Mitotic counting is a vital prognostic marker of tumor proliferation in breast cancer. Deep learning-based mitotic detection is on par with pathologists, but it requires large labeled data for training. We propose a deep classification framework for enhancing mitosis detection by leveraging class label information, via softmax loss, and spatial distribution information among samples, via distance metric learning. We also investigate strategies towards steadily providing informative samples to boost the learning. The efficacy of the proposed framework is established through evaluation on ICPR 2012 and AMIDA 2013 mitotic data. Our framework significantly improves the detection with small training data and achieves on par or superior performance compared to state-of-the-art methods for using the entire training data.
University of Warwick(华威大学);University of Oulu(奥卢大学);The Alan Turing Institute(艾伦·图灵研究所);Aalto University(阿尔托大学)
Mitosis count is an important biomarker for prognosis of various cancers. At present, pathologists typically perform manual counting on a few selected regions of interest in breast whole-slide-images (WSIs) of patient biopsies. This task is very time-consuming, tedious and subjective. Automated mitosis detection methods have made great advances in recent years. However, these methods require exhaustive labeling of a large number of selected regions of interest. This task is very expensive because expert pathologists are needed for reliable and accurate annotations. In this paper, we present a …
For the MIDOG mitosis detection challenge, we created a cascade algorithm consisting of a Mask-RCNN detector, followed by a classification ensemble consisting of ResNet50 and DenseNet201 to refine detected mitotic candidates. The MIDOG training data consists of 200 frames originating from four scanners, three of which are annotated for mitotic instances with centroid annotations. Our main algorithmic choices are as follows: first, to enhance the generalizability of our detector and classification networks, we use a state-of-the-art residual Cycle-GAN to transform each scanner domain to every o…
Supporting Mitosis Detection AI Training with Inter-Observer Eye-Gaze Consistencies
University of California, Los Angeles(加利福尼亚大学洛杉矶分校);University of Illinois, Urbana-Champaign(伊利诺伊大学厄巴纳-香槟分校);UCLA David Geffen School of Medicine(加州大学洛杉矶分校大卫·格芬医学院);Kansas University Medical Center(堪萨斯大学医学中心)
We propose a virtual staining methodology based on Generative Adversarial Networks to map histopathology images of breast cancer tissue from H&E stain to PHH3 and vice versa. We use the resulting synthetic images to build Convolutional Neural Networks (CNN) for automatic detection of mitotic figures, a strong prognostic biomarker used in routine breast cancer diagnosis and grading. We propose several scenarios, in which CNN trained with synthetically generated histopathology images perform on par with or even better than the same baseline model trained with real images. We discuss the potentia…
Guilin University of Electronic Technology(桂林电子科技大学);Guangxi Key Laboratory of Image and Graphic Intelligent Processing(广西图像图形智能处理重点实验室);Ganzhou Municipal Hospital(赣州市人民医院)
Mitosis nuclei count is one of the important indicators for the pathological diagnosis of breast cancer. The manual annotation needs experienced pathologists, which is very time-consuming and inefficient. With the development of deep learning methods, some models with good performance have emerged, but the generalization ability should be further strengthened. In this paper, we propose a two-stage mitosis segmentation and classification method, named SCMitosis. Firstly, the segmentation performance with a high recall rate is achieved by the proposed depthwise separable convolution residual blo…
Helmholtz Zentrum München(亥姆霍兹慕尼黑中心);Technische Universität München(慕尼黑工业大学);Johns Hopkins University(约翰斯·霍普金斯大学)
Intestinal enteroendocrine cells secrete hormones that are vital for the regulation of glucose metabolism but their differentiation from intestinal stem cells is not fully understood. Asymmetric stem cell divisions have been linked to intestinal stem cell homeostasis and secretory fate commitment. We monitored cell divisions using 4D live cell imaging of cultured intestinal crypts to characterize division modes by means of measurable features such as orientation or shape. A statistical analysis of these measurements requires annotation of mitosis events, which is currently a tedious and time-c…
Rethinking Mitosis Detection: Towards Diverse Data and Feature Representation
South China University of Technology(华南理工大学);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));Southern Medical University(南方医科大学);Nanfang Hospital(南方医院);Guangdong Provincial People’s Hospital Ganzhou Hospital(广东省人民医院赣州医院);Guilin University of Electronic Technology(桂林电子科技大学)
