Scribble-based Domain Adaptation via Co-segmentation
School of Biomedical Engineering and Imaging Sciences, King’s College London（伦敦国王学院生物医学工程与成像科学学院）；Wellcome/EPSRC Centre for Interventional and Surgical Sciences, University College London（伦敦大学学院威尔康姆/工程与物理科学研究委员会介入与外科科学中心）；National Hospital for Neurology and Neurosurgery, London（伦敦神经病学与神经外科国家医院）；UCL Ear Institute, University College London（伦敦大学学院UCL耳科研究所）
Reuben Dorent, Samuel Joutard, Jonathan Shapey, Sotirios Bisdas, Neil Kitchen, Robert Bradford, Shakeel Saeed, Marc Modat, Sebastien Ourselin, Tom Vercauteren
Although deep convolutional networks have reached state-of-the-art performance in many medical image segmentation tasks, they have typically demonstrated poor generalisation capability. To be able to generalise from one domain (e.g. one imaging modality) to another, domain adaptation has to be performed. While supervised methods may lead to good performance, they require to fully annotate additional data which may not be an option in practice. In contrast, unsupervised methods don't need additional annotations but are usually unstable and hard to train. In this work, we propose a novel weakly-supervised method. Instead of requiring detailed but time-consuming annotations, scribbles on the target domain are used to perform domain adaptation. This paper introduces a new formulation of domain adaptation based on structured learning and co-segmentation. Our method is easy to train, thanks to the introduction of a regularised loss. The framework is validated on Vestibular Schwannoma segmentation (T1 to T2 scans). Our proposed method outperforms unsupervised approaches and achieves comparable performance to a fully-supervised approach.
TACoS: Weakly Supervised Learning of Two-Dimensional Materials from Scribble Annotations to Precise Segmentation
AnnLab, Institute of Semiconductors, Chinese Academy of Sciences（中国科学院半导体研究所安实验室）；Institute of Semiconductors, Chinese Academy of Sciences（中国科学院半导体研究所）；Center of Materials Science and Optoelectronics Engineering & School of Integrated Circuits, University of Chinese Academy of Sciences（中国科学院大学材料科学与光电技术中心及集成电路学院）
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…
Large-scale data is of crucial importance for learning semantic segmentation models, but annotating per-pixel masks is a tedious and inefficient procedure. We note that for the topic of interactive image segmentation, scribbles are very widely used in academic research and commercial software, and are recognized as one of the most user-friendly ways of interacting. In this paper, we propose to use scribbles to annotate images, and develop an algorithm to train convolutional networks for semantic segmentation supervised by scribbles. Our algorithm is based on a graphical model that jointly prop…
Interactive segmentation enables users to extract masks by providing simple annotations to indicate the target, such as boxes, clicks, or scribbles. Among these interaction formats, scribbles are the most flexible as they can be of arbitrary shapes and sizes. This enables scribbles to provide more indications of the target object. However, previous works mainly focus on click-based configuration, and the scribble-based setting is rarely explored. In this work, we attempt to formulate a standard protocol for scribble-based interactive segmentation. Basically, we design diversified strategies to…
Ulsan National Institute of Science and Technology（蔚山科学技术院）；Korea University（高丽大学）
Segmentation is a fundamental process in microscopic cell image analysis. With the advent of recent advances in deep learning, more accurate and high-throughput cell segmentation has become feasible. However, most existing deep learning-based cell segmentation algorithms require fully annotated ground-truth cell labels, which are time-consuming and labor-intensive to generate. In this paper, we introduce Scribble2Label, a novel weakly-supervised cell segmentation framework that exploits only a handful of scribble annotations without full segmentation labels. The core idea is to combine pseudo-…
ETH Zurich（苏黎世联邦理工学院）；MPI for Informatics（马克斯·普朗克信息学研究所）；KU Leuven（鲁汶大学）
