Shortage of fully annotated datasets has been a limiting factor in developing deep learning based image segmentation algorithms and the problem becomes more pronounced in multi-organ segmentation. In this paper, we propose a unified training strategy that enables a novel multi-scale deep neural network to be trained on multiple partially labeled datasets for multi-organ segmentation. In addition, a new network architecture for multi-scale feature abstraction is proposed to integrate pyramid input and feature analysis into a U-shape pyramid structure. To bridge the semantic gap caused by directly merging features from different scales, an equal convolutional depth mechanism is introduced. Furthermore, we employ a deep supervision mechanism to refine the outputs in different scales. To fully leverage the segmentation features from all the scales, we design an adaptive weighting layer to fuse the outputs in an automatic fashion. All these mechanisms together are integrated into a Pyramid Input Pyramid Output Feature Abstraction Network (PIPO-FAN). Our proposed method was evaluated on four publicly available datasets, including BTCV, LiTS, KiTS and Spleen, where very promising performance has been achieved. The source code of this work is publicly shared at https://github.com/DIAL-RPI/PIPO-FAN for others to easily reproduce the work and build their own models with the introduced mechanisms.
ThreshGuide: Class-Aware Labeled-Guided Thresholding for Semi-Supervised 3D Abdominal Multi-Organ Segmentation
School of Intelligent Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences（中国科学院大学杭州高等研究院智能科学与技术学院）
GuidedNet: Semi-Supervised Multi-Organ Segmentation via Labeled Data Guide Unlabeled Data
Beihang University（北京航空航天大学）；University of Chinese Academy of Sciences（中国科学院大学）；Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences（中国科学院大学杭州高等研究院）；University of Science and Technology Beijing（北京科技大学）
Northwestern Polytechnical University（西北工业大学）；The University of Adelaide（阿德莱德大学）；Alibaba DAMO Academy（阿里巴巴达摩院）；Zhejiang University（浙江大学）
Medical image benchmarks for the segmentation of organs and tumors suffer from the partially labeling issue due to its intensive cost of labor and expertise. Current mainstream approaches follow the practice of one network solving one task. With this pipeline, not only the performance is limited by the typically small dataset of a single task, but also the computation cost linearly increases with the number of tasks. To address this, we propose a Transformer based dynamic on-demand network (TransDoDNet) that learns to segment organs and tumors on multiple partially labeled datasets. Specifical…
Northwestern Polytechnical University（西北工业大学）；The University of Adelaide（阿德莱德大学）
Due to the intensive cost of labor and expertise in annotating 3D medical images at a voxel level, most benchmark datasets are equipped with the annotations of only one type of organs and/or tumors, resulting in the so-called partially labeling issue. To address this, we propose a dynamic on-demand network (DoDNet) that learns to segment multiple organs and tumors on partially labeled datasets. DoDNet consists of a shared encoder-decoder architecture, a task encoding module, a controller for generating dynamic convolution filters, and a single but dynamic segmentation head. The information of …
Foundation Model-guided Iteratively Prompting and Pseudo-Labeling for Partially Labeled Medical Image Segmentation
Department of Biomedical Engineering, Columbia University（哥伦比亚大学生物医学工程系）；Department of Radiation Oncology, Columbia University Irving Medical Center（哥伦比亚大学欧文医学中心放射肿瘤科）；Data Science Institute, Columbia University（哥伦比亚大学数据科学研究所）；Herbert Irving Comprehensive Cancer Center, Columbia University（哥伦比亚大学赫伯特·欧文综合癌症中心）；Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院放射肿瘤科）
Semantic segmentation is an import task in the medical field to identify the exact extent and orientation of significant structures like organs and pathology. Deep neural networks can perform this task well by leveraging the information from a large well-labeled data-set. This paper aims to present a method that mitigates the necessity of an extensive well-labeled data-set. This method also addresses semi-supervision by enabling segmentation based on bounding box annotations, avoiding the need for full pixel-level annotations. The network presented consists of a single U-Net based unbranched a…
Xiamen University（厦门大学）；Chinese PLA General Hospital（中国人民解放军总医院）；Deepwise AI Laboratory（深度智耀人工智能实验室）
