Search Results for author: Wenjia Bai

Found 61 papers, 23 papers with code

DeepMesh: Mesh-based Cardiac Motion Tracking using Deep Learning

no code implementations25 Sep 2023 Qingjie Meng, Wenjia Bai, Declan P O'Regan, and Daniel Rueckert

We propose a novel learning framework, DeepMesh, which propagates a template heart mesh to a subject space and estimates the 3D motion of the heart mesh from CMR images for individual subjects.

Hierarchical Uncertainty Estimation for Medical Image Segmentation Networks

no code implementations16 Aug 2023 Xinyu Bai, Wenjia Bai

Learning a medical image segmentation model is an inherently ambiguous task, as uncertainties exist in both images (noise) and manual annotations (human errors and bias) used for model training.

Image Segmentation Medical Image Segmentation +2

M-FLAG: Medical Vision-Language Pre-training with Frozen Language Models and Latent Space Geometry Optimization

1 code implementation17 Jul 2023 Che Liu, Sibo Cheng, Chen Chen, Mengyun Qiao, Weitong Zhang, Anand Shah, Wenjia Bai, Rossella Arcucci

The proposed method, named Medical vision-language pre-training with Frozen language models and Latent spAce Geometry optimization (M-FLAG), leverages a frozen language model for training stability and efficiency and introduces a novel orthogonality loss to harmonize the latent space geometry.

Image Classification Language Modelling +3

CHeart: A Conditional Spatio-Temporal Generative Model for Cardiac Anatomy

no code implementations30 Jan 2023 Mengyun Qiao, Shuo Wang, Huaqi Qiu, Antonio de Marvao, Declan P. O'Regan, Daniel Rueckert, Wenjia Bai

Two key questions in cardiac image analysis are to assess the anatomy and motion of the heart from images; and to understand how they are associated with non-imaging clinical factors such as gender, age and diseases.

Anatomy Image Segmentation +1

Mesh-based 3D Motion Tracking in Cardiac MRI using Deep Learning

no code implementations5 Sep 2022 Qingjie Meng, Wenjia Bai, Tianrui Liu, Declan P O'Regan, Daniel Rueckert

By developing a differentiable mesh-to-image rasterizer, the method is able to leverage the anatomical shape information from 2D multi-view CMR images for 3D motion estimation.

Motion Estimation

Generative Modelling of the Ageing Heart with Cross-Sectional Imaging and Clinical Data

1 code implementation28 Aug 2022 Mengyun Qiao, Berke Doga Basaran, Huaqi Qiu, Shuo Wang, Yi Guo, Yuanyuan Wang, Paul M. Matthews, Daniel Rueckert, Wenjia Bai

Understanding the morphological and functional changes of the heart during ageing is a key scientific question, the answer to which will help us define important risk factors of cardiovascular disease and monitor disease progression.


Improved post-hoc probability calibration for out-of-domain MRI segmentation

no code implementations4 Aug 2022 Cheng Ouyang, Shuo Wang, Chen Chen, Zeju Li, Wenjia Bai, Bernhard Kainz, Daniel Rueckert

In image segmentation, well-calibrated probabilities allow radiologists to identify regions where model-predicted segmentations are unreliable.

Image Segmentation MRI segmentation +1

Subject-Specific Lesion Generation and Pseudo-Healthy Synthesis for Multiple Sclerosis Brain Images

1 code implementation3 Aug 2022 Berke Doga Basaran, Mengyun Qiao, Paul M. Matthews, Wenjia Bai

In this work, we present a novel foreground-based generative method for modelling the local lesion characteristics that can both generate synthetic lesions on healthy images and synthesize subject-specific pseudo-healthy images from pathological images.

Brain Image Segmentation Data Augmentation +2

MulViMotion: Shape-aware 3D Myocardial Motion Tracking from Multi-View Cardiac MRI

no code implementations29 Jul 2022 Qingjie Meng, Chen Qin, Wenjia Bai, Tianrui Liu, Antonio de Marvao, Declan P O'Regan, Daniel Rueckert

To address this problem, we propose a novel multi-view motion estimation network (MulViMotion), which integrates 2D cine CMR images acquired in short-axis and long-axis planes to learn a consistent 3D motion field of the heart.