Radboud University Medical Center(拉德堡德大学医学中心);Canisius-Wilhelmina Hospital(卡尼修斯-威廉明娜医院);Jeroen Bosch Hospital(耶伦博斯医院)
Manual counting of mitotic tumor cells in tissue sections constitutes one of the strongest prognostic markers for breast cancer. This procedure, however, is time-consuming and error-prone. We developed a method to automatically detect mitotic figures in breast cancer tissue sections based on convolutional neural networks (CNNs). Application of CNNs to hematoxylin and eosin (H&E) stained histological tissue sections is hampered by: (1) noisy and expensive reference standards established by pathologists, (2) lack of generalization due to staining variation across laboratories, and (3) high compu…
Harbin Institute of Technology, Shenzhen(哈尔滨工业大学(深圳))
Tracking living cells in video sequence is difficult, because of cell morphology and high similarities between cells. Tracking-by-detection methods are widely used in multi-cell tracking. We perform multi-cell tracking based on the cell centroid detection, and the performance of the detector has high impact on tracking performance. In this paper, UNet is utilized to extract inter-frame and intra-frame spatio-temporal information of cells. Detection performance of cells in mitotic phase is improved by multi-frame input. Good detection results facilitate multi-cell tracking. A mitosis detection …
PIEAS(巴基斯坦工程与应用科学学院);Islamia College Peshawar(白沙瓦伊斯兰学院)
Empirical evaluation of breast tissue biopsies for mitotic nuclei detection is considered an important prognostic biomarker in tumor grading and cancer progression. However, automated mitotic nuclei detection poses several challenges because of the unavailability of pixel-level annotations, different morphological configurations of mitotic nuclei, their sparse representation, and close resemblance with non-mitotic nuclei. These challenges undermine the precision of the automated detection model and thus make detection difficult in a single phase. This work proposes an end-to-end detection syst…
Friedrich-Alexander-Universität Erlangen-Nürnberg(埃尔朗根-纽伦堡弗里德里希-亚历山大大学);Freie Universität Berlin(柏林自由大学)
Large-scale image data such as digital whole-slide histology images pose a challenging task at annotation software solutions. Today, a number of good solutions with varying scopes exist. For cell annotation, however, we find that many do not match the prerequisites for fast annotations. Especially in the field of mitosis detection, it is assumed that detection accuracy could significantly benefit from larger annotation databases that are currently however very troublesome to produce. Further, multiple independent (blind) expert labels are a big asset for such databases, yet there is currently …
Beijing Institute of Technology(北京理工大学);North China University of Technology(北方工业大学)
Cell detection in histopathology images is of great value in clinical practice. \textit{Convolutional neural networks} (CNNs) have been applied to cell detection to improve the detection accuracy, where cell annotations are required for network training. However, due to the variety and large number of cells, complete annotations that include every cell of interest in the training images can be challenging. Usually, incomplete annotations can be achieved, where positive labeling results are carefully examined to ensure their reliability but there can be other positive instances, i.e., cells of …
AnyCXR: Human Anatomy Segmentation of Chest X-ray at Any Acquisition Position using Multi-stage Domain Randomized Synthetic Data with Imperfect Annotations and Conditional Joint Annotation Regularization Learning
Department of Radiology, Northwestern University, Chicago, IL, USA(西北大学放射科);Data Science Institute, Vanderbilt University, Nashville, TN, USA(范德比尔特大学数据科学研究院);Department of Orthopedics, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, P.R. China(山西医科大学第二医院骨科);Second Clinical Medical College, Shanxi Medical University, Taiyuan, Shanxi, P.R. China(山西医科大学第二临床医学院);School of Computer Science, University of Sydney, Sydney, NSW, Australia(悉尼大学计算机科学学院)
University of Edinburgh(爱丁堡大学);University of California(加利福尼亚大学);Cedars-Sinai Medical Center(西达赛奈医疗中心);University of Essex(埃塞克斯大学);The Alan Turing Institute(艾伦·图灵研究所)
Automated pathology segmentation remains a valuable diagnostic tool in clinical practice. However, collecting training data is challenging. Semi-supervised approaches by combining labelled and unlabelled data can offer a solution to data scarcity. An approach to semi-supervised learning relies on reconstruction objectives (as self-supervision objectives) that learns in a joint fashion suitable representations for the task. Here, we propose Anatomy-Pathology Disentanglement Network (APD-Net), a pathology segmentation model that attempts to learn jointly for the first time: disentanglement of an…
