Diffusion-Based Data Augmentation for Medical Image Segmentation
School of Computer Science and Engineering, Beihang University（北京航空航天大学计算机科学与工程学院）；Dept. of Engineering for Innovation Medicine, University of Verona（威尼斯大学创新医学工程系）
Medical image segmentation models struggle with rare abnormalities due to scarce annotated pathological data. We propose DiffAug a novel framework that combines textguided diffusion-based generation with automatic segmentation validation to address this challenge. Our proposed approach uses latent diffusion models conditioned on medical text descriptions and spatial masks to synthesize abnormalities via inpainting on normal images. Generated samples undergo dynamic quality validation through a latentspace segmentation network that ensures accurate localization while enabling single-step inference. The text prompts, derived from medical literature, guide the generation of diverse abnormality types without requiring manual annotation. Our validation mechanism filters synthetic samples based on spatial accuracy, maintaining quality while operating efficiently through direct latent estimation. Evaluated on three medical imaging benchmarks (CVC-ClinicDB, Kvasir-SEG, REFUGE2), our framework achieves state-of-the-art performance with 8-10% Dice improvements over baselines and reduces false negative rates by up to 28% for challenging cases like small polyps and flat lesions critical for early detection in screening applications.
Consistency regularization describes a class of approaches that have yielded state-of-the-art results for semi-supervised classification. While semi-supervised semantic segmentation proved to be more challenging, a number of successful approaches have been recently proposed. Recent work explored the challenges involved in using consistency regularization for segmentation problems. In their self-supervised work Chen et al. found that colour augmentation prevents a classification network from using image colour statistics as a short-cut for self-supervised learning via instance discrimination. D…
University of Freiburg（弗莱堡大学）；Fraunhofer Institute for Physical Measurement Techniques IPM（弗劳恩霍夫物理测量技术研究所）
Data augmentation methods enrich datasets with augmented data to improve the performance of neural networks. Recently, automated data augmentation methods have emerged, which automatically design augmentation strategies. Existing work focuses on image classification and object detection, whereas we provide the first study on semantic image segmentation and introduce two new approaches: \textit{SmartAugment} and \textit{SmartSamplingAugment}. SmartAugment uses Bayesian Optimization to search over a rich space of augmentation strategies and achieves a new state-of-the-art performance in all sema…
Most modern approaches for domain adaptive semantic segmentation rely on continued access to source data during adaptation, which may be infeasible due to computational or privacy constraints. We focus on source-free domain adaptation for semantic segmentation, wherein a source model must adapt itself to a new target domain given only unlabeled target data. We propose Augmentation Consistency-guided Self-training (AUGCO), a source-free adaptation algorithm that uses the model's pixel-level predictive consistency across diverse, automatically generated views of each target image along with mode…
We propose an approach to domain adaptation for semantic segmentation that is both practical and highly accurate. In contrast to previous work, we abandon the use of computationally involved adversarial objectives, network ensembles and style transfer. Instead, we employ standard data augmentation techniques $-$ photometric noise, flipping and scaling $-$ and ensure consistency of the semantic predictions across these image transformations. We develop this principle in a lightweight self-supervised framework trained on co-evolving pseudo labels without the need for cumbersome extra training ro…
Generalizability is seen as one of the major challenges in deep learning, in particular in the domain of medical imaging, where a change of hospital or in imaging routines can lead to a complete failure of a model. To tackle this, we introduce Consistency Training, a training procedure and alternative to data augmentation based on maximizing models' prediction consistency across augmented and unaugmented data in order to facilitate better out-of-distribution generalization. To this end, we develop a novel region-based segmentation loss function called Segmentation Inconsistency Loss (SIL), whi…
Labeling semantic segmentation datasets is a costly and laborious process if compared with tasks like image classification and object detection. This is especially true for remote sensing applications that not only work with extremely high spatial resolution data but also commonly require the knowledge of experts of the area to perform the manual labeling. Data augmentation techniques help to improve deep learning models under the circumstance of few and imbalanced labeled samples. In this work, we propose a novel data augmentation method focused on exploring the spatial context of remote sens…
Tel Aviv University（特拉维夫大学）；The Chaim Sheba Medical Center（夏姆谢巴医疗中心）；Bar-Ilan University（巴伊兰大学）