Motion Estimation

Generative Myocardial Motion Tracking via Latent Space Exploration with Biomechanics-informed Prior

1 code implementation8 Jun 2022 Chen Qin, Shuo Wang, Chen Chen, Wenjia Bai, Daniel Rueckert

In contrast to most existing approaches which impose explicit generic regularization such as smoothness, in this work we propose a novel method that can implicitly learn an application-specific biomechanics-informed prior and embed it into a neural network-parameterized transformation model.

Image Registration

MaxStyle: Adversarial Style Composition for Robust Medical Image Segmentation

1 code implementation2 Jun 2022 Chen Chen, Zeju Li, Cheng Ouyang, Matt Sinclair, Wenjia Bai, Daniel Rueckert

We propose a novel data augmentation framework called MaxStyle, which maximizes the effectiveness of style augmentation for model OOD performance.

Data Augmentation Image Segmentation +2

Suggestive Annotation of Brain MR Images with Gradient-guided Sampling

no code implementations2 Jun 2022 Chengliang Dai, Shuo Wang, Yuanhan Mo, Elsa Angelini, Yike Guo, Wenjia Bai

We evaluate the framework on two different brain image analysis tasks, namely brain tumour segmentation and whole brain segmentation.

Brain Segmentation Image Segmentation +1

Memory-efficient Segmentation of High-resolution Volumetric MicroCT Images

1 code implementation31 May 2022 YuAn Wang, Laura Blackie, Irene Miguel-Aliaga, Wenjia Bai

In this work, we propose a novel memory-efficient network architecture for 3D high-resolution image segmentation.

Image Segmentation Semantic Segmentation +2

QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results

1 code implementation19 Dec 2021 Raghav Mehta, Angelos Filos, Ujjwal Baid, Chiharu Sako, Richard McKinley, Michael Rebsamen, Katrin Datwyler, Raphael Meier, Piotr Radojewski, Gowtham Krishnan Murugesan, Sahil Nalawade, Chandan Ganesh, Ben Wagner, Fang F. Yu, Baowei Fei, Ananth J. Madhuranthakam, Joseph A. Maldjian, Laura Daza, Catalina Gomez, Pablo Arbelaez, Chengliang Dai, Shuo Wang, Hadrien Reynaud, Yuan-han Mo, Elsa Angelini, Yike Guo, Wenjia Bai, Subhashis Banerjee, Lin-min Pei, Murat AK, Sarahi Rosas-Gonzalez, Ilyess Zemmoura, Clovis Tauber, Minh H. Vu, Tufve Nyholm, Tommy Lofstedt, Laura Mora Ballestar, Veronica Vilaplana, Hugh McHugh, Gonzalo Maso Talou, Alan Wang, Jay Patel, Ken Chang, Katharina Hoebel, Mishka Gidwani, Nishanth Arun, Sharut Gupta, Mehak Aggarwal, Praveer Singh, Elizabeth R. Gerstner, Jayashree Kalpathy-Cramer, Nicolas Boutry, Alexis Huard, Lasitha Vidyaratne, Md Monibor Rahman, Khan M. Iftekharuddin, Joseph Chazalon, Elodie Puybareau, Guillaume Tochon, Jun Ma, Mariano Cabezas, Xavier Llado, Arnau Oliver, Liliana Valencia, Sergi Valverde, Mehdi Amian, Mohammadreza Soltaninejad, Andriy Myronenko, Ali Hatamizadeh, Xue Feng, Quan Dou, Nicholas Tustison, Craig Meyer, Nisarg A. Shah, Sanjay Talbar, Marc-Andre Weber, Abhishek Mahajan, Andras Jakab, Roland Wiest, Hassan M. Fathallah-Shaykh, Arash Nazeri, Mikhail Milchenko1, Daniel Marcus, Aikaterini Kotrotsou, Rivka Colen, John Freymann, Justin Kirby, Christos Davatzikos, Bjoern Menze, Spyridon Bakas, Yarin Gal, Tal Arbel

In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation.

Benchmarking Brain Tumor Segmentation +3

Causality-inspired Single-source Domain Generalization for Medical Image Segmentation

1 code implementation24 Nov 2021 Cheng Ouyang, Chen Chen, Surui Li, Zeju Li, Chen Qin, Wenjia Bai, Daniel Rueckert

In this work, we investigate the single-source domain generalization problem: training a deep network that is robust to unseen domains, under the condition that training data is only available from one source domain, which is common in medical imaging applications.

