arXiv subjects

Yubo Fan

Publications and source records attributed to Yubo Fan.

At least 37 records · Page 2Linked to original sources

arXiv2022

Enhancing Data Diversity for Self-training Based Unsupervised Cross-modality Vestibular Schwannoma and Cochlea Segmentation

Automatic segmentation of vestibular schwannoma (VS) and cochlea from magnetic resonance imaging can facilitate VS treatment planning. Unsupervised segmentation methods have shown promising results without requiring the time-consuming and laborious manual labeling process. In this paper, we present an approach for VS and cochlea segmentation in an unsupervised domain adaptation setting. Specifically, we first develop a cross-site cross-modality unpaired image translation strategy to enrich the diversity of the synthesized data. Then, we devise a rule-based offline augmentation technique to further minimize the domain gap. Lastly, we adopt a self-configuring segmentation framework empowered by self-training to obtain the final results. On the CrossMoDA 2022 validation leaderboard, our method has achieved competitive VS and cochlea segmentation performance with mean Dice scores of 0.8178 $\pm$ 0.0803 and 0.8433 $\pm$ 0.0293, respectively.

cs.CV↗

arXiv2022

Adaptive Contrastive Learning with Dynamic Correlation for Multi-Phase Organ Segmentation

Recent studies have demonstrated the superior performance of introducing ``scan-wise" contrast labels into contrastive learning for multi-organ segmentation on multi-phase computed tomography (CT). However, such scan-wise labels are limited: (1) a coarse classification, which could not capture the fine-grained ``organ-wise" contrast variations across all organs; (2) the label (i.e., contrast phase) is typically manually provided, which is error-prone and may introduce manual biases of defining phases. In this paper, we propose a novel data-driven contrastive loss function that adapts the similar/dissimilar contrast relationship between samples in each minibatch at organ-level. Specifically, as variable levels of contrast exist between organs, we hypothesis that the contrast differences in the organ-level can bring additional context for defining representations in the latent space. An organ-wise contrast correlation matrix is computed with mean organ intensities under one-hot attention maps. The goal of adapting the organ-driven correlation matrix is to model variable levels of feature separability at different phases. We evaluate our proposed approach on multi-organ segmentation with both non-contrast CT (NCCT) datasets and the MICCAI 2015 BTCV Challenge contrast-enhance CT (CECT) datasets. Compared to the state-of-the-art approaches, our proposed contrastive loss yields a substantial and significant improvement of 1.41% (from 0.923 to 0.936, p-value$<$0.01) and 2.02% (from 0.891 to 0.910, p-value$<$0.01) on mean Dice scores across all organs with respect to NCCT and CECT cohorts. We further assess the trained model performance with the MICCAI 2021 FLARE Challenge CECT datasets and achieve a substantial improvement of mean Dice score from 0.927 to 0.934 (p-value$<$0.01). The code is available at: https://github.com/MASILab/DCC_CL

cs.CV↗

arXiv2022

ModDrop++: A Dynamic Filter Network with Intra-subject Co-training for Multiple Sclerosis Lesion Segmentation with Missing Modalities

Multiple Sclerosis (MS) is a chronic neuroinflammatory disease and multi-modality MRIs are routinely used to monitor MS lesions. Many automatic MS lesion segmentation models have been developed and have reached human-level performance. However, most established methods assume the MRI modalities used during training are also available during testing, which is not guaranteed in clinical practice. Previously, a training strategy termed Modality Dropout (ModDrop) has been applied to MS lesion segmentation to achieve the state-of-the-art performance with missing modality. In this paper, we present a novel method dubbed ModDrop++ to train a unified network adaptive to an arbitrary number of input MRI sequences. ModDrop++ upgrades the main idea of ModDrop in two key ways. First, we devise a plug-and-play dynamic head and adopt a filter scaling strategy to improve the expressiveness of the network. Second, we design a co-training strategy to leverage the intra-subject relation between full modality and missing modality. Specifically, the intra-subject co-training strategy aims to guide the dynamic head to generate similar feature representations between the full- and missing-modality data from the same subject. We use two public MS datasets to show the superiority of ModDrop++. Source code and trained models are available at https://github.com/han-liu/ModDropPlusPlus.

eess.IV↗

arXiv2022

Transformer based multiple instance learning for weakly supervised histopathology image segmentation