Deep learning methods, and in particular convolutional neural networks (CNNs), have led to an enormous breakthrough in a wide range of computer vision tasks, primarily by using large-scale annotated datasets. However, obtaining such datasets in the medical domain remains a challenge. In this paper, we present methods for generating synthetic medical images using recently presented deep learning Generative Adversarial Networks (GANs). Furthermore, we show that generated medical images can be used for synthetic data augmentation, and improve the performance of CNN for medical image classificatio…
East China Normal University（华东师范大学）；Huashan Hospital, Fudan University（复旦大学附属华山医院）
Medical image segmentation is one of the fundamental problems for artificial intelligence-based clinical decision systems. Current automatic medical image segmentation methods are often failed to meet clinical requirements. As such, a series of interactive segmentation algorithms are proposed to utilize expert correction information. However, existing methods suffer from some segmentation refining failure problems after long-term interactions and some cost problems from expert annotation, which hinder clinical applications. This paper proposes an interactive segmentation framework, called inte…
University of Augsburg（奥格斯堡大学）；University Hospital Augsburg（奥格斯堡大学医院）
Correct performance assessment is crucial for evaluating modern artificial intelligence algorithms in medicine like deep-learning based medical image segmentation models. However, there is no universal metric library in Python for standardized and reproducible evaluation. Thus, we propose our open-source publicly available Python package MISeval: a metric library for Medical Image Segmentation Evaluation. The implemented metrics can be intuitively used and easily integrated into any performance assessment pipeline. The package utilizes modern CI/CD strategies to ensure functionality and stabil…
Pontifical Catholic University of Rio de Janeiro（里约热内卢天主教大学）；PETROBRAS（巴西国家石油公司）
Nowadays, subsurface salt body localization and delineation, also called semantic segmentation of salt bodies, are among the most challenging geophysicist tasks. Thus, identifying large salt bodies is notoriously tricky and is crucial for identifying hydrocarbon reservoirs and drill path planning. This work proposes a Data Augmentation method based on training two generative models to augment the number of samples in a seismic image dataset for the semantic segmentation of salt bodies. Our method uses deep learning models to generate pairs of seismic image patches and their respective salt mas…
Guangdong Provincial People’s Hospital（广东省人民医院）；Guangdong Academy of Medical Sciences（广东省医学科学院）；Guangdong Cardiovascular Institute（广东省心血管病研究所）；Wuhan University（武汉大学）；Guangzhou Women and Children’s Medical Center（广州市妇女儿童医疗中心）；Guangzhou Medical University（广州医科大学）
Background: Medical images are more difficult to acquire and annotate than natural images, which results in data augmentation technologies often being used in medical image segmentation tasks. Most data augmentation technologies used in medical segmentation were originally developed on natural images and do not take into account the characteristic that the overall layout of medical images is standard and fixed. Methods: Based on the characteristics of medical images, we developed the cutting-splicing data augmentation (CS-DA) method, a novel data augmentation technology for medical image segme…
Due to the limitation of available labeled data, medical image segmentation is a challenging task for deep learning. Traditional data augmentation techniques have been shown to improve segmentation network performances by optimizing the usage of few training examples. However, current augmentation approaches for segmentation do not tackle the strong texture bias of convolutional neural networks, observed in several studies. This work shows on the MoNuSeg dataset that style augmentation, which is already used in classification tasks, helps reducing texture over-fitting and improves segmentation…
Tsinghua University（清华大学）；Peking University Shenzhen Hospital（北京大学深圳医院）
The medical datasets are usually faced with the problem of scarcity and data imbalance. Moreover, annotating large datasets for semantic segmentation of medical lesions is domain-knowledge and time-consuming. In this paper, we propose a new object-blend method(short in soft-CP) that combines the Copy-Paste augmentation method for semantic segmentation of medical lesions offline, ensuring the correct edge information around the lession to solve the issue above-mentioned. We proved the method's validity with several datasets in different imaging modalities. In our experiments on the KiTS19[2] da…
Semantic segmentation is one of the basic topics in computer vision, it aims to assign semantic labels to every pixel of an image. Unbalanced semantic label distribution could have a negative influence on segmentation accuracy. In this paper, we investigate using data augmentation approach to balance the semantic label distribution in order to improve segmentation performance. We propose using generative adversarial networks (GANs) to generate realistic images for improving the performance of semantic segmentation networks. Experimental results show that the proposed method can not only improv…
