One of the biggest challenges for applying machine learning to histopathology is weak supervision: whole-slide images have billions of pixels yet often only one global label. The state of the art therefore relies on strongly-supervised model training using additional local annotations from domain experts. However, in the absence of detailed annotations, most weakly-supervised approaches depend on a frozen feature extractor pre-trained on ImageNet. We identify this as a key weakness and propose to train an in-domain feature extractor on histology images using MoCo v2, a recent self-supervised learning algorithm. Experimental results on Camelyon16 and TCGA show that the proposed extractor greatly outperforms its ImageNet counterpart. In particular, our results improve the weakly-supervised state of the art on Camelyon16 from 91.4% to 98.7% AUC, thereby closing the gap with strongly-supervised models that reach 99.3% AUC. Through these experiments, we demonstrate that feature extractors trained via self-supervised learning can act as drop-in replacements to significantly improve existing machine learning techniques in histology. Lastly, we show that the learned embedding space exhibits biologically meaningful separation of tissue structures.
Semi-supervised learning (semi-SL) is a promising alternative to supervised learning for medical image analysis when obtaining good quality supervision for medical imaging is difficult. However, semi-SL assumes that the underlying distribution of unaudited data matches that of the few labeled samples, which is often violated in practical settings, particularly in medical images. The presence of out-of-distribution (OOD) samples in the unlabeled training pool of semi-SL is inevitable and can reduce the efficiency of the algorithm. Common preprocessing methods to filter out outlier samples may n…
Virtual staining for 3D X-ray histology of bone implants
Institute of Materials Physics（材料物理研究所）；Helmholtz-Zentrum Hereon（海德堡研究中心）；Institute of Metallic Biomaterials（金属生物材料研究所）；Bruker Daltonics SPR（布鲁克尔达特利克斯SPR）；Data-Driven Analysis and Design of Materials（数据驱动的材料分析与设计）；University of Rostock（罗斯托克大学）
VitaminP: cross-modal learning enables whole-cell segmentation from routine histology
Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center（转化分子病理学部门，病理与实验室医学分会，德克萨斯大学MD安德森癌症中心）；Institute for Data Science in Oncology, The University of Texas MD Anderson Cancer Center（肿瘤数据科学研究所，德克萨斯大学MD安德森癌症中心）；The University of Texas MD Anderson Cancer Center（德克萨斯大学MD安德森癌症中心）
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…
Dartmouth College（达特茅斯学院）；Dartmouth-Hitchcock Medical Center（达特茅斯-希区柯克医疗中心）；Geisel School of Medicine at Dartmouth（达特茅斯盖塞尔医学院）
Developing deep learning models to analyze histology images has been computationally challenging, as the massive size of the images causes excessive strain on all parts of the computing pipeline. This paper proposes a novel deep learning-based methodology for improving the computational efficiency of histology image classification. The proposed approach is robust when used with images that have reduced input resolution and can be trained effectively with limited labeled data. Pre-trained on the original high-resolution (HR) images, our method uses knowledge distillation (KD) to transfer learne…
University of Sydney（悉尼大学）；Shanghai Jiao Tong University（上海交通大学）；UNSW（新南威尔士大学）
Gigapixel medical images provide massive data, both morphological textures and spatial information, to be mined. Due to the large data scale in histology, deep learning methods play an increasingly significant role as feature extractors. Existing solutions heavily rely on convolutional neural networks (CNNs) for global pixel-level analysis, leaving the underlying local geometric structure such as the interaction between cells in the tumor microenvironment unexplored. The topological structure in medical images, as proven to be closely related to tumor evolution, can be well characterized by gr…
A solution for co-locating 2D histology images in 3D for histology-to-CT and MR image registration: closing the loop for bone sarcoma treatment planning
ÉTS Montreal（蒙特利尔高等技术学院）；Goodman Cancer Research Centre（古德曼癌症研究中心）；McGill University（麦吉尔大学）
Using only global image-class labels, weakly-supervised learning methods, such as class activation mapping, allow training CNNs to jointly classify an image, and locate regions of interest associated with the predicted class. However, without any guidance at the pixel level, such methods may yield inaccurate regions. This problem is known to be more challenging with histology images than with natural ones, since objects are less salient, structures have more variations, and foreground and background regions have stronger similarities. Therefore, computer vision methods for visual interpretatio…