CNN visualization and interpretation methods, like class-activation maps (CAMs), are typically used to highlight the image regions linked to class predictions. These models allow to simultaneously classify images and extract class-dependent saliency maps, without the need for costly pixel-level annotations. However, they typically yield segmentations with high false-positive rates and, therefore, coarse visualisations, more so when processing challenging images, as encountered in histology. To mitigate this issue, we propose an active learning (AL) framework, which progressively integrates pix…
Training a deep neural network heavily relies on a large amount of training data with accurate annotations. To alleviate this problem, various methods have been proposed to annotate the data automatically. However, automatically generating annotations will inevitably yields noisy labels. In this paper, we propose a Data Selection and joint Training (DST) method to automatically select training samples with accurate annotations. Specifically, DST fits a mixture model according to the original annotation as well as the predicted label for each training sample, and the mixture model is utilized t…
School of Computer Science, the University of Adelaide, Australia(澳大利亚阿德莱德大学计算机学院);Monash University, Australia(澳大利亚莫纳什大学)
Deployment of deep learning models in robotics as sensory information extractors can be a daunting task to handle, even using generic GPU cards. Here, we address three of its most prominent hurdles, namely, i) the adaptation of a single model to perform multiple tasks at once (in this work, we consider depth estimation and semantic segmentation crucial for acquiring geometric and semantic understanding of the scene), while ii) doing it in real-time, and iii) using asymmetric datasets with uneven numbers of annotations per each modality. To overcome the first two issues, we adapt a recently pro…
National Yang Ming Chiao Tung University(国立阳明交通大学);University at Albany, State University of New York(纽约州立大学奥尔巴尼分校)
We develop a Synthetic Fusion Pyramid Network (SPF-Net) with a scale-aware loss function design for accurate crowd counting. Existing crowd-counting methods assume that the training annotation points were accurate and thus ignore the fact that noisy annotations can lead to large model-learning bias and counting error, especially for counting highly dense crowds that appear far away. To the best of our knowledge, this work is the first to properly handle such noise at multiple scales in end-to-end loss design and thus push the crowd counting state-of-the-art. We model the noise of crowd annotat…
Pattern Recognition Lab, Friedrich-Alexander-Universität Erlangen-Nürnberg(埃尔朗根-纽伦堡大学模式识别实验室);Institute of Veterinary Pathology, Free University Berlin(柏林自由大学兽医病理学研究所)
Identification and counting of cells and mitotic figures is a standard task in diagnostic histopathology. Due to the large overall cell count on histological slides and the potential sparse prevalence of some relevant cell types or mitotic figures, retrieving annotation data for sufficient statistics is a tedious task and prone to a significant error in assessment. Automatic classification and segmentation is a classic task in digital pathology, yet it is not solved to a sufficient degree. We present a novel approach for cell and mitotic figure classification, based on a deep convolutional net…
Stanford University(斯坦福大学);University of California Berkeley(加州大学伯克利分校)
We present a dataset of large-scale indoor spaces that provides a variety of mutually registered modalities from 2D, 2.5D and 3D domains, with instance-level semantic and geometric annotations. The dataset covers over 6,000m2 and contains over 70,000 RGB images, along with the corresponding depths, surface normals, semantic annotations, global XYZ images (all in forms of both regular and 360° equirectangular images) as well as camera information. It also includes registered raw and semantically annotated 3D meshes and point clouds. The dataset enables development of joint and cross-modal learn…
Clinical Center(临床中心);National Library of Medicine(美国国家医学图书馆);National Institutes of Health(美国国立卫生研究院)
Despite the recent advances in automatically describing image contents, their applications have been mostly limited to image caption datasets containing natural images (e.g., Flickr 30k, MSCOCO). In this paper, we present a deep learning model to efficiently detect a disease from an image and annotate its contexts (e.g., location, severity and the affected organs). We employ a publicly available radiology dataset of chest x-rays and their reports, and use its image annotations to mine disease names to train convolutional neural networks (CNNs). In doing so, we adopt various regularization tech…