Peking University（北京大学）；Canon Medical Systems（佳能医疗系统公司）
Data augmentation is an effective and universal technique for improving generalization performance of deep neural networks. It could enrich diversity of training samples that is essential in medical image segmentation tasks because 1) the scale of medical image dataset is typically smaller, which may increase the risk of overfitting; 2) the shape and modality of different objects such as organs or tumors are unique, thus requiring customized data augmentation policy. However, most data augmentation implementations are hand-crafted and suboptimal in medical image processing. To fully exploit th…
The University of Tokyo（东京大学）；National Center for Global Health and Medicine（国立国际医疗研究中心）；Kyushu Medical Center（九州医疗中心）
Convolutional Neural Networks (CNNs) can play a key role in Medical Image Analysis under large-scale annotated datasets. However, preparing such massive dataset is demanding. In this context, Generative Adversarial Networks (GANs) can generate realistic but novel samples, and thus effectively cover the real image distribution. In terms of interpolation, the GAN-based medical image augmentation is reliable because medical modalities can display the human body's strong anatomical consistency at fixed position while clearly reflecting inter-subject variability; thus, we propose to use noise-to-im…
ETH Zurich（苏黎世联邦理工学院）；University Hospital of Zurich（苏黎世大学医院）
Supervised learning-based segmentation methods typically require a large number of annotated training data to generalize well at test time. In medical applications, curating such datasets is not a favourable option because acquiring a large number of annotated samples from experts is time-consuming and expensive. Consequently, numerous methods have been proposed in the literature for learning with limited annotated examples. Unfortunately, the proposed approaches in the literature have not yet yielded significant gains over random data augmentation for image segmentation, where random augmenta…
Chalmers University of Technology（查尔姆斯理工大学）；Volvo Cars（沃尔沃汽车）
The state of the art in semantic segmentation is steadily increasing in performance, resulting in more precise and reliable segmentations in many different applications. However, progress is limited by the cost of generating labels for training, which sometimes requires hours of manual labor for a single image. Because of this, semi-supervised methods have been applied to this task, with varying degrees of success. A key challenge is that common augmentations used in semi-supervised classification are less effective for semantic segmentation. We propose a novel data augmentation mechanism call…
Computer-assisted diagnosis (CAD) based on deep learning has become a crucial diagnostic technology in the medical industry, effectively improving diagnosis accuracy. However, the scarcity of brain tumor Magnetic Resonance (MR) image datasets causes the low performance of deep learning algorithms. The distribution of transformed images generated by traditional data augmentation (DA) intrinsically resembles the original ones, resulting in a limited performance in terms of generalization ability. This work improves Progressive Growing of GANs with a structural similarity loss function (PGGAN-SSI…
South China University of Technology（华南理工大学）；University of Utah（犹他大学）
We introduce the idea of inter-slice image augmentation whereby the numbers of the medical images and the corresponding segmentation labels are increased between two consecutive images in order to boost medical image segmentation accuracy. Unlike conventional data augmentation methods in medical imaging, which only increase the number of training samples directly by adding new virtual samples using simple parameterized transformations such as rotation, flipping, scaling, etc., we aim to augment data based on the relationship between two consecutive images, which increases not only the number b…
National Institute of Technology Karnataka（卡纳塔克邦国家技术研究所）
Computer-aided medical image analysis plays a significant role in assisting medical practitioners for expert clinical diagnosis and deciding the optimal treatment plan. At present, convolutional neural networks (CNN) are the preferred choice for medical image analysis. In addition, with the rapid advancements in three-dimensional (3D) imaging systems and the availability of excellent hardware and software support to process large volumes of data, 3D deep learning methods are gaining popularity in medical image analysis. Here, we present an extensive review of the recently evolved 3D deep learn…
Segmentation of findings in the gastrointestinal tract is a challenging but also an important task which is an important building stone for sufficient automatic decision support systems. In this work, we present our solution for the Medico 2020 task, which focused on the problem of colon polyp segmentation. We present our simple but efficient idea of using an augmentation method that uses grids in a pyramid-like manner (large to small) for segmentation. Our results show that the proposed methods work as indented and can also lead to comparable results when competing with other methods.