Densely annotating LiDAR point clouds remains too expensive and time-consuming to keep up with the ever growing volume of data. While current literature focuses on fully-supervised performance, developing efficient methods that take advantage of realistic weak supervision have yet to be explored. In this paper, we propose using scribbles to annotate LiDAR point clouds and release ScribbleKITTI, the first scribble-annotated dataset for LiDAR semantic segmentation. Furthermore, we present a pipeline to reduce the performance gap that arises when using such weak annotations. Our pipeline comprise…
Scribble Hides Class: Promoting Scribble-Based Weakly-Supervised Semantic Segmentation with Its Class Label
Institute of Medical University, Peking University（北京大学医学部）；National Biomedical Imaging Center, Peking University（北京大学生物医学成像中心）；Institute of Biomedical Engineering, Peking University Shenzhen Graduate School（北京大学深圳研究生院生物医学工程研究所）
We present the 2018 DAVIS Challenge on Video Object Segmentation, a public competition specifically designed for the task of video object segmentation. It builds upon the DAVIS 2017 dataset, which was presented in the previous edition of the DAVIS Challenge, and added 100 videos with multiple objects per sequence to the original DAVIS 2016 dataset. Motivated by the analysis of the results of the 2017 edition, the main track of the competition will be the same than in the previous edition (segmentation given the full mask of the objects in the first frame -- semi-supervised scenario). This edit…
Exploiting Inherent Class Label: Towards Robust Scribble Supervised Semantic Segmentation
Institute of Medical Technology, Peking University Health Science Center（北京大学医学部医学技术研究院）；Peking University（北京大学）；National Biomedical Imaging Center, Peking University（北京大学国家生物医学成像科学中心）；Peking University Shenzhen Graduate School（北京大学深圳研究生院）
Volumetric Medical Image Segmentation via Scribble Annotations and Shape Priors
Shanghai Jiao Tong University（上海交通大学）；Ruijin Hospital, Shanghai Jiao Tong University of Medicine（上海交通大学医学院附属瑞金医院）；Shanghai Jiao Tong University of Medicine（上海交通大学医学院）
Curating a large scale fully-annotated dataset can be both labour-intensive and expertise-demanding, especially for medical images. To alleviate this problem, we propose to utilize solely scribble annotations for weakly supervised segmentation. Existing solutions mainly leverage selective losses computed solely on annotated areas and generate pseudo gold standard segmentation by propagating labels to adjacent areas. However, these methods could suffer from the inaccurate and sometimes unrealistic pseudo segmentation due to the insufficient supervision and incomplete shape features. Different f…
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…
University of Maryland, College Park（马里兰大学帕克分校）；Alexandria University, Faculty of Engineering（亚历山大大学工程学院）
In this paper, we cast the scribble-based interactive image segmentation as a semi-supervised learning problem. Our novel approach alleviates the need to solve an expensive generalized eigenvector problem by approximating the eigenvectors using efficiently computed eigenfunctions. The smoothness operator defined on feature densities at the limit n tends to infinity recovers the exact eigenvectors of the graph Laplacian, where n is the number of nodes in the graph. To further reduce the computational complexity without scarifying our accuracy, we select pivots pixels from user annotations. In o…
Shandong University（山东大学）；AICFVE, Beijing Film Academy（北京电影学院AICFVE）；University of Leeds（利兹大学）
Scribble-supervised semantic segmentation has gained much attention recently for its promising performance without high-quality annotations. Due to the lack of supervision, confident and consistent predictions are usually hard to obtain. Typically, people handle these problems to either adopt an auxiliary task with the well-labeled dataset or incorporate the graphical model with additional requirements on scribble annotations. Instead, this work aims to achieve semantic segmentation by scribble annotations directly without extra information and other limitations. Specifically, we propose holis…
