ASLseg: Adapting SAM in the Loop for Semi-supervised Liver Tumor Segmentation
Southern University of Science and Technology（南方科技大学）；The University of Hong Kong（香港大学）；Jiaxing Research Institute, Southern University of Science and Technology（南方科技大学嘉兴研究院）
Liver tumor segmentation is essential for computer-aided diagnosis, surgical planning, and prognosis evaluation. However, obtaining and maintaining a large-scale dataset with dense annotations is challenging. Semi-Supervised Learning (SSL) is a common technique to address these challenges. Recently, Segment Anything Model (SAM) has shown promising performance in some medical image segmentation tasks, but it performs poorly for liver tumor segmentation. In this paper, we propose a novel semi-supervised framework, named ASLseg, which can effectively adapt the SAM to the SSL setting and combine both domain-specific and general knowledge of liver tumors. Specifically, the segmentation model trained with a specific SSL paradigm provides the generated pseudo-labels as prompts to the fine-tuned SAM. An adaptation network is then used to refine the SAM-predictions and generate higher-quality pseudo-labels. Finally, the reliable pseudo-labels are selected to expand the labeled set for iterative training. Extensive experiments on the LiTS dataset demonstrate overwhelming performance of our ASLseg.
Massachusetts Institute of Technology（麻省理工学院）；Harvard University（哈佛大学）；Howard Hughes Medical Institute（霍华德·休斯医学研究所）
Global eradication of malaria depends on the development of drugs effective against the silent, yet obligate liver stage of the disease. The gold standard in drug development remains microscopic imaging of liver stage parasites in in vitro cell culture models. Image analysis presents a major bottleneck in this pipeline since the parasite has significant variability in size, shape, and density in these models. As with other highly variable datasets, traditional segmentation models have poor generalizability as they rely on hand-crafted features; thus, manual annotation of liver stage malaria im…
The success of supervised lesion segmentation algorithms using Computed Tomography (CT) exams depends significantly on the quantity and variability of samples available for training. While annotating such data constitutes a challenge itself, the variability of lesions in the dataset also depends on the prevalence of different types of lesions. This phenomenon adds an inherent bias to lesion segmentation algorithms that can be diminished, among different possibilities, using aggressive data augmentation methods. In this paper, we present a method for implanting realistic lesions in CT slices to…
Washington State University（华盛顿州立大学）；M.D. Anderson Cancer Center, University of Texas（德克萨斯大学MD安德森癌症中心）
Tumor detection in biomedical imaging is a time-consuming process for medical professionals and is not without errors. Thus in recent decades, researchers have developed algorithmic techniques for image processing using a wide variety of mathematical methods, such as statistical modeling, variational techniques, and machine learning. In this paper, we propose a semi-automatic method for liver segmentation of 2D CT scans into three labels denoting healthy, vessel, or tumor tissue based on graph cuts. First, we create a feature vector for each pixel in a novel way that consists of the 59 intensi…
Parameter-Efficient 3D Segmentation of Liver and Liver tumors: Depthwise factorization Scales Better Than Dense Convolution with Spatial Dimensionality
Indian Institute of Technology, Madras（马德拉斯印度理工学院）
In this paper we propose a fully automatic 2-stage cascaded approach for segmentation of liver and its tumors in CT (Computed Tomography) images using densely connected fully convolutional neural network (DenseNet). We independently train liver and tumor segmentation models and cascade them for a combined segmentation of the liver and its tumor. The first stage involves segmentation of liver and the second stage uses the first stage's segmentation results for localization of liver and henceforth tumor segmentations inside liver region. The liver model was trained on the down-sampled axial slic…
