Deep learning-based methods are gaining traction in digital pathology, with an increasing number of publications and challenges that aim at easing the work of systematically and exhaustively analyzing tissue slides. These methods often achieve very high accuracies, at the cost of requiring large annotated datasets to train. This requirement is especially difficult to fulfill in the medical field, where expert knowledge is essential. In this paper we focus on nuclei segmentation, which generally requires experienced pathologists to annotate the nuclear areas in gigapixel histological images. We propose an algorithm for instance segmentation that uses pseudo-label segmentations generated automatically from point annotations, as a method to reduce the burden for pathologists. With the generated segmentation masks, the proposed method trains a modified version of HoVer-Net model to achieve instance segmentation. Experimental results show that the proposed method is robust to inaccuracies in point annotations and comparison with Hover-Net trained with fully annotated instance masks shows that a degradation in segmentation performance does not always imply a degradation in higher order tasks such as tissue classification.
Image datasets with high-quality pixel-level annotations are valuable for semantic segmentation: labelling every pixel in an image ensures that rare classes and small objects are annotated. However, full-image annotations are expensive, with experts spending up to 90 minutes per image. We propose block sub-image annotation as a replacement for full-image annotation. Despite the attention cost of frequent task switching, we find that block annotations can be crowdsourced at higher quality compared to full-image annotation with equal monetary cost using existing annotation tools developed for fu…
Despite the great progress made by deep neural networks in the semantic segmentation task, traditional neural-networkbased methods typically suffer from a shortage of large amounts of pixel-level annotations. Recent progress in fewshot semantic segmentation tackles the issue by only a few pixel-level annotated examples. However, these few-shot approaches cannot easily be applied to multi-way or weak annotation settings. In this paper, we advance the few-shot segmentation paradigm towards a scenario where image-level annotations are available to help the training process of a few pixel-level an…
Medical image segmentation annotations suffer from inter- and intra-observer variations even among experts due to intrinsic differences in human annotators and ambiguous boundaries. Leveraging a collection of annotators' opinions for an image is an interesting way of estimating a gold standard. Although training deep models in a supervised setting with a single annotation per image has been extensively studied, generalizing their training to work with datasets containing multiple annotations per image remains a fairly unexplored problem. In this paper, we propose an approach to handle annotato…
The medical imaging literature has witnessed remarkable progress in high-performing segmentation models based on convolutional neural networks. Despite the new performance highs, the recent advanced segmentation models still require large, representative, and high quality annotated datasets. However, rarely do we have a perfect training dataset, particularly in the field of medical imaging, where data and annotations are both expensive to acquire. Recently, a large body of research has studied the problem of medical image segmentation with imperfect datasets, tackling two major dataset limitat…
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…
Pixel-level annotation demands expensive human efforts and limits the performance of deep networks that usually benefits from more such training data. In this work we aim to achieve high quality instance and semantic segmentation results over a small set of pixel-level mask annotations and a large set of box annotations. The basic idea is exploring detection models to simplify the pixel-level supervised learning task and thus reduce the required amount of mask annotations. Our architecture, named DASNet, consists of three modules: detection, attention, and segmentation. The detection module de…
Brain MR image segmentation is a key task in neuroimaging studies. It is commonly conducted using standard computational tools, such as FSL, SPM, multi-atlas segmentation etc, which are often registration-based and suffer from expensive computation cost. Recently, there is an increased interest using deep neural networks for brain image segmentation, which have demonstrated advantages in both speed and performance. However, neural networks-based approaches normally require a large amount of manual annotations for optimising the massive amount of network parameters. For 3D networks used in volu…
NYU Center for Data Science（纽约大学数据科学中心）；NYU Courant Institute of Mathematical Sciences（纽约大学库朗数学科学研究所）
Deep learning in the presence of noisy annotations has been studied extensively in classification, but much less in segmentation tasks. In this work, we study the learning dynamics of deep segmentation networks trained on inaccurately-annotated data. We discover a phenomenon that has been previously reported in the context of classification: the networks tend to first fit the clean pixel-level labels during an "early-learning" phase, before eventually memorizing the false annotations. However, in contrast to classification, memorization in segmentation does not arise simultaneously for all sem…
Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院保罗·C·劳特伯生物医学成像研究中心）；Peng Cheng Laboratory（鹏城实验室）；Pazhou Laboratory（琶洲实验室）；Guangdong General Hospital, Guangdong Academy of Medical Sciences（广东省人民医院（广东省医学科学院））；Renmin Hospital of Wuhan University（武汉大学人民医院）；School of Electronic and Computer Engineering, Shenzhen Graduate School, Peking University（北京大学深圳研究生院电子与计算机工程学院）；Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院脑认知与脑疾病研究所）；ETS Montreal（蒙特利尔高等技术学院）
Automatic medical image segmentation plays a critical role in scientific research and medical care. Existing high-performance deep learning methods typically rely on large training datasets with high-quality manual annotations, which are difficult to obtain in many clinical applications. Here, we introduce Annotation-effIcient Deep lEarning (AIDE), an open-source framework to handle imperfect training datasets. Methodological analyses and empirical evaluations are conducted, and we demonstrate that AIDE surpasses conventional fully-supervised models by presenting better performance on open dat…
Instance object segmentation and tracking provide comprehensive quantification of objects across microscope videos. The recent single-stage pixel-embedding based deep learning approach has shown its superior performance compared with "segment-then-associate" two-stage solutions. However, one major limitation of applying a supervised pixel-embedding based method to microscope videos is the resource-intensive manual labeling, which involves tracing hundreds of overlapped objects with their temporal associations across video frames. Inspired by the recent generative adversarial network (GAN) base…
The University of Queensland（昆士兰大学）；University of Electronic Science and Technology of China（电子科技大学）
Rich high-quality annotated data is critical for semantic segmentation learning, yet acquiring dense and pixel-wise ground-truth is both labor- and time-consuming. Coarse annotations (e.g., scribbles, coarse polygons) offer an economical alternative, with which training phase could hardly generate satisfactory performance unfortunately. In order to generate high-quality annotated data with a low time cost for accurate segmentation, in this paper, we propose a novel annotation enrichment strategy, which expands existing coarse annotations of training data to a finer scale. Extensive experiments…
Muroran Institute of Technology（室兰工业大学）；Niigata University of Healthcare and Welfare（新泻医疗福祉大学）
Nuclear segmentation, classification and quantification within Haematoxylin & Eosin stained histology images enables the extraction of interpretable cell-based features that can be used in downstream explainable models in computational pathology. The Colon Nuclei Identification and Counting (CoNIC) Challenge is held to help drive forward research and innovation for automatic nuclei recognition in computational pathology. This report describes our proposed method submitted to the CoNIC challenge. Our method employs a multi-task learning framework, which performs a panoptic segmentation task and…
Xidian University（西安电子科技大学）；University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）
3D image segmentation is one of the most important and ubiquitous problems in medical image processing. It provides detailed quantitative analysis for accurate disease diagnosis, abnormal detection, and classification. Currently deep learning algorithms are widely used in medical image segmentation, most algorithms trained models with full annotated datasets. However, obtaining medical image datasets is very difficult and expensive, and full annotation of 3D medical image is a monotonous and time-consuming work. Partially labelling informative slices in 3D images will be a great relief of manu…
The instance segmentation problem intends to precisely detect and delineate objects in images. Most of the current solutions rely on deep convolutional neural networks but despite this fact proposed solutions are very diverse. Some solutions approach the problem as a network problem, where they use several networks or specialize a single network to solve several tasks. A different approach tries to solve the problem as an annotation problem, where the instance information is encoded in a mathematical representation. This work proposes a solution based in the DCME technique to solve the instanc…
A high-performance unsupervised nuclei instance segmentation (HUNIS) method is proposed in this work. HUNIS consists of two-stage block-wise operations. The first stage includes: 1) adaptive thresholding of pixel intensities, 2) incorporation of nuclei size/shape priors and 3) removal of false positive nuclei instances. Then, HUNIS conducts the second stage segmentation by receiving guidance from the first one. The second stage exploits the segmentation masks obtained in the first stage and leverages color and shape distributions for a more accurate segmentation. The main purpose of the two-st…
Generally, microscopy image analysis in biology relies on the segmentation of individual nuclei, using a dedicated stained image, to identify individual cells. However stained nuclei have drawbacks like the need for sample preparation, and specific equipment on the microscope but most importantly, and as it is in most cases, the nuclear stain is not relevant to the biological questions of interest but is solely used for the segmentation task. In this study, we used non-stained brightfield images for nuclei segmentation with the advantage that they can be acquired on any microscope from both li…
