arXiv subjects

Zhangren Tu

Publications and source records attributed to Zhangren Tu.

7 recordsLinked to original sources

arXiv2026

Synthetic Data in MR Spectroscopy: Current Practices, Applications, and Considerations

The use of synthetic data has emerged as an essential tool in Magnetic Resonance Spectroscopy (MRS) research and applications, providing advantages for optimization of acquisition, software validation, deep learning applications, and enhanced reproducibility. Importantly, synthetic data addresses challenges of limited training data availability, particularly for clinical populations, and offers controlled solutions for investigating uncertainties and unexplained variance with in vivo data. This work provides a review and evaluation of current practices in the use and generation of synthetic data within the MRS field. Conducted by the MRS Synthetic Data Working Group under the Code & Data Sharing Committee of the MRS Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM), this manuscript encompasses existing literature, supplemented by collective experience and in-house methodologies.

physics.med-ph↗

arXiv2025

An artificially intelligent magnetic resonance spectroscopy quantification method: Comparison between QNet and LCModel on the cloud computing platform CloudBrain-MRS

Objctives: This work aimed to statistically compare the metabolite quantification of human brain magnetic resonance spectroscopy (MRS) between the deep learning method QNet and the classical method LCModel through an easy-to-use intelligent cloud computing platform CloudBrain-MRS. Materials and Methods: In this retrospective study, two 3 T MRI scanners Philips Ingenia and Achieva collected 61 and 46 in vivo 1H magnetic resonance (MR) spectra of healthy participants, respectively, from the brain region of pregenual anterior cingulate cortex from September to October 2021. The analyses of Bland-Altman, Pearson correlation and reasonability were performed to assess the degree of agreement, linear correlation and reasonability between the two quantification methods. Results: Fifteen healthy volunteers (12 females and 3 males, age range: 21-35 years, mean age/standard deviation = 27.4/3.9 years) were recruited. The analyses of Bland-Altman, Pearson correlation and reasonability showed high to good consistency and very strong to moderate correlation between the two methods for quantification of total N-acetylaspartate (tNAA), total choline (tCho), and inositol (Ins) (relative half interval of limits of agreement = 3.04%, 9.3%, and 18.5%, respectively; Pearson correlation coefficient r = 0.775, 0.927, and 0.469, respectively). In addition, quantification results of QNet are more likely to be closer to the previous reported average values than those of LCModel. Conclusion: There were high or good degrees of consistency between the quantification results of QNet and LCModel for tNAA, tCho, and Ins, and QNet generally has more reasonable quantification than LCModel.

physics.med-ph↗

arXiv2023

XCloud-VIP: Virtual Peak Enables Highly Accelerated NMR Spectroscopy and Faithful Quantitative Measures

Nuclear Magnetic Resonance (NMR) spectroscopy is an important bio-engineering tool to determine the metabolic concentrations, molecule structures and so on. The data acquisition time, however, is very long in multi-dimensional NMR. To accelerate data acquisition, non-uniformly sampling is an effective way but may encounter severe spectral distortions and unfaithful quantitative measures when the acceleration factor is high. By modelling the acquired signal as the superimposed exponentials, we proposed a virtual peak (VIP) approach to selfadapt the prior spectral information, such as the resonance frequency and peak lineshape, and then feed these information into the reconstruction. The proposed method is further implemented with cloud computing to facilitate online, open, and easy access. Results on simulated and experimental data demonstrate that, compared with the low-rank Hankel matrix method, the new approach reconstructs high-fidelity NMR spectra from highly undersampled data and achieves more accurate quantification. The maximum quantitative errors of distances between nuclear pairs and concentrations of metabolites in mixtures have been reduced by 61.1% and 57.7%, respectively.

physics.med-ph↗

arXiv2023

CloudBrain-NMR: An Intelligent Cloud Computing Platform for NMR Spectroscopy Processing, Reconstruction and Analysis