Automatic segmentation of liver and its tumors is an essential step for extracting quantitative imaging biomarkers for accurate tumor detection, diagnosis, prognosis and assessment of tumor response to treatment. MICCAI 2017 Liver Tumor Segmentation Challenge (LiTS) provides a common platform for comparing different automatic algorithms on contrast-enhanced abdominal CT images in tasks including 1) liver segmentation, 2) liver tumor segmentation, and 3) tumor burden estimation. We participate this challenge by developing a hierarchical framework based on deep fully convolutional-deconvolutiona…
Stony Brook University（石溪大学）；University of Brasília（巴西利亚大学）；Emory University（埃默里大学）
An accurate steatosis quantification with pathology tissue samples is of high clinical importance. However, such pathology measurement is manually made in most clinical practices, subject to severe reader variability due to large sampling bias and poor reproducibility. Although some computerized automated methods are developed to quantify the steatosis regions, they present limited analysis capacity for high resolution whole-slide microscopy images and accurate overlapped steatosis division. In this paper, we propose a method that extracts an individual whole tissue piece at high resolution wi…
Parameter-Efficient Fine-Tuning of Foundation Models for Liver Tumor Segmentation in CT
University Health Network（大学健康网络）；Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）；University of Alberta（阿尔伯塔大学）；Alberta Machine Intelligence Institute（阿尔伯塔机器智能研究所）；Islamic Azad University（伊斯兰阿扎德大学）
Johns Hopkins University（约翰斯·霍普金斯大学）；NVIDIA（英伟达）；University of Florida（佛罗里达大学）；The Chinese University of Hong Kong（香港中文大学）
While making a tremendous impact in various fields, deep neural networks usually require large amounts of labeled data for training which are expensive to collect in many applications, especially in the medical domain. Unlabeled data, on the other hand, is much more abundant. Semi-supervised learning techniques, such as co-training, could provide a powerful tool to leverage unlabeled data. In this paper, we propose a novel framework, uncertainty-aware multi-view co-training (UMCT), to address semi-supervised learning on 3D data, such as volumetric data from medical imaging. In our work, co-tra…
Johns Hopkins University（约翰斯·霍普金斯大学）；PAII Inc.（PAII公司）；The First Affiliated Hospital of Nanjing Medical University（南京医科大学第一附属医院）；Ping An Technology（平安科技）；Shanghai Jiao Tong University（上海交通大学）
The boundary of tumors (hepatocellular carcinoma, or HCC) contains rich semantics: capsular invasion, visibility, smoothness, folding and protuberance, etc. Capsular invasion on tumor boundary has proven to be clinically correlated with the prognostic indicator, microvascular invasion (MVI). Investigating tumor boundary semantics has tremendous clinical values. In this paper, we propose the first and novel computational framework that disentangles the task into two components: spatial vertex localization and sequential semantic classification. (1) A HCC tumor segmentor is built for tumor mask …
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…
University of Bristol（布里斯托大学）；Chulalongkorn University（朱拉隆功大学）
Identification of abnormalities in red blood cells (RBC) is key to diagnosing a range of medical conditions from anaemia to liver disease. Currently this is done manually, a time-consuming and subjective process. This paper presents an automated process utilising the advantages of machine learning to increase capacity and standardisation of cell abnormality detection, and its performance is analysed. Three different machine learning technologies were used: a Support Vector Machine (SVM), a classical machine learning technology; TabNet, a deep learning architecture for tabular data; U-Net, a se…
Live(r) Die: Predicting Survival in Colorectal Liver Metastasis
Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada（多伦多大学医学生物物理学系）；Department of Medical Imaging, University of Toronto, Toronto, ON, Canada（多伦多大学医学影像学系）；Sunnybrook Research Institute, Toronto, ON, Canada（辛普森研究学院）
In this paper we present a new method for motion tracking of tumors in liver ultrasound image sequences. Our algorithm has two main steps. In the first step, we apply mean shift algorithm with multiple features to estimate the center of the target in each frame. Target in the first frame is defined using an ellipse. Edge, texture, and intensity features are extracted from the first frame, and then mean shift algorithm is applied to each feature separately to find the center of ellipse related to that feature in the next frame. The center of ellipse will be the weighted average of these centers…
The University of Hong Kong（香港大学）；The University of Hong Kong-Shenzhen Hospital（香港大学深圳医院）