ZScribbleSeg: A comprehensive segmentation framework with modeling of efficient annotation and maximization of scribble supervision
School of Data Science, Fudan University, Shanghai, 200433, China（复旦大学数据科学学院）；Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, USA（约翰霍普金斯大学电气与计算机工程系）
Shandong University（山东大学）；AICFVE, Beijing Film Academy（北京电影学院AICFVE）
Scribble-supervised semantic segmentation has gained much attention recently for its promising performance without high-quality annotations. Many approaches have been proposed. Typically, they handle this problem to either introduce a well-labeled dataset from another related task, turn to iterative refinement and post-processing with the graphical model, or manipulate the scribble label. This work aims to achieve semantic segmentation supervised by scribble label directly without auxiliary information and other intermediate manipulation. Specifically, we impose diffusion on neural representat…
Peng Cheng Laboratory（鹏城实验室）；Harbin Institute of Technology（哈尔滨工业大学）
This paper aims to solve the video object segmentation (VOS) task in a scribble-supervised manner, in which VOS models are not only trained by the sparse scribble annotations but also initialized with the sparse target scribbles for inference. Thus, the annotation burdens for both training and initialization can be substantially lightened. The difficulties of scribble-supervised VOS lie in two aspects. On the one hand, it requires the powerful ability to learn from the sparse scribble annotations during training. On the other hand, it demands strong reasoning capability during inference given …
ETH Zürich（苏黎世联邦理工学院）；University of Cambridge（剑桥大学）
Semantic segmentation of medical images is a crucial step for the quantification of healthy anatomy and diseases alike. The majority of the current state-of-the-art segmentation algorithms are based on deep neural networks and rely on large datasets with full pixel-wise annotations. Producing such annotations can often only be done by medical professionals and requires large amounts of valuable time. Training a medical image segmentation network with weak annotations remains a relatively unexplored topic. In this work we investigate training strategies to learn the parameters of a pixel-wise s…
Deep learning-based semantic segmentation methods have an intrinsic limitation that training a model requires a large amount of data with pixel-level annotations. To address this challenging issue, many researchers give attention to unsupervised domain adaptation for semantic segmentation. Unsupervised domain adaptation seeks to adapt the model trained on the source domain to the target domain. In this paper, we introduce a self-ensembling technique, one of the successful methods for domain adaptation in classification. However, applying self-ensembling to semantic segmentation is very difficu…
The Chinese University of Hong Kong（香港中文大学）；University of Leicester（莱斯特大学）
Domain adaptation is crucial for transferring the knowledge from the source labeled CT dataset to the target unlabeled MR dataset in abdominal multi-organ segmentation. Meanwhile, it is highly desirable to avoid the high annotation cost related to the target dataset and protect the source dataset privacy. Therefore, we propose an effective source-free unsupervised domain adaptation method for cross-modality abdominal multi-organ segmentation without source dataset access. The proposed framework comprises two stages. In the first stage, the feature map statistics-guided model adaptation combine…
The following paper is a reproducibility report for "FDA: Fourier Domain Adaptation for Semantic Segmentation" published in the CVPR 2020 as part of the ML Reproducibility Challenge 2020. The original code was made available by the author. The well-commented version of the code containing all ablation studies performed derived from the original code along with WANDB integration is available at <github.com/thefatbandit/FDA> with proper instructions to execute experiments in README.