Nuclear Magnetic Resonance (NMR) spectroscopy has served as a powerful analytical tool for studying molecular structure and dynamics in chemistry and biology. However, the processing of raw data acquired from NMR spectrometers and subsequent quantitative analysis involves various specialized tools, which necessitates comprehensive knowledge in programming and NMR. Particularly, the emerging deep learning tools is hard to be widely used in NMR due to the sophisticated setup of computation. Thus, NMR processing is not an easy task for chemist and biologists. In this work, we present CloudBrain-NMR, an intelligent online cloud computing platform designed for NMR data reading, processing, reconstruction, and quantitative analysis. The platform is conveniently accessed through a web browser, eliminating the need for any program installation on the user side. CloudBrain-NMR uses parallel computing with graphics processing units and central processing units, resulting in significantly shortened computation time. Furthermore, it incorporates state-of-the-art deep learning-based algorithms offering comprehensive functionalities that allow users to complete the entire processing procedure without relying on additional software. This platform has empowered NMR applications with advanced artificial intelligence processing. CloudBrain-NMR is openly accessible for free usage at https://csrc.xmu.edu.cn/CloudBrain.html

q-bio.QM↗

arXiv2023

CloudBrain-MRS: An Intelligent Cloud Computing Platform for in vivo Magnetic Resonance Spectroscopy Preprocessing, Quantification, and Analysis

Magnetic resonance spectroscopy (MRS) is an important clinical imaging method for diagnosis of diseases. MRS spectrum is used to observe the signal intensity of metabolites or further infer their concentrations. Although the magnetic resonance vendors commonly provide basic functions of spectra plots and metabolite quantification, the widespread clinical research of MRS is still limited due to the lack of easy-to-use processing software or platform. To address this issue, we have developed CloudBrain-MRS, a cloud-based online platform that provides powerful hardware and advanced algorithms. The platform can be accessed simply through a web browser, without the need of any program installation on the user side. CloudBrain-MRS also integrates the classic LCModel and advanced artificial intelligence algorithms and supports batch preprocessing, quantification, and analysis of MRS data from different vendors. Additionally, the platform offers useful functions: 1) Automatically statistical analysis to find biomarkers for diseases; 2) Consistency verification between the classic and artificial intelligence quantification algorithms; 3) Colorful three-dimensional visualization for easy observation of individual metabolite spectrum. Last, both healthy and mild cognitive impairment patient data are used to demonstrate the functions of the platform. To the best of our knowledge, this is the first cloud computing platform for in vivo MRS with artificial intelligence processing. We have shared our cloud platform at MRSHub, providing free access and service for two years. Please visit https://mrshub.org/software_all/#CloudBrain-MRS or https://csrc.xmu.edu.cn/CloudBrain.html.

eess.SP↗

arXiv2022

Alternating Deep Low-Rank Approach for Exponential Function Reconstruction and Its Biomedical Magnetic Resonance Applications

Undersampling can accelerate the signal acquisition but at the cost of bringing in artifacts. Removing these artifacts is a fundamental problem in signal processing and this task is also called signal reconstruction. Through modeling signals as the superimposed exponential functions, deep learning has achieved fast and high-fidelity signal reconstruction by training a mapping from the undersampled exponentials to the fully sampled ones. However, the mismatch, such as the sampling rate of undersampling, the organ and the contrast of imaging, between the training and target data will heavily compromise the reconstruction. To address this issue, we propose Alternating Deep Low-Rank (ADLR), which combines deep learning solvers and classic optimization solvers. Experiments on the reconstruction of synthetic and realistic biomedical magnetic resonance signals demonstrate that ADLR can effectively mitigate the mismatch issue and achieve lower reconstruction errors than state-of-the-art methods.

eess.SP↗

arXiv2022

A Sparse Model-inspired Deep Thresholding Network for Exponential Signal Reconstruction -- Application in Fast Biological Spectroscopy

The non-uniform sampling is a powerful approach to enable fast acquisition but requires sophisticated reconstruction algorithms. Faithful reconstruction from partial sampled exponentials is highly expected in general signal processing and many applications. Deep learning has shown astonishing potential in this field but many existing problems, such as lack of robustness and explainability, greatly limit its applications. In this work, by combining merits of the sparse model-based optimization method and data-driven deep learning, we propose a deep learning architecture for spectra reconstruction from undersampled data, called MoDern. It follows the iterative reconstruction in solving a sparse model to build the neural network and we elaborately design a learnable soft-thresholding to adaptively eliminate the spectrum artifacts introduced by undersampling. Extensive results on both synthetic and biological data show that MoDern enables more robust, high-fidelity, and ultra-fast reconstruction than the state-of-the-art methods. Remarkably, MoDern has a small number of network parameters and is trained on solely synthetic data while generalizing well to biological data in various scenarios. Furthermore, we extend it to an open-access and easy-to-use cloud computing platform (XCloud-MoDern), contributing a promising strategy for further development of biological applications.

cs.LG↗