In this work, we propose a new segmentation network by integrating DenseUNet and bidirectional LSTM together with attention mechanism, termed as DA-BDense-UNet. DenseUNet allows learning enough diverse features and enhancing the representative power of networks by regulating the information flow. Bidirectional LSTM is responsible to explore the relationships between the encoded features and the up-sampled features in the encoding and decoding paths. Meanwhile, we introduce attention gates (AG) into DenseUNet to diminish responses of unrelated background regions and magnify responses of salient…
Liver segmentation on images acquired using computed tomography (CT) and magnetic resonance imaging (MRI) plays an important role in clinical management of liver diseases. Compared to MRI, CT images of liver are more abundant and readily available. However, MRI can provide richer quantitative information of the liver compared to CT. Thus, it is desirable to achieve unsupervised domain adaptation for transferring the learned knowledge from the source domain containing labeled CT images to the target domain containing unlabeled MR images. In this work, we report a novel unsupervised domain adapt…
Spectral Adapters for Segment Anything Model-based Segmentation of Colorectal Liver Metastases in Computed Tomography
Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）；University of Alberta（阿尔伯塔大学）；Alberta Machine Intelligence Institute（阿尔伯塔机器智能研究所）；The University of Texas MD Anderson Cancer Center（德克萨斯大学MD安德森癌症中心）；Toronto General Hospital Research Institute, University Health Network（大学健康网络多伦多总医院研究所）
Zhejiang University（浙江大学）；University of Science and Technology of China（中国科学技术大学）；Zhejiang Lab（之江实验室）；Ritsumeikan University（立命馆大学）；Sir Run Run Shaw Hospital（邵逸夫医院）；The First Affiliated Hospital, College of Medicine, Zhejiang University（浙江大学医学院附属第一医院）
Multi-phase computed tomography (CT) images provide crucial complementary information for accurate liver tumor segmentation (LiTS). State-of-the-art multi-phase LiTS methods usually fused cross-phase features through phase-weighted summation or channel-attention based concatenation. However, these methods ignored the spatial (pixel-wise) relationships between different phases, hence leading to insufficient feature integration. In addition, the performance of existing methods remains subject to the uncertainty in segmentation, which is particularly acute in tumor boundary regions. In this work,…
An Automated Radiomics Framework for Postoperative Survival Prediction in Colorectal Liver Metastases using Preoperative MRI
Department of Medical Biophysics, University of Toronto（多伦多大学医学生物物理学系）；Physical Sciences Platform, Sunnybrook Research Institute（阳光医疗研究学院物理科学平台）；UCL Cancer Institute, University College London（伦敦大学学院癌症研究所）；Systems and Biomedical Engineering Department, Cairo University（开罗大学系统与生物医学工程系）；Department of Surgery, University of Toronto（多伦多大学外科医学系）；Department of Laboratory Medicine and Pathobiology, University of Toronto（多伦多大学实验室医学与病理学系）；Sunnybrook Health Sciences Centre（阳光健康科学中心）；Department of Medical Imaging, University of Toronto（多伦多大学医学影像学系）
College of Engineering, Qatar University（卡塔尔大学工程学院）；Hamad Medical Corporation（哈马德医疗公司）
Machine learning and computer vision techniques have influenced many fields including the biomedical one. The aim of this paper is to investigate the important concept of schedulers in manipulating the learning rate (LR), for the liver segmentation task, throughout the training process, focusing on the newly devised OneCycleLR against the ReduceLRonPlateau. A dataset, published in 2018 and produced by the Medical Segmentation Decathlon Challenge organizers, called Task 8 Hepatic Vessel (MSDC-T8) has been used for testing and validation. The reported results that have the same number of maximum…
Comparative Study of UNet-based Architectures for Liver Tumor Segmentation in Multi-Phase Contrast-Enhanced Computed Tomography
School of Computer Science and Engineering（计算机科学与工程学院）；The Saigon International University（暹罗国际大学）；School of Biomedical Engineering（生物医学工程学院）；International University（国际大学）；Vietnam National University HCMC（越南国家大学胡志明市分校）
LMU München（慕尼黑大学）；University of Tübingen（图宾根大学）；University Freiburg（弗莱堡大学）；Helmholtz Zentrum München（慕尼黑亥姆霍兹中心）