Annotating objects with 3D bounding boxes in LiDAR pointclouds is a costly human driven process in an autonomous driving perception system. In this paper, we present a method to semi-automatically annotate real-world pointclouds collected by deployment vehicles using simulated data. We train a 3D object detector model on labeled simulated data from CARLA jointly with real world pointclouds from our target vehicle. The supervised object detection loss is augmented with a CORAL loss term to reduce the distance between labeled simulated and unlabeled real pointcloud feature representations. The g…
Deep learning-based approaches to delineating 3D structure depend on accurate annotations to train the networks. Yet, in practice, people, no matter how conscientious, have trouble precisely delineating in 3D and on a large scale, in part because the data is often hard to interpret visually and in part because the 3D interfaces are awkward to use. In this paper, we introduce a method that explicitly accounts for annotation inaccuracies. To this end, we treat the annotations as active contour models that can deform themselves while preserving their topology. This enables us to jointly train the…
Annotating cancerous regions in whole-slide images (WSIs) of pathology samples plays a critical role in clinical diagnosis, biomedical research, and machine learning algorithms development. However, generating exhaustive and accurate annotations is labor-intensive, challenging, and costly. Drawing only coarse and approximate annotations is a much easier task, less costly, and it alleviates pathologists' workload. In this paper, we study the problem of refining these approximate annotations in digital pathology to obtain more accurate ones. Some previous works have explored obtaining machine le…
On the Value of PHH3 for Mitotic Figure Detection on H&E-stained Images
Technische Hochschule Ingolstadt(英戈尔施塔特应用技术大学);Gestalt Diagnostics(格式塔诊断公司);University of Veterinary Medicine, Vienna(维也纳兽医大学);Freie Universität Berlin(柏林自由大学);SeaWorld Yas Island(海洋世界亚斯岛);Cornell University(康奈尔大学);USAMV(克卢日-纳波卡兽医与医学大学);Medical University of Vienna(维也纳医科大学);Hoffmann-La Roche(罗氏公司);Ross University School of Veterinary Medicine(罗斯大学兽医学院);University of Florida(佛罗里达大学);University Hospital Erlangen(埃尔兰根大学医院);Friedrich-Alexander-Universität Erlangen-Nürnberg(埃尔朗根-纽伦堡弗里德里希-亚历山大大学);IDEXX Laboratories(爱德士实验室);The Schwarzman Animal Medical Center(施瓦茨曼动物医疗中心)
The estimation of viewpoints and keypoints effectively enhance object detection methods by extracting valuable traits of the object instances. While the output of both processes differ, i.e., angles vs. list of characteristic points, they indeed share the same focus on how the object is placed in the scene, inducing that there is a certain level of correlation between them. Therefore, we propose a convolutional neural network that jointly computes the viewpoint and keypoints for different object categories. By training both tasks together, each task improves the accuracy of the other. Since th…
Disney Research Pittsburgh(迪士尼研究院匹兹堡分院);Max Planck Institute for Informatics(马克斯·普朗克信息学研究所)
Learning a joint language-visual embedding has a number of very appealing properties and can result in variety of practical application, including natural language image/video annotation and search. In this work, we study three different joint language-visual neural network model architectures. We evaluate our models on large scale LSMDC16 movie dataset for two tasks: 1) Standard Ranking for video annotation and retrieval 2) Our proposed movie multiple-choice test. This test facilitate automatic evaluation of visual-language models for natural language video annotation based on human activitie…
Vehicle detection and annotation for streaming video data with complex scenes is an interesting but challenging task for urban traffic surveillance. In this paper, we present a fast framework of Detection and Annotation for Vehicles (DAVE), which effectively combines vehicle detection and attributes annotation. DAVE consists of two convolutional neural networks (CNNs): a fast vehicle proposal network (FVPN) for vehicle-like objects extraction and an attributes learning network (ALN) aiming to verify each proposal and infer each vehicle's pose, color and type simultaneously. These two nets are …
Zhejiang University(浙江大学);Stevens Institute of Technology(史蒂文斯理工学院);Alibaba Group(阿里巴巴集团);Yunnan University(云南大学)
In this paper, we investigate a novel deep-model reusing task. Our goal is to train a lightweight and versatile student model, without human-labelled annotations, that amalgamates the knowledge and masters the expertise of two pretrained teacher models working on heterogeneous problems, one on scene parsing and the other on depth estimation. To this end, we propose an innovative training strategy that learns the parameters of the student intertwined with the teachers, achieved by 'projecting' its amalgamated features onto each teacher's domain and computing the loss. We also introduce two opti…