Instance segmentation in 3D images is a fundamental task in biomedical image analysis. While deep learning models often work well for 2D instance segmentation, 3D instance segmentation still faces critical challenges, such as insufficient training data due to various annotation difficulties in 3D biomedical images. Common 3D annotation methods (e.g., full voxel annotation) incur high workloads and costs for labeling enough instances for training deep learning 3D instance segmentation models. In this paper, we propose a new weak annotation approach for training a fast deep learning 3D instance …
University of Campinas（坎皮纳斯大学）；Université Gustave Eiffel（古斯塔夫·埃菲尔大学）
Despite the progress of interactive image segmentation methods, high-quality pixel-level annotation is still time-consuming and laborious - a bottleneck for several deep learning applications. We take a step back to propose interactive and simultaneous segment annotation from multiple images guided by feature space projection. This strategy is in stark contrast to existing interactive segmentation methodologies, which perform annotation in the image domain. We show that feature space annotation achieves competitive results with state-of-the-art methods in foreground segmentation datasets: iCoS…
The Hong Kong University of Science and Technology（香港科技大学）
Nuclei Segmentation from histology images is a fundamental task in digital pathology analysis. However, deep-learning-based nuclei segmentation methods often suffer from limited annotations. This paper proposes a realistic data augmentation method for nuclei segmentation, named InsMix, that follows a Copy-Paste-Smooth principle and performs morphology-constrained generative instance augmentation. Specifically, we propose morphology constraints that enable the augmented images to acquire luxuriant information about nuclei while maintaining their morphology characteristics (e.g., geometry and lo…
Purdue University（普渡大学）；Indiana University-Purdue University Indianapolis（印第安纳大学-普渡大学印第安纳波利斯分校）；Indiana University（印第安纳大学）
Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of nuclei using convolutional neural networks (CNNs) is described. In particular, since creating labeled volumes manually for training purposes is not practical due to the size and complexity of the 3D data sets, the paper describes a method for generating synthetic microscopy volumes based on a spatially constrained cycle-consistent adversarial network. The prop…
University of Notre Dame（圣母大学）；The Hong Kong Polytechnic University（香港理工大学）；The Chinese University of Hong Kong（香港中文大学）
In recent years, deep learning (DL) methods have become powerful tools for biomedical image segmentation. However, high annotation efforts and costs are commonly needed to acquire sufficient biomedical training data for DL models. To alleviate the burden of manual annotation, in this paper, we propose a new weakly supervised DL approach for biomedical image segmentation using boxes only annotation. First, we develop a method to combine graph search (GS) and DL to generate fine object masks from box annotation, in which DL uses box annotation to compute a rough segmentation for GS and then GS i…
Indian Institute of Information Technology Allahabad（阿拉哈巴德印度信息技术学院）
In the clinical settings, during digital examination of histopathological slides, the pathologist annotate the slides by marking the rough boundary around the suspected tumour region. The marking or annotation is generally represented as a polygonal boundary that covers the extent of the tumour in the slide. These polygonal markings are difficult to imitate through CAD techniques since the tumour regions are heterogeneous and hence segmenting them would require exhaustive pixel wise ground truth annotation. Therefore, for CAD analysis, the ground truths are generally annotated by pathologist e…
Instance segmentation and classification of nuclei is an important task in computational pathology. We show that StarDist, a deep learning nuclei segmentation method originally developed for fluorescence microscopy, can be extended and successfully applied to histopathology images. This is substantiated by conducting experiments on the Lizard dataset, and through entering the Colon Nuclei Identification and Counting (CoNIC) challenge 2022, where our approach achieved the first spot on the leaderboard for the segmentation and classification task for both the preliminary and final test phase.
A three in one bottom-up framework for simultaneous semantic segmentation, instance segmentation and classification of multi-organ nuclei in digital cancer histology
School of Computer Science, Northwestern Polytechnical University（西北工业大学计算机学院）；School of Information Science and Technology, University of Science and Technology of China（中国科学技术大学信息科学技术学院）；College of Science & Engineering, Hamad Bin Khalifa University（哈马德·本·哈利法大学科学与工程学院）
Medical University of Vienna（维也纳医科大学）；Technical University Graz（格拉茨工业大学）；Complexity Science Hub（复杂性科学中心）
Recently, pruning deep neural networks (DNNs) has received a lot of attention for improving accuracy and generalization power, reducing network size, and increasing inference speed on specialized hardwares. Although pruning was mainly tested on computer vision tasks, its application in the context of medical image analysis has hardly been explored. This work investigates the impact of well-known pruning techniques, namely layer-wise and network-wide magnitude pruning, on the nuclei instance segmentation performance in histological images. Our utilized instance segmentation model consists of tw…