Image segmentation enables to extract quantitative measures from scans that can serve as imaging biomarkers for diseases. However, segmentation quality can vary substantially across scans, and therefore yield unfaithful estimates in the follow-up statistical analysis of biomarkers. The core problem is that segmentation and biomarker analysis are performed independently. We propose to propagate segmentation uncertainty to the statistical analysis to account for variations in segmentation confidence. To this end, we evaluate four Bayesian neural networks to sample from the posterior distribution…
University of Science and Technology of China（中国科学技术大学）；University of Miami（迈阿密大学）；the First Affiliated Hospital of USTC（中国科学技术大学附属第一医院）
Automatic deep learning segmentation models has been shown to improve both the segmentation efficiency and the accuracy. However, training a robust segmentation model requires considerably large labeled training samples, which may be impractical. This study aimed to develop a deep learning framework for generating synthetic lesions that can be used to enhance network training. The lesion synthesis network is a modified generative adversarial network (GAN). Specifically, we innovated a partial convolution strategy to construct an Unet-like generator. The discriminator is designed using Wasserst…
SIAT, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）；The Chinese University of Hong Kong（香港中文大学）
Purpose: Segmentation of liver vessels from CT images is indispensable prior to surgical planning and aroused broad range of interests in the medical image analysis community. Due to the complex structure and low contrast background, automatic liver vessel segmentation remains particularly challenging. Most of the related researches adopt FCN, U-net, and V-net variants as a backbone. However, these methods mainly focus on capturing multi-scale local features which may produce misclassified voxels due to the convolutional operator's limited locality reception field. Methods: We propose a robust…
Ecole Polytechnique de Montreal（蒙特利尔综合理工学院）；Mila（米拉（Mila）人工智能研究院）；NVIDIA Corporation（英伟达公司）；Centre hospitalier de l’Université de Montréal（蒙特利尔大学医疗中心）
Often in medical imaging, it is prohibitively challenging to produce enough boundary annotations to train deep neural networks for accurate tumor segmentation. We propose the use of weak labels about whether an image presents tumor or whether it is absent to extend training over images that lack these annotations. Specifically, we propose a semi-supervised framework that employs unpaired image-to-image translation between two domains, presence vs. absence of cancer, as the unsupervised objective. We conjecture that translation helps segmentation -- both require the target to be separated from …
Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Shandong University（山东大学）；Beijing University of Chinese Medicine（北京中医药大学）
The Chinese University of Hong Kong（香港中文大学）；Stanford University（斯坦福大学）
Deep convolutional neural networks have achieved remarkable progress on a variety of medical image computing tasks. A common problem when applying supervised deep learning methods to medical images is the lack of labeled data, which is very expensive and time-consuming to be collected. In this paper, we present a novel semi-supervised method for medical image segmentation, where the network is optimized by the weighted combination of a common supervised loss for labeled inputs only and a regularization loss for both labeled and unlabeled data. To utilize the unlabeled data, our method encourag…
BreastSegNet: Multi-label Segmentation of Breast MRI
Department of Biostatistics \& Bioinformatics, Duke University Department of Electrical；Computer Engineering, Duke University Department of Radiology, Duke University Medical Center Department of Computer Science, Duke University
University of Alberta（阿尔伯塔大学）；Alberta Machine Intelligence Institute（阿尔伯塔机器智能研究所）；National University of Singapore（新加坡国立大学）
Deep learning approaches often require huge datasets to achieve good generalization. This complicates its use in tasks like image-based medical diagnosis, where the small training datasets are usually insufficient to learn appropriate data representations. For such sensitive tasks it is also important to provide the confidence in the predictions. Here, we propose a way to learn and use probabilistic labels to train accurate and calibrated deep networks from relatively small datasets. We observe gains of up to 22% in the accuracy of models trained with these labels, as compared with traditional…