University of Oxford(牛津大学);Federal University of Rio Grande(里奥格兰德联邦大学)
We present in this work the first end-to-end deep learning based method that predicts both 3D hand shape and pose from RGB images in the wild. Our network consists of the concatenation of a deep convolutional encoder, and a fixed model-based decoder. Given an input image, and optionally 2D joint detections obtained from an independent CNN, the encoder predicts a set of hand and view parameters. The decoder has two components: A pre-computed articulated mesh deformation hand model that generates a 3D mesh from the hand parameters, and a re-projection module controlled by the view parameters tha…
Training deep object detectors requires significant amount of human-annotated images with accurate object labels and bounding box coordinates, which are extremely expensive to acquire. Noisy annotations are much more easily accessible, but they could be detrimental for learning. We address the challenging problem of training object detectors with noisy annotations, where the noise contains a mixture of label noise and bounding box noise. We propose a learning framework which jointly optimizes object labels, bounding box coordinates, and model parameters by performing alternating noise correcti…
Max Planck Institute for Informatics(马克斯·普朗克信息学研究所)
Convolutional Neural Network based approaches for monocular 3D human pose estimation usually require a large amount of training images with 3D pose annotations. While it is feasible to provide 2D joint annotations for large corpora of in-the-wild images with humans, providing accurate 3D annotations to such in-the-wild corpora is hardly feasible in practice. Most existing 3D labelled data sets are either synthetically created or feature in-studio images. 3D pose estimation algorithms trained on such data often have limited ability to generalize to real world scene diversity. We therefore propo…
Text spotting end-to-end methods have recently gained attention in the literature due to the benefits of jointly optimizing the text detection and recognition components. Existing methods usually have a distinct separation between the detection and recognition branches, requiring exact annotations for the two tasks. We introduce TextTranSpotter (TTS), a transformer-based approach for text spotting and the first text spotting framework which may be trained with both fully- and weakly-supervised settings. By learning a single latent representation per word detection, and using a novel loss funct…
Contextual Robotics Institute(情境机器人研究所);University of California San Diego(加州大学圣地亚哥分校)
This work introduces a new approach for joint detection of centerlines based on image data by localizing the features jointly in 2D and 3D. In contrast to existing work that focuses on detection of visual cues, we explore feature extraction methods that are directly amenable to the urban driving task. To develop and evaluate our approach, a large urban driving dataset dubbed AV Breadcrumbs is automatically labeled by leveraging vector map representations and projective geometry to annotate over 900,000 images. Our results demonstrate potential for dynamic scene modeling across various urban dr…
City University of Hong Kong(香港城市大学);Baidu USA LLC(百度美国有限责任公司)
Domain Adaptive Object Detection (DAOD) models a joint distribution of images and labels from an annotated source domain and learns a domain-invariant transformation to estimate the target labels with the given target domain images. Existing methods assume that the source domain labels are completely clean, yet large-scale datasets often contain error-prone annotations due to instance ambiguity, which may lead to a biased source distribution and severely degrade the performance of the domain adaptive detector de facto. In this paper, we represent the first effort to formulate noisy DAOD and pr…
University of Edinburgh(爱丁堡大学);Google Research(谷歌研究院)
Training object class detectors typically requires a large set of images with objects annotated by bounding boxes. However, manually drawing bounding boxes is very time consuming. In this paper we greatly reduce annotation time by proposing center-click annotations: we ask annotators to click on the center of an imaginary bounding box which tightly encloses the object instance. We then incorporate these clicks into existing Multiple Instance Learning techniques for weakly supervised object localization, to jointly localize object bounding boxes over all training images. Extensive experiments o…