Medical image segmentation models are typically supervised by expert annotations at the pixel-level, which can be expensive to acquire. In this work, we propose a method that combines the high quality of pixel-level expert annotations with the scale of coarse DNN-generated saliency maps for training multi-label semantic segmentation models. We demonstrate the application of our semi-supervised method, which we call CheXseg, on multi-label chest X-ray interpretation. We find that CheXseg improves upon the performance (mIoU) of fully-supervised methods that use only pixel-level expert annotation…
Background: The quantitative analysis of microscope videos often requires instance segmentation and tracking of cellular and subcellular objects. The traditional method consists of two stages: (1) performing instance object segmentation of each frame, and (2) associating objects frame-by-frame. Recently, pixel-embedding-based deep learning approaches these two steps simultaneously as a single stage holistic solution. In computer vision, annotated training data with consistent segmentation and tracking is resource intensive, the severity of which is multiplied in microscopy imaging due to (1) d…
Queen Mary University of London（伦敦玛丽女王大学）；Karolinska University Hospital（卡罗林斯卡大学医院）
We present a novel neural network architecture, US-Net, for robust nuclei instance segmentation in histopathology images. The proposed framework integrates the nuclei detection and segmentation networks by sharing their outputs through the same foundation network, and thus enhancing the performance of both. The detection network takes into account the high-level semantic cues with contextual information, while the segmentation network focuses more on the low-level details like the edges. Extensive experiments reveal that our proposed framework can strengthen the performance of both branch netw…
Imperial College London（帝国理工学院）；BioMedIA Group, Department of Computing（计算系BioMedIA小组）
Few-shot semantic segmentation (FSS) has great potential for medical imaging applications. Most of the existing FSS techniques require abundant annotated semantic classes for training. However, these methods may not be applicable for medical images due to the lack of annotations. To address this problem we make several contributions: (1) A novel self-supervised FSS framework for medical images in order to eliminate the requirement for annotations during training. Additionally, superpixel-based pseudo-labels are generated to provide supervision; (2) An adaptive local prototype pooling module pl…
Carleton University（卡尔顿大学）；Canada CIFAR AI Chair（加拿大CIFAR人工智能讲席）
Medical image segmentation methods typically rely on numerous dense annotated images for model training, which are notoriously expensive and time-consuming to collect. To alleviate this burden, weakly supervised techniques have been exploited to train segmentation models with less expensive annotations. In this paper, we propose a novel point-supervised contrastive variance method (PSCV) for medical image semantic segmentation, which only requires one pixel-point from each organ category to be annotated. The proposed method trains the base segmentation network by using a novel contrastive vari…
Northwestern Polytechnical University（西北工业大学）；The University of Adelaide（阿德莱德大学）；Australian Institute for Machine Learning（澳大利亚机器学习研究所）
Manual annotation of medical images is highly subjective, leading to inevitable and huge annotation biases. Deep learning models may surpass human performance on a variety of tasks, but they may also mimic or amplify these biases. Although we can have multiple annotators and fuse their annotations to reduce stochastic errors, we cannot use this strategy to handle the bias caused by annotators' preferences. In this paper, we highlight the issue of annotator-related biases on medical image segmentation tasks, and propose a Preference-involved Annotation Distribution Learning (PADL) framework to …
University of Michigan（密歇根大学）；Indian Institute of Technology - Bombay（印度理工学院孟买分校）
For medical image segmentation, most fully convolutional networks (FCNs) need strong supervision through a large sample of high-quality dense segmentations, which is taxing in terms of costs, time and logistics involved. This burden of annotation can be alleviated by exploiting weak inexpensive annotations such as bounding boxes and anatomical landmarks. However, it is very difficult to \textit{a priori} estimate the optimal balance between the number of annotations needed for each supervision type that leads to maximum performance with the least annotation cost. To optimize this cost-performa…
Technical University of Munich（慕尼黑工业大学）；German Aerospace Center（德国航空航天中心）；Wageningen University（瓦赫宁根大学）；Ecole Polytechnique Fédérale de Lausanne（洛桑联邦理工学院）
Training Convolutional Neural Networks (CNNs) for very high resolution images requires a large quantity of high-quality pixel-level annotations, which is extremely labor- and time-consuming to produce. Moreover, professional photo interpreters might have to be involved for guaranteeing the correctness of annotations. To alleviate such a burden, we propose a framework for semantic segmentation of aerial images based on incomplete annotations, where annotators are asked to label a few pixels with easy-to-draw scribbles. To exploit these sparse scribbled annotations, we propose the FEature and Sp…
Nanyang Technological University（南洋理工大学）；The University of Adelaide（阿德莱德大学）
Weakly supervised semantic segmentation receives much research attention since it alleviates the need to obtain a large amount of dense pixel-wise ground-truth annotations for the training images. Compared with other forms of weak supervision, image labels are quite efficient to obtain. In our work, we focus on the weakly supervised semantic segmentation with image label annotations. Recent progress for this task has been largely dependent on the quality of generated pseudo-annotations. In this work, inspired by spatial neural-attention for image captioning, we propose a decoupled spatial neur…