Hispathological image segmentation algorithms play a critical role in computer aided diagnosis technology. The development of weakly supervised segmentation algorithm alleviates the problem of medical image annotation that it is time-consuming and labor-intensive. As a subset of weakly supervised learning, Multiple Instance Learning (MIL) has been proven to be effective in segmentation. However, there is a lack of related information between instances in MIL, which limits the further improvement of segmentation performance. In this paper, we propose a novel weakly supervised method for pixel-level segmentation in histopathology images, which introduces Transformer into the MIL framework to capture global or long-range dependencies. The multi-head self-attention in the Transformer establishes the relationship between instances, which solves the shortcoming that instances are independent of each other in MIL. In addition, deep supervision is introduced to overcome the limitation of annotations in weakly supervised methods and make the better utilization of hierarchical information. The state-of-the-art results on the colon cancer dataset demonstrate the superiority of the proposed method compared with other weakly supervised methods. It is worth believing that there is a potential of our approach for various applications in medical images.

cs.CV↗

arXiv2022

3D Segmentation Guided Style-based Generative Adversarial Networks for PET Synthesis

Potential radioactive hazards in full-dose positron emission tomography (PET) imaging remain a concern, whereas the quality of low-dose images is never desirable for clinical use. So it is of great interest to translate low-dose PET images into full-dose. Previous studies based on deep learning methods usually directly extract hierarchical features for reconstruction. We notice that the importance of each feature is different and they should be weighted dissimilarly so that tiny information can be captured by the neural network. Furthermore, the synthesis on some regions of interest is important in some applications. Here we propose a novel segmentation guided style-based generative adversarial network (SGSGAN) for PET synthesis. (1) We put forward a style-based generator employing style modulation, which specifically controls the hierarchical features in the translation process, to generate images with more realistic textures. (2) We adopt a task-driven strategy that couples a segmentation task with a generative adversarial network (GAN) framework to improve the translation performance. Extensive experiments show the superiority of our overall framework in PET synthesis, especially on those regions of interest.

eess.IV↗

arXiv2022

Unsupervised Domain Adaptation for Vestibular Schwannoma and Cochlea Segmentation via Semi-supervised Learning and Label Fusion

Automatic methods to segment the vestibular schwannoma (VS) tumors and the cochlea from magnetic resonance imaging (MRI) are critical to VS treatment planning. Although supervised methods have achieved satisfactory performance in VS segmentation, they require full annotations by experts, which is laborious and time-consuming. In this work, we aim to tackle the VS and cochlea segmentation problem in an unsupervised domain adaptation setting. Our proposed method leverages both the image-level domain alignment to minimize the domain divergence and semi-supervised training to further boost the performance. Furthermore, we propose to fuse the labels predicted from multiple models via noisy label correction. In the MICCAI 2021 crossMoDA challenge, our results on the final evaluation leaderboard showed that our proposed method has achieved promising segmentation performance with mean dice score of 79.9% and 82.5% and ASSD of 1.29 mm and 0.18 mm for VS tumor and cochlea, respectively. The cochlea ASSD achieved by our method has outperformed all other competing methods as well as the supervised nnU-Net.

cs.CV↗

arXiv2021

Cross-Modality Domain Adaptation for Vestibular Schwannoma and Cochlea Segmentation

Automatic methods to segment the vestibular schwannoma (VS) tumors and the cochlea from magnetic resonance imaging (MRI) are critical to VS treatment planning. Although supervised methods have achieved satisfactory performance in VS segmentation, they require full annotations by experts, which is laborious and time-consuming. In this work, we aim to tackle the VS and cochlea segmentation problem in an unsupervised domain adaptation setting. Our proposed method leverages both the image-level domain alignment to minimize the domain divergence and semi-supervised training to further boost the performance. Furthermore, we propose to fuse the labels predicted from multiple models via noisy label correction. Our results on the challenge validation leaderboard showed that our unsupervised method has achieved promising VS and cochlea segmentation performance with mean dice score of 0.8261 $\pm$ 0.0416; The mean dice value for the tumor is 0.8302 $\pm$ 0.0772. This is comparable to the weakly-supervised based method.

eess.IV↗

arXiv2021

Atlas-Based Segmentation of Intracochlear Anatomy in Metal Artifact Affected CT Images of the Ear with Co-trained Deep Neural Networks

We propose an atlas-based method to segment the intracochlear anatomy (ICA) in the post-implantation CT (Post-CT) images of cochlear implant (CI) recipients that preserves the point-to-point correspondence between the meshes in the atlas and the segmented volumes. To solve this problem, which is challenging because of the strong artifacts produced by the implant, we use a pair of co-trained deep networks that generate dense deformation fields (DDFs) in opposite directions. One network is tasked with registering an atlas image to the Post-CT images and the other network is tasked with registering the Post-CT images to the atlas image. The networks are trained using loss functions based on voxel-wise labels, image content, fiducial registration error, and cycle-consistency constraint. The segmentation of the ICA in the Post-CT images is subsequently obtained by transferring the predefined segmentation meshes of the ICA in the atlas image to the Post-CT images using the corresponding DDFs generated by the trained registration networks. Our model can learn the underlying geometric features of the ICA even though they are obscured by the metal artifacts. We show that our end-to-end network produces results that are comparable to the current state of the art (SOTA) that relies on a two-steps approach that first uses conditional generative adversarial networks to synthesize artifact-free images from the Post-CT images and then uses an active shape model-based method to segment the ICA in the synthetic images. Our method requires a fraction of the time needed by the SOTA, which is important for end-user acceptance.

