Self2Seg: Single-Image Self-Supervised Joint Segmentation and Denoising
University of Innsbruck（因斯布鲁克大学）；VASCage-Research Centre on Vascular Ageing and Stroke（VASCage血管衰老与中风研究中心）；MRC Laboratory of Molecular Biology（医学研究委员会分子生物学实验室）；Institut Pascal（帕斯卡尔研究所）；Université Clermont Auvergne（克莱蒙奥弗涅大学）；Institut de Mathématiques de Bordeaux（波尔多数学研究所）
Nadja Gruber, Johannes Schwab, Noémie Debroux, Nicolas Papadakis, Markus Haltmeier
We develop Self2Seg, a self-supervised method for the joint segmentation and denoising of a single image. To this end, we combine the advantages of variational segmentation with self-supervised deep learning. One major benefit of our method lies in the fact, that in contrast to data-driven methods, where huge amounts of labeled samples are necessary, Self2Seg segments an image into meaningful regions without any training database. Moreover, we demonstrate that self-supervised denoising itself is significantly improved through the region-specific learning of Self2Seg. Therefore, we introduce a novel self-supervised energy functional in which denoising and segmentation are coupled in a way that both tasks benefit from each other. We propose a unified optimisation strategy and numerically show that for noisy microscopy images our proposed joint approach outperforms its sequential counterpart as well as alternative methods focused purely on denoising or segmentation.
Center for Systems Biology（系统生物学中心）；Max Planck Institute of Molecular Cell Biology and Genetics（马克斯·普朗克分子细胞生物学与遗传学研究所）；Max Planck Institute for Physics of Complex Systems（马克斯·普朗克复杂系统物理研究所）
Microscopy image analysis often requires the segmentation of objects, but training data for this task is typically scarce and hard to obtain. Here we propose DenoiSeg, a new method that can be trained end-to-end on only a few annotated ground truth segmentations. We achieve this by extending Noise2Void, a self-supervised denoising scheme that can be trained on noisy images alone, to also predict dense 3-class segmentations. The reason for the success of our method is that segmentation can profit from denoising, especially when performed jointly within the same network. The network becomes a de…
School of Information Science and Technology, ShanghaiTech University（上海科技大学信息科学与技术学院）；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 segmentation is an important problem in medical image analysis due to the high cost of pixelwise annotation. Prior methods, while often focusing on weak labels of 2D images, exploit few structural cues of volumetric medical images. To address this, we propose a novel weakly-supervised segmentation strategy capable of better capturing 3D shape prior in both model prediction and learning. Our main idea is to extract a self-taught shape representation by leveraging weak labels, and then integrate this representation into segmentation prediction for shape refinement. To this end,…
In this work we present a method for lung nodules segmentation, their texture classification and subsequent follow-up recommendation from the CT image of lung. Our method consists of neural network model based on popular U-Net architecture family but modified for the joint nodule segmentation and its texture classification tasks and an ensemble-based model for the follow-up recommendation. This solution was evaluated within the LNDb medical imaging challenge and produced the best nodule segmentation result on the final leaderboard.