Standard segmentation of medical images based on full-supervised convolutional networks demands accurate dense annotations. Such learning framework is built on laborious manual annotation with restrict demands for expertise, leading to insufficient high-quality labels. To overcome such limitation and exploit massive weakly labeled data, we relaxed the rigid labeling requirement and developed a semi-supervised learning framework based on a teacher-student fashion for organ and lesion segmentation with partial dense-labeled supervision and supplementary loose bounding-box supervision which are e…
With the tremendous advances of Convolutional Neural Networks (ConvNets) on object recognition, we can now obtain reliable enough machine-labeled annotations easily by predictions from off-the-shelf ConvNets. In this work, we present an abstraction memory based framework for few-shot learning, building upon machine-labeled image annotations. Our method takes some large-scale machine-annotated datasets (e.g., OpenImages) as an external memory bank. In the external memory bank, the information is stored in the memory slots with the form of key-value, where image feature is regarded as key and la…
Ludwig Maximilians University（路德维希-马克西米利安大学）；Technical University Munich（慕尼黑工业大学）
The wide range of research in deep learning-based medical image segmentation pushed the boundaries in a multitude of applications. A clinically relevant problem that received less attention is the handling of scans with irregular anatomy, e.g., after organ resection. State-of-the-art segmentation models often lead to organ hallucinations, i.e., false-positive predictions of organs, which cannot be alleviated by oversampling or post-processing. Motivated by the increasing need to develop robust deep learning models, we propose HALOS for abdominal organ segmentation in MR images that handles cas…
University of Chinese Academy of Sciences（中国科学院大学）；ByteDance Inc（字节跳动公司）；Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所）
Albeit with varying degrees of progress in the field of Semi-Supervised Semantic Segmentation, most of its recent successes are involved in unwieldy models and the lightweight solution is still not yet explored. We find that existing knowledge distillation techniques pay more attention to pixel-level concepts from labeled data, which fails to take more informative cues within unlabeled data into account. Consequently, we offer the first attempt to provide lightweight SSSS models via a novel multi-granularity distillation (MGD) scheme, where multi-granularity is captured from three aspects: i) …
Cooperative Medianet Innovation Center, Shanghai Jiao Tong University（上海交通大学媒体网络协同创新中心）
Annotating multiple organs in 3D medical images is time-consuming and costly. Meanwhile, there exist many single-organ datasets with one specific organ annotated. This paper investigates how to learn a multi-organ segmentation model leveraging a set of binary-labeled datasets. A novel Multi-teacher Single-student Knowledge Distillation (MS-KD) framework is proposed, where the teacher models are pre-trained single-organ segmentation networks, and the student model is a multi-organ segmentation network. Considering that each teacher focuses on different organs, a region-based supervision method,…
Deep Mutual Learning among Partially Labeled Datasets for Multi-Organ Segmentation
Digital Medical Research Center, School of Basic Medical Science, Fudan University（复旦大学基础医学院数字医学研究中心）；Shanghai Key Lab of Medical Image Computing and Computer Assisted Intervention（上海市医学影像计算与计算机辅助介入重点实验室）
Boosting Overlapping Organoid Instance Segmentation Using Pseudo-Label Unmixing and Synthesis-Assisted Learning
School of Biomedical Engineering, Sun Yat-sen University（中山大学生物医学工程学院）；Peng Cheng Laboratory（鹏城实验室）；The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital（深圳大学第一附属医院、深圳第二人民医院）；The Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University（临床医学研究中心、南通大学附属医院、南通大学医学院）；Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences（慈溪生物医学工程研究所、宁波材料技术与工程研究所、中国科学院）
Pelvic floor MRI segmentation based on semi-supervised deep learning
Institute of Medical Technology, Peking University Health Science Center, Peking University（北京大学医学部医学技术研究院，北京大学）；Biomedical Engineering Department, Peking University（北京大学生物医学工程系）；University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University（上海交通大学密西根学院）；School of Electrical and Electronic Engineering, Nanyang Technological University（南洋理工大学电子与电气工程学院）；Department of Mechanical Engineering, University of Michigan（密歇根大学机械工程系）；Department of Obstetrics and Gynecology, University of Michigan（密歇根大学妇产科）
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；Southeast University（东南大学）