eess.IV↗

arXiv2018

Unsupervised Learning for Cell-level Visual Representation in Histopathology Images with Generative Adversarial Networks

The visual attributes of cells, such as the nuclear morphology and chromatin openness, are critical for histopathology image analysis. By learning cell-level visual representation, we can obtain a rich mix of features that are highly reusable for various tasks, such as cell-level classification, nuclei segmentation, and cell counting. In this paper, we propose a unified generative adversarial networks architecture with a new formulation of loss to perform robust cell-level visual representation learning in an unsupervised setting. Our model is not only label-free and easily trained but also capable of cell-level unsupervised classification with interpretable visualization, which achieves promising results in the unsupervised classification of bone marrow cellular components. Based on the proposed cell-level visual representation learning, we further develop a pipeline that exploits the varieties of cellular elements to perform histopathology image classification, the advantages of which are demonstrated on bone marrow datasets.

cs.CV↗

arXiv2018

Unsupervised End-to-end Learning for Deformable Medical Image Registration

We propose a registration algorithm for 2D CT/MRI medical images with a new unsupervised end-to-end strategy using convolutional neural networks. The contributions of our algorithm are threefold: (1) We transplant traditional image registration algorithms to an end-to-end convolutional neural network framework, while maintaining the unsupervised nature of image registration problems. The image-to-image integrated framework can simultaneously learn both image features and transformation matrix for registration. (2) Training with additional data without any label can further improve the registration performance by approximately 10 %. (3) The registration speed is 100x faster than traditional methods. The proposed network is easy to implement and can be trained efficiently. Experiments demonstrate that our system achieves state-of-the-art results on 2D brain registration and achieves comparable results on 2D liver registration. It can be extended to register other organs beyond liver and brain such as kidney, lung, and heart.

cs.CV↗

arXiv2017

Gland Instance Segmentation Using Deep Multichannel Neural Networks

Objective: A new image instance segmentation method is proposed to segment individual glands (instances) in colon histology images. This process is challenging since the glands not only need to be segmented from a complex background, they must also be individually identified. Methods: We leverage the idea of image-to-image prediction in recent deep learning by designing an algorithm that automatically exploits and fuses complex multichannel information - regional, location, and boundary cues - in gland histology images. Our proposed algorithm, a deep multichannel framework, alleviates heavy feature design due to the use of convolutional neural networks and is able to meet multifarious requirements by altering channels. Results: Compared with methods reported in the 2015 MICCAI Gland Segmentation Challenge and other currently prevalent instance segmentation methods, we observe state-of-the-art results based on the evaluation metrics. Conclusion: The proposed deep multichannel algorithm is an effective method for gland instance segmentation. Significance: The generalization ability of our model not only enable the algorithm to solve gland instance segmentation problems, but the channel is also alternative that can be replaced for a specific task.

cs.CV↗

arXiv2017

Sleep Stage Classification Based on Multi-level Feature Learning and Recurrent Neural Networks via Wearable Device

This paper proposes a practical approach for automatic sleep stage classification based on a multi-level feature learning framework and Recurrent Neural Network (RNN) classifier using heart rate and wrist actigraphy derived from a wearable device. The feature learning framework is designed to extract low- and mid-level features. Low-level features capture temporal and frequency domain properties and mid-level features learn compositions and structural information of signals. Since sleep staging is a sequential problem with long-term dependencies, we take advantage of RNNs with Bidirectional Long Short-Term Memory (BLSTM) architectures for sequence data learning. To simulate the actual situation of daily sleep, experiments are conducted with a resting group in which sleep is recorded in resting state, and a comprehensive group in which both resting sleep and non-resting sleep are included.We evaluate the algorithm based on an eight-fold cross validation to classify five sleep stages (W, N1, N2, N3, and REM). The proposed algorithm achieves weighted precision, recall and F1 score of 58.0%, 60.3%, and 58.2% in the resting group and 58.5%, 61.1%, and 58.5% in the comprehensive group, respectively. Various comparison experiments demonstrate the effectiveness of feature learning and BLSTM. We further explore the influence of depth and width of RNNs on performance. Our method is specially proposed for wearable devices and is expected to be applicable for long-term sleep monitoring at home. Without using too much prior domain knowledge, our method has the potential to generalize sleep disorder detection.

