Noisy labels can significantly affect the performance of deep neural networks (DNNs). In medical image segmentation tasks, annotations are error-prone due to the high demand in annotation time and in the annotators' expertise. Existing methods mostly assume noisy labels in different pixels are \textit{i.i.d}. However, segmentation label noise usually has strong spatial correlation and has prominent bias in distribution. In this paper, we propose a novel Markov model for segmentation noisy annotations that encodes both spatial correlation and bias. Further, to mitigate such label noise, we propose a label correction method to recover true label progressively. We provide theoretical guarantees of the correctness of the proposed method. Experiments show that our approach outperforms current state-of-the-art methods on both synthetic and real-world noisy annotations.
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…
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…
National Cheng Kung University（国立成功大学）；IBM Research Europe（IBM欧洲研究院）
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…
Supervised training of object detectors requires well-annotated large-scale datasets, whose production is costly. Therefore, some efforts have been made to obtain annotations in economical ways, such as cloud sourcing. However, datasets obtained by these methods tend to contain noisy annotations such as inaccurate bounding boxes and incorrect class labels. In this study, we propose a new problem setting of training object detectors on datasets with entangled noises of annotations of class labels and bounding boxes. Our proposed method efficiently decouples the entangled noises, corrects the no…
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…
Deep convolutional neural networks have driven substantial advancements in the automatic understanding of images. Requiring a large collection of images and their associated annotations is one of the main bottlenecks limiting the adoption of deep networks. In the task of medical image segmentation, requiring pixel-level semantic annotations performed by human experts exacerbate this difficulty. This paper proposes a new framework to train a fully convolutional segmentation network from a large set of cheap unreliable annotations and a small set of expert-level clean annotations. We propose a s…
One of the problems on the way to successful implementation of neural networks is the quality of annotation. For instance, different annotators can annotate images in a different way and very often their decisions do not match exactly and in extreme cases are even mutually exclusive which results in noisy annotations and, consequently, inaccurate predictions. To avoid that problem in the task of computed tomography (CT) imaging segmentation we propose a clearing algorithm for annotations. It consists of 3 stages: - annotators scoring, which assigns a higher confidence level to better annotator…
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…
In recent years, deep learning techniques (e.g., U-Net, DeepLab) have achieved tremendous success in image segmentation. The performance of these models heavily relies on high-quality ground truth segment labels. Unfortunately, in many real-world problems, ground truth segment labels often have geometric annotation errors due to manual annotation mistakes, GPS errors, or visually interpreting background imagery at a coarse resolution. Such location errors will significantly impact the training performance of existing deep learning algorithms. Existing research on label errors either models gro…
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…
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…
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…
Leverage Weakly Annotation to Pixel-wise Annotation via Zero-shot Segment Anything Model for Molecular-empowered Learning
Data Science Institute, Vanderbilt University（范德堡大学数据科学研究所）；Department of Computer Science, Vanderbilt University（范德堡大学计算机科学系）；NVIDIA Corporation（英伟达公司）；Department of Electrical and Computer Engineering, Vanderbilt University Medical Center（范德堡大学医学中心电气与计算机工程系）；Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center（范德堡大学医学中心病理学、微生物学与免疫学系）
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…
Recently, the availability of remote sensing imagery from aerial vehicles and satellites constantly improved. For an automated interpretation of such data, deep-learning-based object detectors achieve state-of-the-art performance. However, established object detectors require complete, precise, and correct bounding box annotations for training. In order to create the necessary training annotations for object detectors, imagery can be georeferenced and combined with data from other sources, such as points of interest localized by GPS sensors. Unfortunately, this combination often leads to poor …
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…
How to Efficiently Annotate Images for Best-Performing Deep Learning Based Segmentation Models: An Empirical Study with Weak and Noisy Annotations and Segment Anything Model
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 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…
Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所）；University of Chinese Academy of Sciences（中国科学院大学）；CAS Center for Excellence in Brain Science and Intelligence Technology（中国科学院脑科学与智能技术卓越创新中心）
Deep learning methods require massive of annotated data for optimizing parameters. For example, datasets attached with accurate bounding box annotations are essential for modern object detection tasks. However, labeling with such pixel-wise accuracy is laborious and time-consuming, and elaborate labeling procedures are indispensable for reducing man-made noise, involving annotation review and acceptance testing. In this paper, we focus on the impact of noisy location annotations on the performance of object detection approaches and aim to, on the user side, reduce the adverse effect of the noi…
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…
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…
National Institutes of Health Clinical Center（美国国立卫生研究院临床中心）；Beijing Institute of Big Data Research（北京大数据研究院）
Image segmentation is a fundamental problem in medical image analysis. In recent years, deep neural networks achieve impressive performances on many medical image segmentation tasks by supervised learning on large manually annotated data. However, expert annotations on big medical datasets are tedious, expensive or sometimes unavailable. Weakly supervised learning could reduce the effort for annotation but still required certain amounts of expertise. Recently, deep learning shows a potential to produce more accurate predictions than the original erroneous labels. Inspired by this, we introduce…
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…
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…
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 …
ShanghaiTech University（上海科技大学）；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）
Learning segmentation from noisy labels is an important task for medical image analysis due to the difficulty in acquiring highquality annotations. Most existing methods neglect the pixel correlation and structural prior in segmentation, often producing noisy predictions around object boundaries. To address this, we adopt a superpixel representation and develop a robust iterative learning strategy that combines noise-aware training of segmentation network and noisy label refinement, both guided by the superpixels. This design enables us to exploit the structural constraints in segmentation lab…
The University of Adelaide（阿德莱德大学）；NVIDIA（英伟达）；Caltech（加州理工学院）；Zhejiang University（浙江大学）
Instance segmentation is a fundamental vision task that aims to recognize and segment each object in an image. However, it requires costly annotations such as bounding boxes and segmentation masks for learning. In this work, we propose a fully unsupervised learning method that learns class-agnostic instance segmentation without any annotations. We present FreeSOLO, a self-supervised instance segmentation framework built on top of the simple instance segmentation method SOLO. Our method also presents a novel localization-aware pre-training framework, where objects can be discovered from complic…
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…
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…
Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所）；University of Chinese Academy of Sciences（中国科学院大学）
How deep neural networks (DNNs) learn from noisy labels has been studied extensively in image classification but much less in image segmentation. So far, our understanding of the learning behavior of DNNs trained by noisy segmentation labels remains limited. In this study, we address this deficiency in both binary segmentation of biological microscopy images and multi-class segmentation of natural images. We generate extremely noisy labels by randomly sampling a small fraction (e.g., 10%) or flipping a large fraction (e.g., 90%) of the ground truth labels. When trained with these noisy labels,…
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…
Temporally consistent dense video annotations are scarce and hard to collect. In contrast, image segmentation datasets (and pre-trained models) are ubiquitous, and easier to label for any novel task. In this paper, we introduce a method to adapt still image segmentation models to video in an unsupervised manner, by using an optical flow-based consistency measure. To ensure that the inferred segmented videos appear more stable in practice, we verify that the consistency measure is well correlated with human judgement via a user study. Training a new multi-input multi-output decoder using this m…