University of California, Los Angeles（加州大学洛杉矶分校）；NVIDIA（英伟达）
Fully convolutional neural networks (CNNs) have proven to be effective at representing and classifying textural information, thus transforming image intensity into output class masks that achieve semantic image segmentation. In medical image analysis, however, expert manual segmentation often relies on the boundaries of anatomical structures of interest. We propose boundary aware CNNs for medical image segmentation. Our networks are designed to account for organ boundary information, both by providing a special network edge branch and edge-aware loss terms, and they are trainable end-to-end. W…
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…
Ecole nationale Supérieure en Informatique（国立高等计算机学院）；Université de Bourgogne（勃艮第大学）
Segmentation of medical images is an essential part in the process of diagnostics. Physicians require an automatic, robust and valid results. Hidden Markov Random Fields (HMRF) provide powerful model. This latter models the segmentation problem as the minimization of an energy function. Cuckoo search (CS) algorithm is one of the recent nature-inspired meta-heuristic algorithms. It has shown its efficiency in many engineering optimization problems. In this paper, we use three cuckoo search algorithm to achieve medical image segmentation.
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 …
Recent advances of semantic image segmentation greatly benefit from deeper and larger Convolutional Neural Network (CNN) models. Compared to image segmentation in the wild, properties of both medical images themselves and of existing medical datasets hinder training deeper and larger models because of overfitting. To this end, we propose a novel two-stream UNET architecture for automatic end-to-end medical image segmentation, in which intensity value and gradient vector flow (GVF) are two inputs for each stream, respectively. We demonstrate that two-stream CNNs with more low-level features gre…
Imperial College London（帝国理工学院）；University of Edinburgh（爱丁堡大学）；Fudan University（复旦大学）；City, University of London（伦敦城市大学）；Technical University of Munich（慕尼黑工业大学）
The success of neural networks on medical image segmentation tasks typically relies on large labeled datasets for model training. However, acquiring and manually labeling a large medical image set is resource-intensive, expensive, and sometimes impractical due to data sharing and privacy issues. To address this challenge, we propose AdvChain, a generic adversarial data augmentation framework, aiming at improving both the diversity and effectiveness of training data for medical image segmentation tasks. AdvChain augments data with dynamic data augmentation, generating randomly chained photo-met…
Nanjing University（南京大学）；Medical School of Nanjing University（南京大学医学院）；National Institute of Healthcare Data Science, Nanjing University（南京大学国家健康数据科学研究院）；UNC Chapel Hill（北卡罗来纳大学教堂山分校）
Conventional data augmentation realized by performing simple pre-processing operations (\eg, rotation, crop, \etc) has been validated for its advantage in enhancing the performance for medical image segmentation. However, the data generated by these conventional augmentation methods are random and sometimes harmful to the subsequent segmentation. In this paper, we developed a novel automatic learning-based data augmentation method for medical image segmentation which models the augmentation task as a trial-and-error procedure using deep reinforcement learning (DRL). In our method, we innovativ…
Medical image annotation typically requires expert knowledge and hence incurs time-consuming and expensive data annotation costs. To alleviate this burden, we propose a novel learning scenario, Exemplar Learning (EL), to explore automated learning processes for medical image segmentation with a single annotated image example. This innovative learning task is particularly suitable for medical image segmentation, where all categories of organs can be presented in one single image and annotated all at once. To address this challenging EL task, we propose an Exemplar Learning-based Synthesis Net (…
University of Liverpool（利物浦大学）；Xi’an Jiaotong-Liverpool University (XJTLU)（西交利物浦大学）；Duke Kunshan University（昆山杜克大学）