Deep learning (DL) has shown promise for faster, high quality accelerated MRI reconstruction. However, supervised DL methods depend on extensive amounts of fully-sampled (labeled) data and are sensitive to out-of-distribution (OOD) shifts, particularly low signal-to-noise ratio (SNR) acquisitions. To alleviate this challenge, we propose Noise2Recon, a model-agnostic, consistency training method for joint MRI reconstruction and denoising that can use both fully-sampled (labeled) and undersampled (unlabeled) scans in semi-supervised and self-supervised settings. With limited or no labeled traini…
AICES Graduate School, RWTH Aachen University（亚琛工业大学 AICES 研究生院）；University of Münster（明斯特大学）
Nowadays, modern electron microscopes deliver images at atomic scale. The precise atomic structure encodes information about material properties. Thus, an important ingredient in the image analysis is to locate the centers of the atoms shown in micrographs as precisely as possible. Here, we consider scanning transmission electron microscopy (STEM), which acquires data in a rastering pattern, pixel by pixel. Due to this rastering combined with the magnification to atomic scale, movements of the specimen even at the nanometer scale lead to random image distortions that make precise atom localiza…
Transfer learning and joint learning approaches are extensively used to improve the performance of Convolutional Neural Networks (CNNs). In medical imaging applications in which the target dataset is typically very small, transfer learning improves feature learning while joint learning has shown effectiveness in improving the network's generalization and robustness. In this work, we study the combination of these two approaches for the problem of liver lesion segmentation and classification. For this purpose, 332 abdominal CT slices containing lesion segmentation and classification of three le…
Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）
We developed a new joint probabilistic segmentation and image distribution matching generative adversarial network (PSIGAN) for unsupervised domain adaptation (UDA) and multi-organ segmentation from magnetic resonance (MRI) images. Our UDA approach models the co-dependency between images and their segmentation as a joint probability distribution using a new structure discriminator. The structure discriminator computes structure of interest focused adversarial loss by combining the generated pseudo MRI with probabilistic segmentations produced by a simultaneously trained segmentation sub-networ…
University of Science and Technology of China（中国科学技术大学）
The capability of image semantic segmentation may be deteriorated due to noisy input image, where image denoising prior to segmentation helps. Both image denoising and semantic segmentation have been developed significantly with the advance of deep learning. Thus, we are interested in the synergy between them by using a holistic deep model. We observe that not only denoising helps combat the drop of segmentation accuracy due to noise, but also pixel-wise semantic information boosts the capability of denoising. We then propose a boosting network to perform denoising and segmentation alternately…
Semantic segmentation labels are expensive and time consuming to acquire. Hence, pretraining is commonly used to improve the label-efficiency of segmentation models. Typically, the encoder of a segmentation model is pretrained as a classifier and the decoder is randomly initialized. Here, we argue that random initialization of the decoder can be suboptimal, especially when few labeled examples are available. We propose a decoder pretraining approach based on denoising, which can be combined with supervised pretraining of the encoder. We find that decoder denoising pretraining on the ImageNet d…
Unsupervised image segmentation and denoising are two fundamental tasks in image processing. Usually, graph based models such as multicut are used for segmentation and variational models are employed for denoising. Our approach addresses both problems at the same time. We propose a novel ILP formulation of the first derivative Potts model with the $\ell_1$ data term, where binary variables are introduced to deal with the $\ell_0$ norm of the regularization term. The ILP is then solved by a standard off-the-shelf MIP solver. Numerical experiments are compared with the multicut problem.
Texas A&M University（得克萨斯农工大学）；Nanyang Technological University（南洋理工大学）；The University of Sydney（悉尼大学）
Several recent works discussed application-driven image restoration neural networks, which are capable of not only removing noise in images but also preserving their semantic-aware details, making them suitable for various high-level computer vision tasks as the pre-processing step. However, such approaches require extra annotations for their high-level vision tasks, in order to train the joint pipeline using hybrid losses. The availability of those annotations is yet often limited to a few image sets, potentially restricting the general applicability of these methods to denoising more unseen …