stat.ML↗

arXiv2017

Learning Multi-level Features For Sensor-based Human Action Recognition

This paper proposes a multi-level feature learning framework for human action recognition using a single body-worn inertial sensor. The framework consists of three phases, respectively designed to analyze signal-based (low-level), components (mid-level) and semantic (high-level) information. Low-level features capture the time and frequency domain property while mid-level representations learn the composition of the action. The Max-margin Latent Pattern Learning (MLPL) method is proposed to learn high-level semantic descriptions of latent action patterns as the output of our framework. The proposed method achieves the state-of-the-art performances, 88.7%, 98.8% and 72.6% (weighted F1 score) respectively, on Skoda, WISDM and OPP datasets.

cs.CV↗

arXiv2016

Gland Instance Segmentation by Deep Multichannel Neural Networks

In this paper, we propose a new image instance segmentation method that segments individual glands (instances) in colon histology images. This is a task called instance segmentation that has recently become increasingly important. The problem is challenging since not only do the glands need to be segmented from the complex background, they are also required to be individually identified. Here we leverage the idea of image-to-image prediction in recent deep learning by building a framework that automatically exploits and fuses complex multichannel information, regional, location and boundary patterns in gland histology images. Our proposed system, deep multichannel framework, alleviates heavy feature design due to the use of convolutional neural networks and is able to meet multifarious requirement by altering channels. Compared to methods reported in the 2015 MICCAI Gland Segmentation Challenge and other currently prevalent methods of instance segmentation, we observe state-of-the-art results based on a number of evaluation metrics.

cs.CV↗

arXiv2014

Reconstructing human organ cross-sectional imaging along any axis

Cross-sectional imaging of human organ serves as a critical tool to provide diagnostic results of many diseases. Based on a unique body coordinate system, we present a method that we use to reconstruct any cross-sectional imaging of organ regardless of its original section going along which scanning or cutting axis. In clinical medicine, this method enables a patient to undergo only one scanning, and then the doctor can observe the structure of lesion sections along any axis, and it can help find changes of lesions at the same section from different scanning results and thus quantify diagnosis by cross-sectional imaging. Significant progress has thus been made towards quantitative diagnosis cross-sectional imaging.

physics.med-ph↗

arXiv2013

Three-Dimensional Reconstruction of Erythrocyte in the Capillary

The dynamic analysis of erythrocyte deformability is used as an important means for early diagnosis of blood diseases and blood rheology. Yet no effective method is available in terms of three-dimensional reconstruction of erythrocytes in a capillary. In this study, ultrathin serial sections of skeletal muscle tissue are obtained from the ultramicrotome, the tomographic images of an erythrocyte in a capillary are captured by the transmission electron microscope, and then a method to position and restore is devised to demonstrate the physiological relationship between two adjacent tomographic images of an erythrocyte. Both the modeling and the physical verification reveal that this method is effective, which means that it can be used to make three-dimensional reconstruction of an erythrocyte in a capillary. An example of reconstructed deformation of erythrocyte based on the serial ultrathin sections is shown at the end of this paper.

physics.med-ph↗

arXiv2011

Natural gaits of the non-pathological flat foot and high-arched foot

There has been a controversy as to whether or not the non-pathological flat foot and high-arched foot have an effect on human walking activities. The 3D foot scanning system was employed to obtain static footprints from subjects adopting a half-weight-bearing stance. Based upon their footprints, the subjects were divided into two groups: the flat-footed and the high-arched. The plantar pressure measurement system was used to measure and record the subjects' successive natural gaits. Two indices were proposed: distribution of vertical ground reaction force (VGRF) of plantar and the rate of the footprint areas. Using these two indices to compare the natural gaits of the two subject groups, we found that (1) in stance phase, there is a significant difference (p<0.01) in the distributions of VGRF of plantar; (2) in a stride cycle, there is also a significant difference (p<0.01) in the rates of the footprint areas. Our analysis suggests that when walking, the VGRF of the plantar brings greater muscle tension to the flat-footed while a smaller rate of the footprint areas brings greater stability to the high-arched.

physics.med-ph↗

arXiv2010

Bone in vivo: Surface mapping technique

Bone surface mapping technique is proposed on the bases of two kinds of uniqueness of bone in vivo, (i) magnitude of the principal moments of inertia, (ii) the direction cosines of principal axes of inertia relative to inertia reference frame. We choose the principal axes of inertia as the bone coordinate system axes. The geographical marks such as the prime meridian of the bone in vivo are defined and methods such as tomographic reconstruction and boundary development are employed so that the surface of bone in vivo can be mapped. Experimental results show that the surface mapping technique can both reflect the shape and help study the surface changes of bone in vivo. The prospect of such research into the surface shape and changing laws of organ, tissue or cell will be promising.

physics.bio-ph↗