Arizona State University（亚利桑那州立大学）；Barrow Neurological Institute（巴罗神经学研究所）；St. Joseph’s Hospital and Medical Center（圣约瑟夫医院和医疗中心）
Confocal laser endomicroscopy (CLE) allow on-the-fly in vivo intraoperative imaging in a discreet field of view, especially for brain tumors, rather than extracting tissue for examination ex vivo with conventional light microscopy. Fluorescein sodium-driven CLE imaging is more interactive, rapid, and portable than conventional hematoxylin and eosin (H&E)-staining. However, it has several limitations: CLE images may be contaminated with artifacts (motion, red blood cells, noise), and neuropathologists are mainly trained on colorful stained histology slides like H&E while the CLE images are gray…
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…
Phi-SegNet: Phase-Integrated Supervision for Medical Image Segmentation
mHealth Lab, Department of Biomedical Engineering, Bangladesh University of Engineering and Technology（孟加拉工程与技术大学生物医学工程系mHealth实验室）；Department of Electrical and Computer Engineering, Johns Hopkins University（约翰霍普金斯大学电气与计算机工程系）；Center for Bioengineering Innovation and Design, Department of Biomedical Engineering, Johns Hopkins University（约翰霍普金斯大学生物工程创新与设计中心，生物医学工程系）
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 …
Universitat Politècnica de València（瓦伦西亚理工大学）；ETS Montreal（蒙特利尔高等技术学院）
Prostate cancer is one of the main diseases affecting men worldwide. The gold standard for diagnosis and prognosis is the Gleason grading system. In this process, pathologists manually analyze prostate histology slides under microscope, in a high time-consuming and subjective task. In the last years, computer-aided-diagnosis (CAD) systems have emerged as a promising tool that could support pathologists in the daily clinical practice. Nevertheless, these systems are usually trained using tedious and prone-to-error pixel-level annotations of Gleason grades in the tissue. To alleviate the need of…
Harbin Institute of Technology（哈尔滨工业大学）；Peng Cheng Laboratory（鹏城实验室）
Significant progress has been made in self-supervised image denoising (SSID) in the recent few years. However, most methods focus on dealing with spatially independent noise, and they have little practicality on real-world sRGB images with spatially correlated noise. Although pixel-shuffle downsampling has been suggested for breaking the noise correlation, it breaks the original information of images, which limits the denoising performance. In this paper, we propose a novel perspective to solve this problem, i.e., seeking for spatially adaptive supervision for real-world sRGB image denoising. …
Bosch Center for Artificial Intelligence（博世人工智能中心）；University of Bonn（波恩大学）；Max Planck Institute for Informatics（马克斯·普朗克信息学研究所）
Despite their recent successes, GAN models for semantic image synthesis still suffer from poor image quality when trained with only adversarial supervision. Historically, additionally employing the VGG-based perceptual loss has helped to overcome this issue, significantly improving the synthesis quality, but at the same time limiting the progress of GAN models for semantic image synthesis. In this work, we propose a novel, simplified GAN model, which needs only adversarial supervision to achieve high quality results. We re-design the discriminator as a semantic segmentation network, directly u…
Unpaired Image-to-Image Translation (I2IT) tasks often suffer from lack of data, a problem which self-supervised learning (SSL) has recently been very popular and successful at tackling. Leveraging auxiliary tasks such as rotation prediction or generative colorization, SSL can produce better and more robust representations in a low data regime. Training such tasks along an I2IT task is however computationally intractable as model size and the number of task grow. On the other hand, learning sequentially could incur catastrophic forgetting of previously learned tasks. To alleviate this, we intr…
This study investigates weakly supervised image segmentation using loose bounding box supervision. It presents a multiple instance learning strategy based on polar transformation to assist image segmentation when loose bounding boxes are employed as supervision. In this strategy, weighted smooth maximum approximation is introduced to incorporate the observation that pixels closer to the origin of the polar transformation are more likely to belong to the object in the bounding box. The proposed approach was evaluated on a public medical dataset using Dice coefficient. The results demonstrate it…
