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 analyzes the correspondence of cell positions in the detection maps output of the co-detection CNN. Experiments demonstrated that the proposed method can match positions by analyzing the co-detection CNN. Even though the method uses only weak supervision, the performance of our method was almost the same as the state-of-the-art supervised method.
PatchSorter: A High Throughput Deep Learning Digital Pathology Tool for Object Labeling
Vetsuisse Faculty, University of Bern（伯尔尼大学兽医系）；Case Western Reserve University（凯斯西储大学）；Toth Technology LLC（托思科技有限责任公司）；Duke University（杜克大学）；Institute of Pathology, Lausanne University Hospital（洛桑大学医院病理研究所）；Bern Center for Precision Medicine, University of Bern（伯尔尼大学伯尔尼精准医学中心）；Emory University（埃默里大学）；Georgia Institute of Technology（佐治亚理工学院）；Atlanta Veterans Medical Center（亚特兰大退伍军人医疗中心）；The Netherlands Cancer Institute（荷兰癌症研究所）；University Hospital of Geneva（日内瓦大学医院）
本文发布开源数字病理标注工具 PatchSorter，通过结合深度学习与直观 Web 界面，在超过 100,000 个对象上实现较人工无辅助标注逾 7 倍的速度提升且几乎不损失准确性。
City University of Hong Kong（香港城市大学）；The Hong Kong University of Science and Technology（香港科技大学）；The First Affiliated Hospital of Wenzhou Medical University（温州医科大学附属第一医院）
Semantic segmentation of functional magnetic resonance imaging (fMRI) makes great sense for pathology diagnosis and decision system of medical robots. The multi-channel fMRI provides more information of the pathological features. But the increased amount of data causes complexity in feature detections. This paper proposes a principal component analysis (PCA)-aided fully convolutional network to particularly deal with multi-channel fMRI. We transfer the learned weights of contemporary classification networks to the segmentation task by fine-tuning. The results of the convolutional network are c…
Acquiring the most representative examples via active learning (AL) can benefit many data-dependent computer vision tasks by minimizing efforts of image-level or pixel-wise annotations. In this paper, we propose a novel Collaborative Panoptic-Regional Active Learning framework (CPRAL) to address the semantic segmentation task. For a small batch of images initially sampled with pixel-wise annotations, we employ panoptic information to initially select unlabeled samples. Considering the class imbalance in the segmentation dataset, we import a Regional Gaussian Attention module (RGA) to achieve s…
Semi-supervised Medical Image Segmentation Method Based on Cross-pseudo Labeling Leveraging Strong and Weak Data Augmentation Strategies
Hangzhou Dianzi University（杭州电子科技大学）；Zhejiang University of Finance and Economics（浙江财经大学）；Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）；Shenzhen Children's Hospital（深圳市儿童医院）；Shenzhen Research Institute of Big Data（深圳市大数据研究院）
Shenzhen Research Institute of Big Data（深圳大数据研究院）；The Chinese University of Hong Kong at Shenzhen（香港中文大学（深圳））；Sun Yat-sen University（中山大学）；Pazhou Lab（琶洲实验室）
Recently deep neural networks, which require a large amount of annotated samples, have been widely applied in nuclei instance segmentation of H\&E stained pathology images. However, it is inefficient and unnecessary to label all pixels for a dataset of nuclei images which usually contain similar and redundant patterns. Although unsupervised and semi-supervised learning methods have been studied for nuclei segmentation, very few works have delved into the selective labeling of samples to reduce the workload of annotation. Thus, in this paper, we propose a novel full nuclei segmentation framewor…
North Shore Country Day（北岸乡村日校）；Northwestern University（西北大学）
Data labeling is often the most challenging task when developing computational pathology models. Pathologist participation is necessary to generate accurate labels, and the limitations on pathologist time and demand for large, labeled datasets has led to research in areas including weakly supervised learning using patient-level labels, machine assisted annotation and active learning. In this paper we explore self-supervised learning to reduce labeling burdens in computational pathology. We explore this in the context of classification of breast cancer tissue using the Barlow Twins approach, an…
Multi-graph Graph Matching for Coronary Artery Semantic Labeling
Kennesaw State University（肯尼索州立大学）；The First Affiliated Hospital of Nanjing Medical University（南京医科大学第一附属医院）；Michigan Technological University（密歇根理工大学）；Medical University of South Carolina（南卡罗来纳医科大学）
Domain adaptation helps transfer the knowledge gained from a labeled source domain to an unlabeled target domain. During the past few years, different domain adaptation techniques have been published. One common flaw of these approaches is that while they might work well on one input type, such as images, their performance drops when applied to others, such as text or time-series. In this paper, we introduce Proportional Progressive Pseudo Labeling (PPPL), a simple, yet effective technique that can be implemented in a few lines of code to build a more general domain adaptation technique that c…
This paper proposes a novel and efficient method for Learning from Label Proportions (LLP), whose goal is to train a classifier only by using the class label proportions of instance sets, called bags. We propose a novel LLP method based on an online pseudo-labeling method with regret minimization. As opposed to the previous LLP methods, the proposed method effectively works even if the bag sizes are large. We demonstrate the effectiveness of the proposed method using some benchmark datasets.