Center for Systems Biology Dresden (CSBD)（德累斯顿系统生物学中心）；Max-Planck Institute of Molecular Cell Biology and Genetics（马克斯·普朗克分子细胞生物学与遗传学研究所）
Deep learning (DL) has arguably emerged as the method of choice for the detection and segmentation of biological structures in microscopy images. However, DL typically needs copious amounts of annotated training data that is for biomedical projects typically not available and excessively expensive to generate. Additionally, tasks become harder in the presence of noise, requiring even more high-quality training data. Hence, we propose to use denoising networks to improve the performance of other DL-based image segmentation methods. More specifically, we present ideas on how state-of-the-art sel…
Institute for Signals, Systems and Computational Intelligence, sinc(i) CONICET-UNL（信号、系统与计算智能研究所，sinc(i) 阿根廷国家科学与技术研究理事会-国立利托拉尔大学）；Imperial College London（伦敦帝国理工学院）
We introduce Post-DAE, a post-processing method based on denoising autoencoders (DAE) to improve the anatomical plausibility of arbitrary biomedical image segmentation algorithms. Some of the most popular segmentation methods (e.g. based on convolutional neural networks or random forest classifiers) incorporate additional post-processing steps to ensure that the resulting masks fulfill expected connectivity constraints. These methods operate under the hypothesis that contiguous pixels with similar aspect should belong to the same class. Even if valid in general, this assumption does not consid…
Peking University（北京大学）；Beijing Institute of Big Data Research（北京大数据研究院）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
Blood vessel segmentation is crucial for many diagnostic and research applications. In recent years, CNN-based models have leaded to breakthroughs in the task of segmentation, however, such methods usually lose high-frequency information like object boundaries and subtle structures, which are vital to vessel segmentation. To tackle this issue, we propose Boundary Enhancement and Feature Denoising (BEFD) module to facilitate the network ability of extracting boundary information in semantic segmentation, which can be integrated into arbitrary encoder-decoder architecture in an end-to-end way. B…
Nowadays, Deep learning techniques show dramatic performance on computer vision area, and they even outperform human. But it is also vulnerable to some small perturbation called an adversarial attack. This is a problem combined with the safety of artificial intelligence, which has recently been studied a lot. These attacks have shown that they can fool models of image classification, semantic segmentation, and object detection. We point out this attack can be protected by denoise autoencoder, which is used for denoising the perturbation and restoring the original images. We experiment with var…
Research institute for signals, systems and computational intelligence, sinc(i)（信号、系统与计算智能研究所（sinc(i)））；FICH-UNL（拉普拉塔国立大学工程学院）；CONICET（阿根廷国家科学与技术研究理事会）
Deep convolutional neural networks (CNN) proved to be highly accurate to perform anatomical segmentation of medical images. However, some of the most popular CNN architectures for image segmentation still rely on post-processing strategies (e.g. Conditional Random Fields) to incorporate connectivity constraints into the resulting masks. These post-processing steps are based on the assumption that objects are usually continuous and therefore nearby pixels should be assigned the same object label. Even if it is a valid assumption in general, these methods do not offer a straightforward way to in…
Deep convolutional neural networks (DCNNs) have contributed many breakthroughs in segmentation tasks, especially in the field of medical imaging. However, \textit{domain shift} and \textit{corrupted annotations}, which are two common problems in medical imaging, dramatically degrade the performance of DCNNs in practice. In this paper, we propose a novel robust cross-denoising framework using two peer networks to address domain shift and corrupted label problems with a peer-review strategy. Specifically, each network performs as a mentor, mutually supervised to learn from reliable samples selec…
Visual anomaly detection, an important problem in computer vision, is usually formulated as a one-class classification and segmentation task. The student-teacher (S-T) framework has proved to be effective in solving this challenge. However, previous works based on S-T only empirically applied constraints on normal data and fused multi-level information. In this study, we propose an improved model called DeSTSeg, which integrates a pre-trained teacher network, a denoising student encoder-decoder, and a segmentation network into one framework. First, to strengthen the constraints on anomalous da…