Data Augmentation Domain Generalization +3

DeepMCAT: Large-Scale Deep Clustering for Medical Image Categorization

no code implementations30 Sep 2021 Turkay Kart, Wenjia Bai, Ben Glocker, Daniel Rueckert

In recent years, the research landscape of machine learning in medical imaging has changed drastically from supervised to semi-, weakly- or unsupervised methods.

Clustering Deep Clustering +1

Joint Motion Correction and Super Resolution for Cardiac Segmentation via Latent Optimisation

no code implementations8 Jul 2021 Shuo Wang, Chen Qin, Nicolo Savioli, Chen Chen, Declan O'Regan, Stuart Cook, Yike Guo, Daniel Rueckert, Wenjia Bai

In cardiac magnetic resonance (CMR) imaging, a 3D high-resolution segmentation of the heart is essential for detailed description of its anatomical structures.

Anatomy Cardiac Segmentation +1

Cooperative Training and Latent Space Data Augmentation for Robust Medical Image Segmentation

2 code implementations2 Jul 2021 Chen Chen, Kerstin Hammernik, Cheng Ouyang, Chen Qin, Wenjia Bai, Daniel Rueckert

In this paper, we present a cooperative framework for training image segmentation models and a latent space augmentation method for generating hard examples.

Data Augmentation Image Reconstruction +3

A General Framework for Revealing Human Mind with auto-encoding GANs

no code implementations10 Feb 2021 Pan Wang, Rui Zhou, Shuo Wang, Ling Li, Wenjia Bai, Jialu Fan, Chunlin Li, Peter Childs, Yike Guo

For this reason, we propose an end-to-end brain decoding framework which translates brain activity into an image by latent space alignment.

Brain Decoding

Suggestive Annotation of Brain Tumour Images with Gradient-guided Sampling

no code implementations26 Jun 2020 Chengliang Dai, Shuo Wang, Yuanhan Mo, Kaichen Zhou, Elsa Angelini, Yike Guo, Wenjia Bai

Machine learning has been widely adopted for medical image analysis in recent years given its promising performance in image segmentation and classification tasks.

BIG-bench Machine Learning Image Segmentation +1

Deep Generative Model-based Quality Control for Cardiac MRI Segmentation

no code implementations23 Jun 2020 Shuo Wang, Giacomo Tarroni, Chen Qin, Yuanhan Mo, Chengliang Dai, Chen Chen, Ben Glocker, Yike Guo, Daniel Rueckert, Wenjia Bai

Our approach provides a real-time and model-agnostic quality control for cardiac MRI segmentation, which has the potential to be integrated into clinical image analysis workflows.

Image Segmentation MRI segmentation +1

Realistic Adversarial Data Augmentation for MR Image Segmentation

1 code implementation23 Jun 2020 Chen Chen, Chen Qin, Huaqi Qiu, Cheng Ouyang, Shuo Wang, Liang Chen, Giacomo Tarroni, Wenjia Bai, Daniel Rueckert

In this work, we propose an adversarial data augmentation method for training neural networks for medical image segmentation.

Data Augmentation Image Segmentation +2

Biomechanics-informed Neural Networks for Myocardial Motion Tracking in MRI

1 code implementation8 Jun 2020 Chen Qin, Shuo Wang, Chen Chen, Huaqi Qiu, Wenjia Bai, Daniel Rueckert

The learnt VAE regulariser then can be coupled with any deep learning based registration network to regularise the solution space to be biomechanically plausible.

Image Registration

Efficient Deep Representation Learning by Adaptive Latent Space Sampling

no code implementations19 Mar 2020 Yuanhan Mo, Shuo Wang, Chengliang Dai, Rui Zhou, Zhongzhao Teng, Wenjia Bai, Yike Guo

Supervised deep learning requires a large amount of training samples with annotations (e. g. label class for classification task, pixel- or voxel-wised label map for segmentation tasks), which are expensive and time-consuming to obtain.

General Classification Image Classification +2

Suggestive Labelling for Medical Image Analysis by Adaptive Latent Space Sampling

no code implementations MIDL 2019 Yuanhan Mo, Shuo Wang, Chengliang Dai, Zhongzhao Teng, Wenjia Bai, Yike Guo

Supervised deep learning for medical imaging analysis requires a large amount of training samples with annotations (e. g. label class for classification task, pixel- or voxel-wised label map for medical segmentation tasks), which are expensive and time-consuming to obtain.