CLASS-M: Adaptive stain separation-based contrastive learning with pseudo-labeling for histopathological image classification
University of Utah（犹他大学）；Scientific Computing and Imaging Institute（科学计算与成像研究所）；University of British Columbia（不列颠哥伦比亚大学）；College of Medicine, The Catholic University of Korea（韩国天主教大学医学院）
Guangdong Cardiovascular Institute（广东省心血管病研究所）；School of Computer Science and Engineering, South China University of Technology（华南理工大学计算机科学与工程学院）
Tissue-level semantic segmentation is a vital step in computational pathology. Fully-supervised models have already achieved outstanding performance with dense pixel-level annotations. However, drawing such labels on the giga-pixel whole slide images is extremely expensive and time-consuming. In this paper, we use only patch-level classification labels to achieve tissue semantic segmentation on histopathology images, finally reducing the annotation efforts. We proposed a two-step model including a classification and a segmentation phases. In the classification phase, we proposed a CAM-based mo…
Harvard Medical School（哈佛医学院）；University of Toronto（多伦多大学）
Tissue phenotyping is a fundamental task in learning objective characterizations of histopathologic biomarkers within the tumor-immune microenvironment in cancer pathology. However, whole-slide imaging (WSI) is a complex computer vision in which: 1) WSIs have enormous image resolutions with precludes large-scale pixel-level efforts in data curation, and 2) diversity of morphological phenotypes results in inter- and intra-observer variability in tissue labeling. To address these limitations, current efforts have proposed using pretrained image encoders (transfer learning from ImageNet, self-sup…
Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）；Northeastern University（东北大学）；Caliber Imaging and Diagnostics（Caliber影像与诊断公司）；SUNY Downstate Medical Center（纽约州立大学下州医学中心）；Skin Medical Research Diagnostics, P.L.L.C.（皮肤医学研究诊断有限责任公司）；University of Modena and Reggio Emilia（摩德纳-雷焦艾米利亚大学）
In-vivo optical microscopy is advancing into routine clinical practice for non-invasively guiding diagnosis and treatment of cancer and other diseases, and thus beginning to reduce the need for traditional biopsy. However, reading and analysis of the optical microscopic images are generally still qualitative, relying mainly on visual examination. Here we present an automated semantic segmentation method called "Multiscale Encoder-Decoder Network (MED-Net)" that provides pixel-wise labeling into classes of patterns in a quantitative manner. The novelty in our approach is the modeling of textura…
Disco: Densely-overlapping Cell Instance Segmentation via Adjacency-aware Collaborative Coloring
Shanghai Academy of Artificial Intelligence for Science（上海人工智能科学研究院）；Fudan University（复旦大学）；Shanghai Innovation Institute（上海创新研究院）；School of Life Sciences and Biotechnology, Shanghai Jiao Tong University（上海交通大学生命科学与生物技术学院）；Lingang Laboratory（临港实验室）；Renji Hospital, School of Medicine, Shanghai Jiao Tong University（仁济医院，上海交通大学医学院）
Modern object detection architectures are moving towards employing self-supervised learning (SSL) to improve performance detection with related pretext tasks. Pretext tasks for monocular 3D object detection have not yet been explored yet in literature. The paper studies the application of established self-supervised bounding box recycling by labeling random windows as the pretext task. The classifier head of the 3D detector is trained to classify random windows containing different proportions of the ground truth objects, thus handling the foreground-background imbalance. We evaluate the prete…
Technion Israel Institute of Technology（以色列理工学院）；Rambam Health Care Campus（兰巴姆医疗中心）
The integration of artificial intelligence into digital pathology has the potential to automate and improve various tasks, such as image analysis and diagnostic decision-making. Yet, the inherent variability of tissues, together with the need for image labeling, lead to biased datasets that limit the generalizability of algorithms trained on them. One of the emerging solutions for this challenge is synthetic histological images. However, debiasing real datasets require not only generating photorealistic images but also the ability to control the features within them. A common approach is to us…