Annotating multiple organs in medical images is both costly and time-consuming; therefore, existing multi-organ datasets with labels are often low in sample size and mostly partially labeled, that is, a dataset has a few organs labeled but not all organs. In this paper, we investigate how to learn a single multi-organ segmentation network from a union of such datasets. To this end, we propose two types of novel loss function, particularly designed for this scenario: (i) marginal loss and (ii) exclusion loss. Because the background label for a partially labeled image is, in fact, a `merged' lab…
National University of Sciences and Technology（国家科技大学）；National Center for Artificial Intelligence（国家人工智能中心）
Autonomous surgical procedures, in particular minimal invasive surgeries, are the next frontier for Artificial Intelligence research. However, the existing challenges include precise identification of the human anatomy and the surgical settings, and modeling the environment for training of an autonomous agent. To address the identification of human anatomy and the surgical settings, we propose a deep learning based semantic segmentation algorithm to identify and label the tissues and organs in the endoscopic video feed of the human torso region. We present an annotated dataset, m2caiSeg, creat…
Johns Hopkins University（约翰斯·霍普金斯大学）；University of Oxford（牛津大学）；The Johns Hopkins Medical Institute（约翰斯·霍普金斯医学研究所）；Google AI（谷歌AI）；ByteDance Inc.（字节跳动公司）；Facebook（脸书）；PAII Inc.（PAII公司）
Accurate multi-organ abdominal CT segmentation is essential to many clinical applications such as computer-aided intervention. As data annotation requires massive human labor from experienced radiologists, it is common that training data are partially labeled, e.g., pancreas datasets only have the pancreas labeled while leaving the rest marked as background. However, these background labels can be misleading in multi-organ segmentation since the "background" usually contains some other organs of interest. To address the background ambiguity in these partially-labeled datasets, we propose Prior…
Label-efficient multi-organ segmentation with a diffusion model
College of Big Data and Internet, Shenzhen Technology University（深圳技术大学大数据与互联网学院）；School of Artificial Intelligence, Beijing University of Posts and Telecommunications（北京邮电大学人工智能学院）；Department of Radiology, Beijing Tiantan Hospital, Capital Medical University（首都医科大学附属北京天坛医院放射科）
Samsung AI Center（三星人工智能中心）；Steklov Institute of Mathematics at St. Petersburg（圣彼得堡斯捷克洛夫数学研究所）；Neuromation OU
We present the winning solution for the Inclusive Images Competition organized as part of the Conference on Neural Information Processing Systems (NeurIPS 2018) Competition Track. The competition was organized to study ways to cope with domain shift in image processing, specifically geographical shift: the training and two test sets in the competition had different geographical distributions. Our solution has proven to be relatively straightforward and simple: it is an ensemble of several CNNs where only the last layer is fine-tuned with the help of a small labeled set of tuning labels made av…
University of Guelph（圭尔夫大学）；Vector Institute（向量研究所）
In Digital Pathology (DP), labeled data is generally very scarce due to the requirement that medical experts provide annotations. We address this issue by learning transferable features from weakly labeled data, which are collected from various parts of the body and are organized by non-medical experts. In this paper, we show that features learned from such weakly labeled datasets are indeed transferable and allow us to achieve highly competitive patch classification results on the colorectal cancer (CRC) dataset [1] and the PatchCamelyon (PCam) dataset [2] while using an order of magnitude le…
RPTU Kaiserslautern-Landau（莱茵兰-普法尔茨州凯泽斯劳滕-兰道应用技术大学）；Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）；Heidelberg University（海德堡大学）；German Research Center for Artificial Intelligence (DFKI)（德国人工智能研究中心（DFKI））
Morphological atlases are an important tool in organismal studies, and modern high-throughput Computed Tomography (CT) facilities can produce hundreds of full-body high-resolution volumetric images of organisms. However, creating an atlas from these volumes requires accurate organ segmentation. In the last decade, machine learning approaches have achieved incredible results in image segmentation tasks, but they require large amounts of annotated data for training. In this paper, we propose a self-training framework for multi-organ segmentation in tomographic images of Medaka fish. We utilize t…