Automatic segmentation of brain glioma from multimodal MRI scans plays a key role in clinical trials and practice. Unfortunately, manual segmentation is very challenging, time-consuming, costly, and often inaccurate despite human expertise due to the high variance and high uncertainty in the human annotations. In the present work, we develop an end-to-end deep-learning-based segmentation method using a multi-decoder architecture by jointly learning three separate sub-problems using a partly shared encoder. We also propose to apply smoothing methods to the input images to generate denoised vers…
Northeastern University（东北大学）；Chengdu University of Information Technology（成都信息工程大学）；University of Lübeck（吕贝克大学）；Shengjing Hospital, China Medical University（中国医科大学附属盛京医院）；Liaoning Shihua University（辽宁石油化工大学）；University of New South Wales（新南威尔士大学）
Environmental microorganisms (EMs) are ubiquitous around us and have an important impact on the survival and development of human society. However, the high standards and strict requirements for the preparation of environmental microorganism (EM) data have led to the insufficient of existing related databases, not to mention the databases with GT images. This problem seriously affects the progress of related experiments. Therefore, This study develops the Environmental Microorganism Dataset Sixth Version (EMDS-6), which contains 21 types of EMs. Each type of EM contains 40 original and 40 GT i…
Indian Institute of Technology Madras（印度理工学院马德拉斯分校）；Sree Chitra Tirunal Institute for Medical Sciences and Technology（Sree Chitra Tirunal医学科学与技术研究所）
The work presented explores the use of denoising autoencoders (DAE) for brain lesion detection, segmentation and false positive reduction. Stacked denoising autoencoders (SDAE) were pre-trained using a large number of unlabeled patient volumes and fine tuned with patches drawn from a limited number of patients (n=20, 40, 65). The results show negligible loss in performance even when SDAE was fine tuned using 20 patients. Low grade glioma (LGG) segmentation was achieved using a transfer learning approach wherein a network pre-trained with High Grade Glioma (HGG) data was fine tuned using LGG im…
This paper is a presentation of a new method for denoising images using Haralick features and further segmenting the characters using artificial neural networks. The image is divided into kernels, each of which is converted to a GLCM (Gray Level Co-Occurrence Matrix) on which a Haralick Feature generation function is called, the result of which is an array with fourteen elements corresponding to fourteen features The Haralick values and the corresponding noise/text classification form a dictionary, which is then used to de-noise the image through kernel comparison. Segmentation is the process …
Technical Report for ICRA 2025 GOOSE 2D Semantic Segmentation Challenge: Leveraging Color Shift Correction, RoPE-Swin Backbone, and Quantile-based Label Denoising Strategy for Robust Outdoor Scene Understanding
Institute of Intelligent Systems（智能系统研究所）；College of Artificial Intelligence, National Yang Ming Chiao Tung University（人工智能学院，阳明交通大学）；Institute of Data Science, National Cheng Kung University（数据科学研究所，成功大学）
Huazhong University of Science and Technology（华中科技大学）
Optical neuroimaging is a vital tool for understanding the brain structure and the connection between regions and nuclei. However, the image noise introduced in the sample preparation and the imaging system hinders the extraction of the possible knowlege from the dataset, thus denoising for the optical neuroimaging is usually necessary. The supervised denoisng methods often outperform the unsupervised ones, but the training of the supervised denoising models needs the corresponding clean labels, which is not always avaiable due to the high labeling cost. On the other hand, those semantic label…
Sparse coding of images is traditionally done by cutting them into small patches and representing each patch individually over some dictionary given a pre-determined number of nonzero coefficients to use for each patch. In lack of a way to effectively distribute a total number (or global budget) of nonzero coefficients across all patches, current sparse recovery algorithms distribute the global budget equally across all patches despite the wide range of differences in structural complexity among them. In this work we propose a new framework for joint sparse representation and recovery of all i…
Interdisciplinary Center for Scientific Computing, Heidelberg University；Department of Mathematics, Humboldt University of Berlin（mathematics department, Humboldt University of Berlin）；Institute for Mathematics, Heidelberg University（mathematics institute, Heidelberg University）；University of Trier（Trier university）