In this paper we present a solution to the task of "unsupervised domain adaptation (UDA) of a given pre-trained semantic segmentation model without relying on any source domain representations". Previous UDA approaches for semantic segmentation either employed simultaneous training of the model in the source and target domains, or they relied on an additional network, replaying source domain knowledge to the model during adaptation. In contrast, we present our novel Unsupervised BatchNorm Adaptation (UBNA) method, which adapts a given pre-trained model to an unseen target domain without using …
Semantic segmentation models struggle to generalize in the presence of domain shift. In this paper, we introduce contrastive learning for feature alignment in cross-domain adaptation. We assemble both in-domain contrastive pairs and cross-domain contrastive pairs to learn discriminative features that align across domains. Based on the resulting well-aligned feature representations we introduce a label expansion approach that is able to discover samples from hard classes during the adaptation process to further boost performance. The proposed approach consistently outperforms state-of-the-art m…
Institute of Industrial Science, The University of Tokyo（东京大学生产技术研究所）；OMRON SINIC X Corporation（欧姆龙SINIC X公司）
Hand segmentation is a crucial task in first-person vision. Since first-person images exhibit strong bias in appearance among different environments, adapting a pre-trained segmentation model to a new domain is required in hand segmentation. Here, we focus on appearance gaps for hand regions and backgrounds separately. We propose (i) foreground-aware image stylization and (ii) consensus pseudo-labeling for domain adaptation of hand segmentation. We stylize source images independently for the foreground and background using target images as style. To resolve the domain shift that the stylizatio…
Unsupervised Domain Adaptation (UDA) can tackle the challenge that convolutional neural network(CNN)-based approaches for semantic segmentation heavily rely on the pixel-level annotated data, which is labor-intensive. However, existing UDA approaches in this regard inevitably require the full access to source datasets to reduce the gap between the source and target domains during model adaptation, which are impractical in the real scenarios where the source datasets are private, and thus cannot be released along with the well-trained source models. To cope with this issue, we propose a source-…
In this paper, we focus on a less explored, but more realistic and complex problem of domain adaptation in LiDAR semantic segmentation. There is a significant drop in performance of an existing segmentation model when training (source domain) and testing (target domain) data originate from different LiDAR sensors. To overcome this shortcoming, we propose an unsupervised domain adaptation framework that leverages unlabeled target domain data for self-supervision, coupled with an unpaired mask transfer strategy to mitigate the impact of domain shifts. Furthermore, we introduce the gated adapter …
Huawei Cloud（华为云）；Huawei Technologies（华为技术有限公司）；Dalian University of Technology（大连理工大学）
Multi-source unsupervised domain adaptation~(MSDA) aims at adapting models trained on multiple labeled source domains to an unlabeled target domain. In this paper, we propose a novel multi-source domain adaptation framework based on collaborative learning for semantic segmentation. Firstly, a simple image translation method is introduced to align the pixel value distribution to reduce the gap between source domains and target domain to some extent. Then, to fully exploit the essential semantic information across source domains, we propose a collaborative learning method for domain adaptation w…
Probabilistic Domain Adaptation for Biomedical Image Segmentation
Georg-August-University Göttingen（哥廷根大学）；Institute of Computer Science（计算机科学学院）；Campus Institute Data Science (CIDAS)（校园数据科学研究所）；CAIMed - Lower Saxony Center for AI & Causal Methods in Medicine（下萨克森人工智能与因果医学中心）；Cluster of Excellence Multiscale Bioimaging (MBExC)（多尺度生物成像卓越中心）
Curating a large set of fully annotated training data can be costly, especially for the tasks of medical image segmentation. Scribble, a weaker form of annotation, is more obtainable in practice, but training segmentation models from limited supervision of scribbles is still challenging. To address the difficulties, we propose a new framework for scribble learning-based medical image segmentation, which is composed of mix augmentation and cycle consistency and thus is referred to as CycleMix. For augmentation of supervision, CycleMix adopts the mixup strategy with a dedicated design of random …
Instance segmentation is a problem of significance in computer vision. However, preparing annotated data for this task is extremely time-consuming and costly. By combining the advantages of 3D scanning, reasoning, and GAN-based domain adaptation techniques, we introduce a novel pipeline named SRDA to obtain large quantities of training samples with very minor effort. Our pipeline is well-suited to scenes that can be scanned, i.e. most indoor and some outdoor scenarios. To evaluate our performance, we build three representative scenes and a new dataset, with 3D models of various common objects …