Joint Motion Estimation and Segmentation from Undersampled Cardiac MR Image

no code implementations20 Aug 2019 Chen Qin, Wenjia Bai, Jo Schlemper, Steffen E. Petersen, Stefan K. Piechnik, Stefan Neubauer, Daniel Rueckert

Accelerating the acquisition of magnetic resonance imaging (MRI) is a challenging problem, and many works have been proposed to reconstruct images from undersampled k-space data.

Image Reconstruction Motion Estimation

Unsupervised Multi-modal Style Transfer for Cardiac MR Segmentation

no code implementations20 Aug 2019 Chen Chen, Cheng Ouyang, Giacomo Tarroni, Jo Schlemper, Huaqi Qiu, Wenjia Bai, Daniel Rueckert

In this work, we present a fully automatic method to segment cardiac structures from late-gadolinium enhanced (LGE) images without using labelled LGE data for training, but instead by transferring the anatomical knowledge and features learned on annotated balanced steady-state free precession (bSSFP) images, which are easier to acquire.

Image Segmentation Semantic Segmentation +2

VS-Net: Variable splitting network for accelerated parallel MRI reconstruction

1 code implementation19 Jul 2019 Jinming Duan, Jo Schlemper, Chen Qin, Cheng Ouyang, Wenjia Bai, Carlo Biffi, Ghalib Bello, Ben Statton, Declan P. O'Regan, Daniel Rueckert

In this work, we propose a deep learning approach for parallel magnetic resonance imaging (MRI) reconstruction, termed a variable splitting network (VS-Net), for an efficient, high-quality reconstruction of undersampled multi-coil MR data.

MRI Reconstruction Rolling Shutter Correction

Self-Supervised Learning for Cardiac MR Image Segmentation by Anatomical Position Prediction

no code implementations5 Jul 2019 Wenjia Bai, Chen Chen, Giacomo Tarroni, Jinming Duan, Florian Guitton, Steffen E. Petersen, Yike Guo, Paul M. Matthews, Daniel Rueckert

In the recent years, convolutional neural networks have transformed the field of medical image analysis due to their capacity to learn discriminative image features for a variety of classification and regression tasks.

Image Segmentation Self-Supervised Learning +2

Improving the generalizability of convolutional neural network-based segmentation on CMR images

1 code implementation2 Jul 2019 Chen Chen, Wenjia Bai, Rhodri H. Davies, Anish N. Bhuva, Charlotte Manisty, James C. Moon, Nay Aung, Aaron M. Lee, Mihir M. Sanghvi, Kenneth Fung, Jose Miguel Paiva, Steffen E. Petersen, Elena Lukaschuk, Stefan K. Piechnik, Stefan Neubauer, Daniel Rueckert

We demonstrate that a neural network trained on a single-site single-scanner dataset from the UK Biobank can be successfully applied to segmenting cardiac MR images across different sites and different scanners without substantial loss of accuracy.

Image Segmentation Semantic Segmentation

Explainable Anatomical Shape Analysis through Deep Hierarchical Generative Models

1 code implementation28 Jun 2019 Carlo Biffi, Juan J. Cerrolaza, Giacomo Tarroni, Wenjia Bai, Antonio de Marvao, Ozan Oktay, Christian Ledig, Loic Le Folgoc, Konstantinos Kamnitsas, Georgia Doumou, Jinming Duan, Sanjay K. Prasad, Stuart A. Cook, Declan P. O'Regan, Daniel Rueckert

At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space.


Multi-Task Learning for Left Atrial Segmentation on GE-MRI

1 code implementation31 Oct 2018 Chen Chen, Wenjia Bai, Daniel Rueckert

Segmentation of the left atrium (LA) is crucial for assessing its anatomy in both pre-operative atrial fibrillation (AF) ablation planning and post-operative follow-up studies.

Anatomy General Classification +1

A Comprehensive Approach for Learning-based Fully-Automated Inter-slice Motion Correction for Short-Axis Cine Cardiac MR Image Stacks

no code implementations3 Oct 2018 Giacomo Tarroni, Ozan Oktay, Matthew Sinclair, Wenjia Bai, Andreas Schuh, Hideaki Suzuki, Antonio de Marvao, Declan O'Regan, Stuart Cook, Daniel Rueckert

If long axis (LA) images are available, PSMs are generated for them and combined to create the target PSM; if not, the target PSM is produced from the same stack using a 3D model trained from motion-free stacks.