Beijing University of Posts and Telecommunications（北京邮电大学）；Guilin University of Electronic Technology（桂林电子科技大学）
Abdominal organ segmentation has many important clinical applications, such as organ quantification, surgical planning, and disease diagnosis. However, manually annotating organs from CT scans is time-consuming and labor-intensive. Semi-supervised learning has shown the potential to alleviate this challenge by learning from a large set of unlabeled images and limited labeled samples. In this work, we follow the self-training strategy and employ a high-performance hybrid architecture (PHTrans) consisting of CNN and Swin Transformer for the teacher model to generate precise pseudo labels for unl…
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…
Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）；University of Tübingen（蒂宾根大学）；Boston University（波士顿大学）
It is well known that semantic segmentation can be used as an effective intermediate representation for learning driving policies. However, the task of street scene semantic segmentation requires expensive annotations. Furthermore, segmentation algorithms are often trained irrespective of the actual driving task, using auxiliary image-space loss functions which are not guaranteed to maximize driving metrics such as safety or distance traveled per intervention. In this work, we seek to quantify the impact of reducing segmentation annotation costs on learned behavior cloning agents. We analyze s…
Memorial Sloan Kettering Cancer Center（纪念斯隆-凯特琳癌症中心）
Our contribution is a unified cross-modality feature disentagling approach for multi-domain image translation and multiple organ segmentation. Using CT as the labeled source domain, our approach learns to segment multi-modal (T1-weighted and T2-weighted) MRI having no labeled data. Our approach uses a variational auto-encoder (VAE) to disentangle the image content from style. The VAE constrains the style feature encoding to match a universal prior (Gaussian) that is assumed to span the styles of all the source and target modalities. The extracted image style is converted into a latent style sc…
Armed Forces Yangju Hospital（杨州武装部队医院）；Seoul National University（首尔国立大学）
For more clinical applications of deep learning models for medical image segmentation, high demands on labeled data and computational resources must be addressed. This study proposes a coarse-to-fine framework with two teacher models and a student model that combines knowledge distillation and cross teaching, a consistency regularization based on pseudo-labels, for efficient semi-supervised learning. The proposed method is demonstrated on the abdominal multi-organ segmentation task in CT images under the MICCAI FLARE 2022 challenge, with mean Dice scores of 0.8429 and 0.8520 in the validation …
Deep networks have achieved excellent results in perceptual tasks, yet their ability to generalize to variations not seen during training has come under increasing scrutiny. In this work we focus on their ability to have invariance towards the presence or absence of details. For example, humans are able to watch cartoons, which are missing many visual details, without being explicitly trained to do so. As another example, 3D rendering software is a relatively recent development, yet people are able to understand such rendered scenes even though they are missing details (consider a film like To…
Nuclei segmentation is a fundamental task that is critical for various computational pathology applications including nuclei morphology analysis, cell type classification, and cancer grading. Conventional vision-based methods for nuclei segmentation struggle in challenging cases and deep learning approaches have proven to be more robust and generalizable. However, CNNs require large amounts of labeled histopathology data. Moreover, conventional CNN-based approaches lack structured prediction capabilities which are required to distinguish overlapping and clumped nuclei. Here, we present an appr…
Federated Learning with Partially Labeled Data: A Conditional Distillation Approach
Department of Computer Science and Information Engineering, National Taiwan University（计算机科学与信息工程系，国立台湾大学）；Graduate School of Informatics, Nagoya University（资讯研究生院，名古屋大学）；Institute of Applied Mathematical Sciences, National Taiwan University（应用数学科学研究所，国立台湾大学）；NVIDIA Corporation（NVIDIA公司）
Duke University School of Medicine（杜克大学医学院）；Duke University（杜克大学）；Universitat de Girona（赫罗纳大学）；Université de Bourgogne（勃艮第大学）；Università degli studi di Cassino（卡西诺大学）