Self is the Best Learner: CT-free Ultra-Low-Dose PET Organ Segmentation via Collaborating Denoising and Segmentation Learning
School of Biomedical Engineering, Southern Medical University（生物医学工程学院，南方医科大学）；School of Biomedical Engineering, Shanghai Jiao Tong University（生物医学工程学院，上海交通大学）；Nanfang PET Center, Nanfang Hospital Southern Medical University（南芳PET中心，南方医科大学南芳医院）；Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University（广东省医学图像处理重点实验室，南方医科大学）；Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University（广东省医学影像与诊断技术工程实验室，南方医科大学）；Pazhou Lab（琶洲实验室）
Pancreatic Tumor Segmentation as Anomaly Detection in CT Images Using Denoising Diffusion Models
School of Electrical and Computer Engineering, University of Oklahoma（俄克拉荷马大学电气与计算机工程学院）；University of Oklahoma Health Sciences Center（俄克拉荷马大学健康科学中心）；School of Computer Science, University of Oklahoma（俄克拉荷马大学计算机科学学院）
Teacher Encoder-Student Decoder Denoising Guided Segmentation Network for Anomaly Detection
School of Computer Science, Chengdu University of Information Science and Technology（成都信息科技大学计算机科学学院）；Purdue University（普渡大学）；University at Albany（阿尔巴尼大学）
Retinal OCT Synthesis with Denoising Diffusion Probabilistic Models for Layer Segmentation
Institute of Imaging and Computer Vision, RWTH Aachen University（成像与计算机视觉研究所，亚琛RWTH大学）；Bio-manufacturing Engineering Laboratory of Tsinghua SIGS, Tsinghua University（清华大学SIGS生物制造工程实验室）；Shenzhen Eye Hospital（深圳眼科医院）；Department of Ophthalmology, RWTH Aachen University（眼科部，亚琛RWTH大学）
Prototype-Based Pseudo-Label Denoising for Source-Free Domain Adaptation in Remote Sensing Semantic Segmentation
College of Computer Science, Sichuan University（四川大学计算机科学学院）；College of Computer Science and Cyber Security, Chengdu University of Technology（成都理工大学计算机科学与网络安全学院）
An image processing unit (IPU), or image signal processor (ISP) for high dynamic range (HDR) imaging usually consists of demosaicing, white balancing, lens shading correction, color correction, denoising, and tone-mapping. Besides noise from the imaging sensors, almost every step in the ISP introduces or amplifies noise in different ways, and denoising operators are designed to reduce the noise from these sources. Designed for dynamic range compressing, tone-mapping operators in an ISP can significantly amplify the noise level, especially for images captured in low-light conditions, making den…
Harbin Institute of Technology at Shenzhen（哈尔滨工业大学（深圳））；Peng Cheng Laboratory（鹏城实验室）
Based on the Denoising Diffusion Probabilistic Model (DDPM), medical image segmentation can be described as a conditional image generation task, which allows to compute pixel-wise uncertainty maps of the segmentation and allows an implicit ensemble of segmentations to boost the segmentation performance. However, DDPM requires many iterative denoising steps to generate segmentations from Gaussian noise, resulting in extremely inefficient inference. To mitigate the issue, we propose a principled acceleration strategy, called pre-segmentation diffusion sampling DDPM (PD-DDPM), which is specially …
Diffusion frameworks have achieved comparable performance with previous state-of-the-art image generation models. Researchers are curious about its variants in discriminative tasks because of its powerful noise-to-image denoising pipeline. This paper proposes DiffusionInst, a novel framework that represents instances as instance-aware filters and formulates instance segmentation as a noise-to-filter denoising process. The model is trained to reverse the noisy groundtruth without any inductive bias from RPN. During inference, it takes a randomly generated filter as input and outputs mask in one…
Demosaicking and denoising are the first steps of any camera image processing pipeline and are key for obtaining high quality RGB images. A promising current research trend aims at solving these two problems jointly using convolutional neural networks. Due to the unavailability of ground truth data these networks cannot be currently trained using real RAW images. Instead, they resort to simulated data. In this paper we present a method to learn demosaicking directly from mosaicked images, without requiring ground truth RGB data. We apply this to learn joint demosaicking and denoising only from…
University of Science and Technology of China（中国科学技术大学）；Microsoft Research Asia（微软亚洲研究院）
Self-training is a competitive approach in domain adaptive segmentation, which trains the network with the pseudo labels on the target domain. However inevitably, the pseudo labels are noisy and the target features are dispersed due to the discrepancy between source and target domains. In this paper, we rely on representative prototypes, the feature centroids of classes, to address the two issues for unsupervised domain adaptation. In particular, we take one step further and exploit the feature distances from prototypes that provide richer information than mere prototypes. Specifically, we use…