One of the main obstacles to 3D semantic segmentation is the significant amount of endeavor required to generate expensive point-wise annotations for fully supervised training. To alleviate manual efforts, we propose GIDSeg, a novel approach that can simultaneously learn segmentation from sparse annotations via reasoning global-regional structures and individual-vicinal properties. GIDSeg depicts global- and individual- relation via a dynamic edge convolution network coupled with a kernelized identity descriptor. The ensemble effects are obtained by endowing a fine-grained receptive field to a…
Challenging computer vision tasks, in particular semantic image segmentation, require large training sets of annotated images. While obtaining the actual images is often unproblematic, creating the necessary annotation is a tedious and costly process. Therefore, one often has to work with unreliable annotation sources, such as Amazon Mechanical Turk or (semi-)automatic algorithmic techniques. In this work, we present a Gaussian process (GP) based technique for simultaneously identifying which images of a training set have unreliable annotation and learning a segmentation model in which the neg…
MPI for Informatics（马克斯·普朗克信息学研究所）；Saarland Informatics Campus（萨尔兰信息学园区）；ETH Zürich（苏黎世联邦理工学院）；CISPA（亥姆霍兹信息安全中心）；MPI for Intelligent Systems（马克斯·普朗克智能系统研究所）；University of Tübingen（蒂宾根大学）
For best performance, today's semantic segmentation methods use large and carefully labeled datasets, requiring expensive annotation budgets. In this work, we show that coarse annotation is a low-cost but highly effective alternative for training semantic segmentation models. Considering the urban scene segmentation scenario, we leverage cheap coarse annotations for real-world captured data, as well as synthetic data to train our model and show competitive performance compared with finely annotated real-world data. Specifically, we propose a coarse-to-fine self-training framework that generate…
University of Notre Dame（圣母大学）；Harper Cancer Research Institute（哈珀癌症研究所）
Image segmentation is a fundamental problem in biomedical image analysis. Recent advances in deep learning have achieved promising results on many biomedical image segmentation benchmarks. However, due to large variations in biomedical images (different modalities, image settings, objects, noise, etc), to utilize deep learning on a new application, it usually needs a new set of training data. This can incur a great deal of annotation effort and cost, because only biomedical experts can annotate effectively, and often there are too many instances in images (e.g., cells) to annotate. In this pap…
Collecting image annotations remains a significant burden when deploying CNN in a specific applicative context. This is especially the case when the annotation consists in binary masks covering object instances. Our work proposes to delineate instances in three steps, based on a semi-automatic approach: (1) the extreme points of an object (left-most, right-most, top, bottom pixels) are manually defined, thereby providing the object bounding-box, (2) a universal automatic segmentation tool like Deep Extreme Cut is used to turn the bounded object into a segmentation mask that matches the extreme…
IIIT Hyderabad（海得拉巴国际信息技术研究所）；University of Oxford（牛津大学）
Recent approaches for weakly supervised instance segmentations depend on two components: (i) a pseudo label generation model that provides instances which are consistent with a given annotation; and (ii) an instance segmentation model, which is trained in a supervised manner using the pseudo labels as ground-truth. Unlike previous approaches, we explicitly model the uncertainty in the pseudo label generation process using a conditional distribution. The samples drawn from our conditional distribution provide accurate pseudo labels due to the use of semantic class aware unary terms, boundary aw…
Recently, weakly-supervised image segmentation using weak annotations like scribbles has gained great attention, since such annotations are much easier to obtain compared to time-consuming and label-intensive labeling at the pixel/voxel level. However, because scribbles lack structure information of region of interest (ROI), existing scribble-based methods suffer from poor boundary localization. Furthermore, most current methods are designed for 2D image segmentation, which do not fully leverage the volumetric information if directly applied to image slices. In this paper, we propose a scribbl…
ShanghaiTech University（上海科技大学）；Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences（中国科学院上海微系统与信息技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Shanghai Engineering Research Center of Intelligent Vision and Imaging（上海智能视觉与成像工程技术研究中心）
Weakly supervised nuclei segmentation is a critical problem for pathological image analysis and greatly benefits the community due to the significant reduction of labeling cost. Adopting point annotations, previous methods mostly rely on less expressive representations for nuclei instances and thus have difficulty in handling crowded nuclei. In this paper, we propose to decouple weakly supervised semantic and instance segmentation in order to enable more effective subtask learning and to promote instance-aware representation learning. To achieve this, we design a modular deep network with two …