Motion Compensation

Recurrent neural networks for aortic image sequence segmentation with sparse annotations

no code implementations1 Aug 2018 Wenjia Bai, Hideaki Suzuki, Chen Qin, Giacomo Tarroni, Ozan Oktay, Paul M. Matthews, Daniel Rueckert

In this work, we propose an image sequence segmentation algorithm by combining a fully convolutional network with a recurrent neural network, which incorporates both spatial and temporal information into the segmentation task.


Deep nested level sets: Fully automated segmentation of cardiac MR images in patients with pulmonary hypertension

no code implementations27 Jul 2018 Jinming Duan, Jo Schlemper, Wenjia Bai, Timothy J. W. Dawes, Ghalib Bello, Georgia Doumou, Antonio de Marvao, Declan P. O'Regan, Daniel Rueckert

In this paper we introduce a novel and accurate optimisation method for segmentation of cardiac MR (CMR) images in patients with pulmonary hypertension (PH).

Joint Learning of Motion Estimation and Segmentation for Cardiac MR Image Sequences

1 code implementation11 Jun 2018 Chen Qin, Wenjia Bai, Jo Schlemper, Steffen E. Petersen, Stefan K. Piechnik, Stefan Neubauer, Daniel Rueckert

Cardiac motion estimation and segmentation play important roles in quantitatively assessing cardiac function and diagnosing cardiovascular diseases.

Cardiac Segmentation Motion Estimation +1

Learning-Based Quality Control for Cardiac MR Images

no code implementations25 Mar 2018 Giacomo Tarroni, Ozan Oktay, Wenjia Bai, Andreas Schuh, Hideaki Suzuki, Jonathan Passerat-Palmbach, Antonio de Marvao, Declan P. O'Regan, Stuart Cook, Ben Glocker, Paul M. Matthews, Daniel Rueckert

The results show the capability of the proposed pipeline to correctly detect incomplete or corrupted scans (e. g. on UK Biobank, sensitivity and specificity respectively 88% and 99% for heart coverage estimation, 85% and 95% for motion detection), allowing their exclusion from the analysed dataset or the triggering of a new acquisition.

Motion Detection Specificity

Ensembles of Multiple Models and Architectures for Robust Brain Tumour Segmentation

no code implementations4 Nov 2017 Konstantinos Kamnitsas, Wenjia Bai, Enzo Ferrante, Steven McDonagh, Matthew Sinclair, Nick Pawlowski, Martin Rajchl, Matthew Lee, Bernhard Kainz, Daniel Rueckert, Ben Glocker

Deep learning approaches such as convolutional neural nets have consistently outperformed previous methods on challenging tasks such as dense, semantic segmentation.

Semantic Segmentation

Automated cardiovascular magnetic resonance image analysis with fully convolutional networks

1 code implementation25 Oct 2017 Wenjia Bai, Matthew Sinclair, Giacomo Tarroni, Ozan Oktay, Martin Rajchl, Ghislain Vaillant, Aaron M. Lee, Nay Aung, Elena Lukaschuk, Mihir M. Sanghvi, Filip Zemrak, Kenneth Fung, Jose Miguel Paiva, Valentina Carapella, Young Jin Kim, Hideaki Suzuki, Bernhard Kainz, Paul M. Matthews, Steffen E. Petersen, Stefan K. Piechnik, Stefan Neubauer, Ben Glocker, Daniel Rueckert

By combining FCN with a large-scale annotated dataset, the proposed automated method achieves a high performance on par with human experts in segmenting the LV and RV on short-axis CMR images and the left atrium (LA) and right atrium (RA) on long-axis CMR images.

Multi-Atlas Segmentation using Partially Annotated Data: Methods and Annotation Strategies

no code implementations29 Apr 2016 Lisa M. Koch, Martin Rajchl, Wenjia Bai, Christian F. Baumgartner, Tong Tong, Jonathan Passerat-Palmbach, Paul Aljabar, Daniel Rueckert

Multi-atlas segmentation is a widely used tool in medical image analysis, providing robust and accurate results by learning from annotated atlas datasets.

Cardiac Segmentation

Patch-based Evaluation of Image Segmentation

no code implementations CVPR 2014 Christian Ledig, Wenzhe Shi, Wenjia Bai, Daniel Rueckert

The ideal similarity measure should be unbiased to segmentations of different volume and complexity, and be able to quantify and visualise segmentation bias.

Hippocampus Image Segmentation +1

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