Accurate hand pose estimation at joint level has several uses on human-robot interaction, user interfacing and virtual reality applications. Yet, it currently is not a solved problem. The novel deep learning techniques could make a great improvement on this matter but they need a huge amount of annotated data. The hand pose datasets released so far present some issues that make them impossible to use on deep learning methods such as the few number of samples, high-level abstraction annotations or samples consisting in depth maps. In this work, we introduce a multiview hand pose dataset in whic…
SenseTime Research(商汤科技研究院);The Chinese University of Hong Kong(香港中文大学)
The performance of object detection, to a great extent, depends on the availability of large annotated datasets. To alleviate the annotation cost, the research community has explored a number of ways to exploit unlabeled or weakly labeled data. However, such efforts have met with limited success so far. In this work, we revisit the problem with a pragmatic standpoint, trying to explore a new balance between detection performance and annotation cost by jointly exploiting fully and weakly annotated data. Specifically, we propose a weakly- and semi-supervised object detection framework (WSSOD), w…
Queen Mary University of London(伦敦玛丽女王大学);Vision Semantics Ltd(视觉语义有限公司)
Recognising semantic pedestrian attributes in surveillance images is a challenging task for computer vision, particularly when the imaging quality is poor with complex background clutter and uncontrolled viewing conditions, and the number of labelled training data is small. In this work, we formulate a Joint Recurrent Learning (JRL) model for exploring attribute context and correlation in order to improve attribute recognition given small sized training data with poor quality images. The JRL model learns jointly pedestrian attribute correlations in a pedestrian image and in particular their se…
Department of Radiology and Imaging Sciences, National Institutes of Health Clinical Center(美国国立卫生研究院临床中心放射与影像科学系)
The recent rapid and tremendous success of deep convolutional neural networks (CNN) on many challenging computer vision tasks largely derives from the accessibility of the well-annotated ImageNet and PASCAL VOC datasets. Nevertheless, unsupervised image categorization (i.e., without the ground-truth labeling) is much less investigated, yet critically important and difficult when annotations are extremely hard to obtain in the conventional way of "Google Search" and crowd sourcing. We address this problem by presenting a looped deep pseudo-task optimization (LDPO) framework for joint mining of …
University of Chinese Academy of Sciences(中国科学院大学);Institute of Automation, Chinese Academy of Sciences(中国科学院自动化研究所)
Iris segmentation and localization in non-cooperative environment is challenging due to illumination variations, long distances, moving subjects and limited user cooperation, etc. Traditional methods often suffer from poor performance when confronted with iris images captured in these conditions. Recent studies have shown that deep learning methods could achieve impressive performance on iris segmentation task. In addition, as iris is defined as an annular region between pupil and sclera, geometric constraints could be imposed to help locating the iris more accurately and improve the segmentat…
Bridging Annotation Gaps: Transferring Labels to Align Object Detection Datasets
National University of Singapore I2R, A*STAR(新加坡国立大学I2R,A*STAR);University of Cambridge(剑桥大学);National University of Singapore ASUS Intelligent Cloud Services(新加坡国立大学ASUS智能云服务)
Inria(法国国家信息与自动化研究所);École normale supérieure(巴黎高等师范学院);CNRS(法国国家科学研究中心);PSL Research University(巴黎文理研究大学);University Grenoble Alpes(格勒诺布尔阿尔卑斯大学);Grenoble INP(格勒诺布尔国立高等物理、数学与信息学院)
Spatio-temporal action detection in videos is typically addressed in a fully-supervised setup with manual annotation of training videos required at every frame. Since such annotation is extremely tedious and prohibits scalability, there is a clear need to minimize the amount of manual supervision. In this work we propose a unifying framework that can handle and combine varying types of less-demanding weak supervision. Our model is based on discriminative clustering and integrates different types of supervision as constraints on the optimization. We investigate applications of such a model to t…
Computer Vision Center(计算机视觉中心);Universitat de Barcelona(巴塞罗那大学)
Current state-of-the-art in 3D human pose and shape recovery relies on deep neural networks and statistical morphable body models, such as the Skinned Multi-Person Linear model (SMPL). However, regardless of the advantages of having both body pose and shape, SMPL-based solutions have shown difficulties to predict 3D bodies accurately. This is mainly due to the unconstrained nature of SMPL, which may generate unrealistic body meshes. Because of this, regression of SMPL parameters is a difficult task, often addressed with complex regularization terms. In this paper we propose to embed SMPL withi…