained to detect and classify cells on images of H&E-stained tissue sections. Pathologists' labels consisting of exhaustive nuclei locations and tumor regions were used to trained the model in a supervised fashion. We show that combining two models, each working at a different magnification allows the system to capture both cell-level details and surrounding context to enable successful detection and classification of cells as either tumor-…