Organ segmentation of medical images is a key step in virtual imaging trials. However, organ segmentation datasets are limited in terms of quality (because labels cover only a few organs) and quantity (since case numbers are limited). In this study, we explored the tradeoffs between quality and quantity. Our goal is to create a unified approach for multi-organ segmentation of body CT, which will facilitate the creation of large numbers of accurate virtual phantoms. Initially, we compared two segmentation architectures, 3D-Unet and DenseVNet, which were trained using XCAT data that is fully lab…
Aligning Machine and Human Visual Representations across Abstraction Levels
Google DeepMind Machine Learning Group（谷歌DeepMind机器学习组）；Technische Universität Berlin（技术大学柏林）；BIFOLD；Berlin Institute for the Foundations of Learning and Data（柏林学习与数据基础研究所）；Max Planck Institute for Human Cognitive and Brain Sciences（人类认知与脑科学Max Planck研究所）；Max Planck Institute for Human Development（人类发展Max Planck研究所）；TUD Dresden University of Technology（德累斯顿技术大学）；Anthropic；Department of Artificial Intelligence, Korea University（人工智能系，韩国大学）；Max Planck Institute for Informatics（信息Max Planck研究所）
University of Florence（佛罗伦萨大学）；University of Siena（锡耶纳大学）
Multi-organ segmentation of X-ray images is of fundamental importance for computer aided diagnosis systems. However, the most advanced semantic segmentation methods rely on deep learning and require a huge amount of labeled images, which are rarely available due to both the high cost of human resources and the time required for labeling. In this paper, we present a novel multi-stage generation algorithm based on Generative Adversarial Networks (GANs) that can produce synthetic images along with their semantic labels and can be used for data augmentation. The main feature of the method is that,…
Two-Stage Hybrid Supervision Framework for Fast, Low-resource, and Accurate Organ and Pan-cancer Segmentation in Abdomen CT
Beijing University of Posts and Telecommunications（北京邮电大学）；Dalian University of Technology（大连理工大学）；Guilin University of Electronic Technology（桂林电子科技大学）
Multi-organ segmentation: a progressive exploration of learning paradigms under scarce annotation
School of Basic Medical Science, Fudan University（复旦大学基础医学院）；Digital Medical Research Center（数字医学研究中心）；Shanghai Key Lab of Medical Image Computing and Computer Assisted Intervention（上海市医学影像计算与计算机辅助介入重点实验室）
Centrum Wiskunde & Informatica（荷兰国家数学与计算机科学研究所）；Xomnia B.V.（Xomnia公司）；Erasmus University Medical Center（伊拉斯谟大学医学中心）；Delft University of Technology（代尔夫特理工大学）；Leiden University Medical Center（莱顿大学医学中心）
Deep learning models benefit from training with a large dataset (labeled or unlabeled). Following this motivation, we present an approach to learn a deep learning model for the automatic segmentation of Organs at Risk (OARs) in cervical cancer radiation treatment from a large clinically available dataset of Computed Tomography (CT) scans containing data inhomogeneity, label noise, and missing annotations. We employ simple heuristics for automatic data cleaning to minimize data inhomogeneity and label noise. Further, we develop a semi-supervised learning approach utilizing a teacher-student set…
The First Affiliated Hospital of Anhui Medical University（安徽医科大学第一附属医院）；Huawei Cloud Computing Technology Co. Ltd（华为云计算技术有限公司）；University of Science and Technology of China（中国科学技术大学）
There exists a large number of datasets for organ segmentation, which are partially annotated and sequentially constructed. A typical dataset is constructed at a certain time by curating medical images and annotating the organs of interest. In other words, new datasets with annotations of new organ categories are built over time. To unleash the potential behind these partially labeled, sequentially-constructed datasets, we propose to incrementally learn a multi-organ segmentation model. In each incremental learning (IL) stage, we lose the access to previous data and annotations, whose knowledg…
University of Texas Southwestern Medical Center（德克萨斯大学西南医学中心）
Data cleaning consumes about 80% of the time spent on data analysis for clinical research projects. This is a much bigger problem in the era of big data and machine learning in the field of medicine where large volumes of data are being generated. We report an initial effort towards automated patient data cleaning using deep learning: the standardization of organ labeling in radiation therapy. Organs are often labeled inconsistently at different institutions (sometimes even within the same institution) and at different time periods, which poses a problem for clinical research, especially for m…