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…
ProBAG: Prototype-Guided Boundary-Aware Graph Diffusion for Weakly Supervised Histopathology Segmentation
AI VIETNAM Lab（AI越南实验室）；Washington University School of Medicine（华盛顿大学医学院）；Jeonbuk National University（全北国立大学）；Perelman School of Medicine, University of Pennsylvania（宾夕法尼亚大学佩雷尔曼医学院）
Data labeling in supervised learning is considered an expensive and infeasible tool in some conditions. The self-supervised learning method is proposed to tackle the learning effectiveness with fewer labeled data, however, there is a lack of confidence in the size of labeled data needed to achieve adequate results. This study aims to draw a baseline on the proportion of the labeled data that models can appreciate to yield competent accuracy when compared to training with additional labels. The study implements the kaggle.com' cats-vs-dogs dataset, Mnist and Fashion-Mnist to investigate the sel…
Segmentation of histological images is one of the most crucial tasks for many biomedical analyses including quantification of certain tissue type. However, challenges are posed by high variability and complexity of structural features in such images, in addition to imaging artifacts. Further, the conventional approach of manual thresholding is labor-intensive, and highly sensitive to inter- and intra-image intensity variations. An accurate and robust automated segmentation method is of high interest. We propose and evaluate an elegant convolutional neural network (CNN) designed for segmentatio…
We present an algorithm for multi-scale tumor (chimeric cell) detection in high resolution slide scans. The broad range of tumor sizes in our dataset pose a challenge for current Convolutional Neural Networks (CNN) which often fail when image features are very small (8 pixels). Our approach modifies the effective receptive field at different layers in a CNN so that objects with a broad range of varying scales can be detected in a single forward pass. We define rules for computing adaptive prior anchor boxes which we show are solvable under the equal proportion interval principle. Two mechanism…
Data-driven Nucleus Subclassification on Colon H&E using Style-transferred Digital Pathology
Vanderbilt University（范德堡大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；National Institutes of Health（美国国立卫生研究院）；Vanderbilt University Medical Center（范德堡大学医学中心）；Vanderbilt University School of Medicine（范德堡大学医学院）；Veterans Affairs Tennessee Valley Healthcare System（田纳西河谷退伍军人事务医疗系统）
Cardiac segmentation is an essential step for the diagnosis of cardiovascular diseases. However, pixel-wise dense labeling is both costly and time-consuming. Scribble, as a form of sparse annotation, is more accessible than full annotations. However, it's particularly challenging to train a segmentation network with weak supervision from scribbles. To tackle this problem, we propose a new scribble-guided method for cardiac segmentation, based on the Positive-Unlabeled (PU) learning framework and global consistency regularization, and termed as ShapePU. To leverage unlabeled pixels via PU learn…
Labeled data is a critical resource for training and evaluating machine learning models. However, many real-life datasets are only partially labeled. We propose a semi-supervised machine learning training strategy to improve event detection performance on sequential data, such as video recordings, when only sparse labels are available, such as event start times without their corresponding end times. Our method uses noisy guesses of the events' end times to train event detection models. Depending on how conservative these guesses are, mislabeled samples may be introduced into the training set. …