Simulators can efficiently generate large amounts of labeled synthetic data with perfect supervision for hard-to-label tasks like semantic segmentation. However, they introduce a domain gap that severely hurts real-world performance. We propose to use self-supervised monocular depth estimation as a proxy task to bridge this gap and improve sim-to-real unsupervised domain adaptation (UDA). Our Geometric Unsupervised Domain Adaptation method (GUDA) learns a domain-invariant representation via a multi-task objective combining synthetic semantic supervision with real-world geometric constraints on…
Shanghai Jiao Tong University（上海交通大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；East China Normal University（华东师范大学）
Shape information is a strong and valuable prior in segmenting organs in medical images. However, most current deep learning based segmentation algorithms have not taken shape information into consideration, which can lead to bias towards texture. We aim at modeling shape explicitly and using it to help medical image segmentation. Previous methods proposed Variational Autoencoder (VAE) based models to learn the distribution of shape for a particular organ and used it to automatically evaluate the quality of a segmentation prediction by fitting it into the learned shape distribution. Based on w…
IMT School for Advanced Studies Lucca（IMT卢卡高等研究院）；University of Edinburgh（爱丁堡大学）
Large, fine-grained image segmentation datasets, annotated at pixel-level, are difficult to obtain, particularly in medical imaging, where annotations also require expert knowledge. Weakly-supervised learning can train models by relying on weaker forms of annotation, such as scribbles. Here, we learn to segment using scribble annotations in an adversarial game. With unpaired segmentation masks, we train a multi-scale GAN to generate realistic segmentation masks at multiple resolutions, while we use scribbles to learn their correct position in the image. Central to the model's success is a nove…
Domain adaptation is an important task to enable learning when labels are scarce. While most works focus only on the image modality, there are many important multi-modal datasets. In order to leverage multi-modality for domain adaptation, we propose cross-modal learning, where we enforce consistency between the predictions of two modalities via mutual mimicking. We constrain our network to make correct predictions on labeled data and consistent predictions across modalities on unlabeled target-domain data. Experiments in unsupervised and semi-supervised domain adaptation settings prove the eff…
Radboud University Medical Center（拉德堡德大学医学中心）；The Netherlands Cancer Institute（荷兰癌症研究所）；Nanjing University of Information Science and Technology（南京信息工程大学）
Domain adaptation has been widely adopted to transfer styles across multi-vendors and multi-centers, as well as to complement the missing modalities. In this challenge, we proposed an unsupervised domain adaptation framework for cross-modality vestibular schwannoma (VS) and cochlea segmentation and Koos grade prediction. We learn the shared representation from both ceT1 and hrT2 images and recover another modality from the latent representation, and we also utilize proxy tasks of VS segmentation and brain parcellation to restrict the consistency of image structures in domain adaptation. After …
Deep learning approaches for semantic segmentation rely primarily on supervised learning approaches and require substantial efforts in producing pixel-level annotations. Further, such approaches may perform poorly when applied to unseen image domains. To cope with these limitations, both unsupervised domain adaptation (UDA) with full source supervision but without target supervision and semi-supervised learning (SSL) with partial supervision have been proposed. While such methods are effective at aligning different feature distributions, there is still a need to efficiently exploit unlabeled d…
University of Electronic Science and Technology of China（电子科技大学）；Shanghai Artificial Intelligence Laboratory（上海人工智能实验室）；Sichuan Cancer Hospital and Institute（四川省肿瘤医院（四川省肿瘤研究所））；Sichuan Cancer Center（四川省癌症中心）；Sichuan University（四川大学）；West China Hospital（华西医院）；Johns Hopkins University（约翰斯·霍普金斯大学）；SenseTime Research（商汤科技研究院）；Rutgers University（罗格斯大学）
Whole abdominal organ segmentation is important in diagnosing abdomen lesions, radiotherapy, and follow-up. However, oncologists' delineating all abdominal organs from 3D volumes is time-consuming and very expensive. Deep learning-based medical image segmentation has shown the potential to reduce manual delineation efforts, but it still requires a large-scale fine annotated dataset for training, and there is a lack of large-scale datasets covering the whole abdomen region with accurate and detailed annotations for the whole abdominal organ segmentation. In this work, we establish a new large-s…
From Few to More: Scribble-based Medical Image Segmentation via Masked Context Modeling and Continuous Pseudo Labels
National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology, School of Computer Science and Engineering, Northwestern Polytechnical University（集成空天地海大数据应用技术国家工程实验室，计算机科学与工程学院，西北工业大学）