Single-source domain generalization (SDG) in medical image segmentation is a challenging yet essential task as domain shifts are quite common among clinical image datasets. Previous attempts most conduct global-only/random augmentation. Their augmented samples are usually insufficient in diversity and informativeness, thus failing to cover the possible target domain distribution. In this paper, we rethink the data augmentation strategy for SDG in medical image segmentation. Motivated by the class-level representation invariance and style mutability of medical images, we hypothesize that unseen…
University of Augsburg（奥格斯堡大学）；University Hospital Augsburg（奥格斯堡大学医院）
In the last decade, research on artificial intelligence has seen rapid growth with deep learning models, especially in the field of medical image segmentation. Various studies demonstrated that these models have powerful prediction capabilities and achieved similar results as clinicians. However, recent studies revealed that the evaluation in image segmentation studies lacks reliable model performance assessment and showed statistical bias by incorrect metric implementation or usage. Thus, this work provides an overview and interpretation guide on the following metrics for medical image segmen…
In this paper, we propose a novel medical image segmentation using iterative deep learning framework. We have combined an iterative learning approach and an encoder-decoder network to improve segmentation results, which enables to precisely localize the regions of interest (ROIs) including complex shapes or detailed textures of medical images in an iterative manner. The proposed iterative deep convolutional encoder-decoder network consists of two main paths: convolutional encoder path and convolutional decoder path with iterative learning. Experimental results show that the proposed iterative …
Yes, it can. Data augmentation is perhaps the oldest preprocessing step in computer vision literature. Almost every computer vision model trained on imaging data uses some form of augmentation. In this paper, we use the inter-vertebral disk segmentation task alongside a deep residual U-Net as the learning model, to explore the effectiveness of augmentation. In the extreme, we observed that a model trained on patches extracted from just one scan, with each patch augmented 50 times; achieved a Dice score of 0.73 in a validation set of 40 cases. Qualitative evaluation indicated a clinically usabl…
With the COVID-19 global pandemic, computer-assisted diagnoses of medical images have gained much attention, and robust methods of Semantic Segmentation of Computed Tomography (CT) became highly desirable. Semantic Segmentation of CT is one of many research fields of automatic detection of COVID-19 and has been widely explored since the COVID-19 outbreak. In this work, we propose an extensive analysis of how different data augmentation techniques improve the training of encoder-decoder neural networks on this problem. Twenty different data augmentation techniques were evaluated on five differe…
The recently proposed panoptic segmentation task presents a significant challenge of image understanding with computer vision by unifying semantic segmentation and instance segmentation tasks. In this paper we present an efficient and novel panoptic data augmentation (PanDA) method which operates exclusively in pixel space, requires no additional data or training, and is computationally cheap to implement. By retraining original state-of-the-art models on PanDA augmented datasets generated with a single frozen set of parameters, we show robust performance gains in panoptic segmentation, instan…
Deep models often suffer from severe performance drop due to the appearance shift in the real clinical setting. Most of the existing learning-based methods rely on images from multiple sites/vendors or even corresponding labels. However, collecting enough unknown data to robustly model segmentation cannot always hold since the complex appearance shift caused by imaging factors in daily application. In this paper, we propose a novel style-invariant method for cardiac image segmentation. Based on the zero-shot style transfer to remove appearance shift and test-time augmentation to explore divers…
Alibaba DAMO Academy（阿里巴巴达摩院）；The University of Adelaide（阿德莱德大学）
Recently, significant progress has been made on semantic segmentation. However, the success of supervised semantic segmentation typically relies on a large amount of labelled data, which is time-consuming and costly to obtain. Inspired by the success of semi-supervised learning methods in image classification, here we propose a simple yet effective semi-supervised learning framework for semantic segmentation. We demonstrate that the devil is in the details: a set of simple design and training techniques can collectively improve the performance of semi-supervised semantic segmentation significa…
Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）
Today deep convolutional neural networks (CNNs) push the limits for most computer vision problems, define trends, and set state-of-the-art results. In remote sensing tasks such as object detection and semantic segmentation, CNNs reach the SotA performance. However, for precise performance, CNNs require much high-quality training data. Rare objects and the variability of environmental conditions strongly affect prediction stability and accuracy. To overcome these data restrictions, it is common to consider various approaches including data augmentation techniques. This study focuses on the deve…
Semantic image segmentation aims to obtain object labels with precise boundaries, which usually suffers from overfitting. Recently, various data augmentation strategies like regional dropout and mix strategies have been proposed to address the problem. These strategies have proved to be effective for guiding the model to attend on less discriminative parts. However, current strategies operate at the image level, and objects and the background are coupled. Thus, the boundaries are not well augmented due to the fixed semantic scenario. In this paper, we propose ObjectAug to perform object-level …
Semantic segmentation using convolutional neural networks (CNN) is a crucial component in image analysis. Training a CNN to perform semantic segmentation requires a large amount of labeled data, where the production of such labeled data is both costly and labor intensive. Semi-supervised learning algorithms address this issue by utilizing unlabeled data and so reduce the amount of labeled data needed for training. In particular, data augmentation techniques such as CutMix and ClassMix generate additional training data from existing labeled data. In this paper we propose a new approach for data…
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…
Adaptive Spatial Augmentation for Semi-supervised Semantic Segmentation
Shaanxi Provincial Key Laboratory of Speech and Image Information Processing（陕西语音图像信息处理省级重点实验室）；National Engineering Laboratory for Integrated Aerospace-Ground-Ocean Big Data Application Technology（集成空天海大数据应用技术国家工程实验室）；School of Computer Science, Northwestern Polytechnical University（西北工业大学计算机学院）；College of Information Engineering, Northwest A&F University（西北农林科技大学信息工程学院）
Instance segmentation is applied widely in image editing, image analysis and autonomous driving, etc. However, insufficient data is a common problem in practical applications. The Visual Inductive Priors(VIPriors) Instance Segmentation Challenge has focused on this problem. VIPriors for Data-Efficient Computer Vision Challenges ask competitors to train models from scratch in a data-deficient setting, but there are some visual inductive priors that can be used. In order to address the VIPriors instance segmentation problem, we designed a Task-Specific Data Augmentation(TS-DA) strategy and Infer…
Adaptive Augmentation-Aware Latent Learning for Robust LiDAR Semantic Segmentation
University of Science and Technology of China（中国科学技术大学）；National Key Laboratory of Deep Space Exploration, Deep Space Exploration Laboratory（深空探测全国重点实验室（深空探测实验室））
We develop and approach to unsupervised semantic medical image segmentation that extends previous work with generative adversarial networks. We use existing edge detection methods to construct simple edge diagrams, train a generative model to convert them into synthetic medical images, and construct a dataset of synthetic images with known segmentations using variations on extracted edge diagrams. This synthetic dataset is then used to train a supervised image segmentation model. We test our approach on a clinical dataset of kidney ultrasound images and the benchmark ISIC 2018 skin lesion data…
We propose an attention mechanism for 3D medical image segmentation. The method, named segmentation-by-detection, is a cascade of a detection module followed by a segmentation module. The detection module enables a region of interest to come to attention and produces a set of object region candidates which are further used as an attention model. Rather than dealing with the entire volume, the segmentation module distills the information from the potential region. This scheme is an efficient solution for volumetric data as it reduces the influence of the surrounding noise which is especially im…
