高分辨核磁共振实验与数据处理的自动化关键技术研究
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摘要
自1945年核磁共振(Nuclear Magnetic Resonance, NMR)现象被发现以来,核磁共振技术的发展犹如一棵常青树,目前已经成为应用最为广泛的分析技术之一。核磁共振技术之所以能具有如此强大的生命力主要是由于其能提供大量的化学结构信息和动力学信息,而高分辨率的谱图正是提供这些信息的基础。随着核磁共振在代谢组学等领域的不断发展应用,如何自动地获得高分辨率的核磁共振谱图越来越受到人们的重视,这也是核磁共振波谱仪研发的一个重要挑战和机遇。
本论文从实验和数据处理两个方面,开展自动获取高分辨核磁共振谱图的研究工作。在具有自主知识产权的核磁共振波谱仪上,实现了自动获取高分辨核磁共振谱图所需的三项关键技术：自动匀场方法,自动相位校正方法以及自动基线校正方法,并在此基础上提出了一些更优化的改进方案。
在自动化核磁共振实验的研究工作中,我们针对高分辨核磁共振实验必须具备的前提条件之一——均匀的静磁场展开研究。在自主开发的核磁共振波波谱仪中实现了各种自动匀场方法包括基于搜索算法的自动匀场方法,一维和三维梯度匀场方法,及结合线形的梯度匀场方法。并在此基础上,提出了一些改进方法,如：在三维梯度匀场方法中,采用了改进的脉冲序列,使得谱仪可以利用XY匀场线圈来产生相位编码梯度,从而实现了在普通探头上的三维梯度匀场；此外,针对梯度匀场中匀场电流值越界和三维梯度匀场时间过长的两个问题,分别提出了相应的解决方案。
在自动数据处理方面,我们首先实现了核磁共振数据处理软件中的常规算法,并在此基础上发展了若干改进方法,包括一种适用性和准确性都非常高的自动相位校正方法,以及可以适用于基线失真较大谱图的自动基线校正方法。新的自动相位校正方法采用了粗调和细调相结合的方案,在粗调过程中利用了“基线-谱峰”分界点差异最小化的方法获得一个大致准确的校正结果,基于这个结果判断出各个谱峰的特性,即将谱图中的谱峰区分为正峰、负峰和畸变峰。然后利用最小化自定义的负值惩罚函数进行细调,从而获得更准确的自动相位校正结果。最后,通过实验验证出新的自动相位校正方法不仅适用于各种NMR谱图,而且几乎不受信噪比、基线失真等因素的影响。表明此方法不仅普适性强,而且具有很好的鲁棒性以及准确性。新的自动基线校正方法的基础是改进的基线识别算法和迭代的基线模型构建算法。其中,改进的基线识别算法不仅结合了三种常用的基线识别算法,而且还利用谱峰轮廓拟合的方法来准确地识别出谱图中的宽峰信号。而在迭代的基线模型构建算法中,我们不仅利用了识别出的基线区间,还在迭代的过程中自动地寻出谱图中谱峰重叠非常严重区间中的“准基线点”,利用这些“准基线点”我们可以构建出更符合实际情况的基线模型,从而得到更好的基线校正结果。实验证明这种新的自动基线校正方法能够更有效地处理谱峰密集和基线失真严重的复杂NMR谱图。
Nuclear Magnetic Resonance technology has been developing rapidly since1945and has become one of the most successful analytical techniques. High resolution is the basis of the fact that the NMR spectra can provide the information of chemical structure and dynamics. In recent years, the rapid development of NMR in the field of metabolomics has raised a question of how to get the spectra automatically, which is an important challenge and opportunity for NMR spectrometer manufacturers.
In this thesis, the question of how to get the high resolution spectra automatically is discussed through both experiment and data processing. A variety of methods of automatic shimming and automatic data processing methods are implemented in the spectrometer with independent intellectual property rights.
The research of automatic shimming includes shimming based on search algorithm, gradient shimming and gradient shimming with lineshape optimization. In the gradient shimming, an improved pulse sequence is utilized to make three dimensional gradients shimming available in the probe without XY gradient coils. Moreover, some improvements are also made to address two issues of gradient shimming:One is that the shimming current will be out of range, and the other one is that a long time is needed in three dimensional automated shimming.
In the research of automatic data processing, a robust automatic phase correction method and a new automatic baseline correction method are proposed. In the automatic phase correction method, a new strategy combining'coarse tuning' with 'fine tuning' is introduced to correct various spectra accurately. In the'coarse tuning' procedure, the preliminary phased spectra are obtained by minimizing the objective function based on the height difference of'critical signal points'in peaks'tails. After that, the peaks in the preliminary corrected spectra can be categorized into three classes:positive, negative, and distorted. Based on the classification result, a new custom negative penalty function used in the step of 'fine tuning' is constructed to avoid the negative points in the spectra excluded in the negative peaks and distorted peaks. Finally, the fine phased spectra can be obtained by minimizing the custom negative penalty function. This automatic method is proven to be very robust for it is tolerant to low signal-to-noise ratio, large baseline distortion and independent of the starting search points of phasing parameters. The new baseline correction method is based on an improved baseline recognition method and a new iterative baseline modeling method. The presented baseline recognition method takes advantages of three baseline recognition algorithms in order to recognize all signals in spectra. While in the iterative baseline modeling method, except for the well-recognized baseline points in signal-free regions, the 'quasi-baseline points' in the signal-crowded regions are also identified and then utilized to improve robustness by preventing the negative regions. The experimental results on both simulated data and real metabolomics spectra with over-crowded peaks show the efficiency of this automatic method.
本论文从实验和数据处理两个方面,开展自动获取高分辨核磁共振谱图的研究工作。在具有自主知识产权的核磁共振波谱仪上,实现了自动获取高分辨核磁共振谱图所需的三项关键技术：自动匀场方法,自动相位校正方法以及自动基线校正方法,并在此基础上提出了一些更优化的改进方案。
在自动化核磁共振实验的研究工作中,我们针对高分辨核磁共振实验必须具备的前提条件之一——均匀的静磁场展开研究。在自主开发的核磁共振波波谱仪中实现了各种自动匀场方法包括基于搜索算法的自动匀场方法,一维和三维梯度匀场方法,及结合线形的梯度匀场方法。并在此基础上,提出了一些改进方法,如：在三维梯度匀场方法中,采用了改进的脉冲序列,使得谱仪可以利用XY匀场线圈来产生相位编码梯度,从而实现了在普通探头上的三维梯度匀场；此外,针对梯度匀场中匀场电流值越界和三维梯度匀场时间过长的两个问题,分别提出了相应的解决方案。
在自动数据处理方面,我们首先实现了核磁共振数据处理软件中的常规算法,并在此基础上发展了若干改进方法,包括一种适用性和准确性都非常高的自动相位校正方法,以及可以适用于基线失真较大谱图的自动基线校正方法。新的自动相位校正方法采用了粗调和细调相结合的方案,在粗调过程中利用了“基线-谱峰”分界点差异最小化的方法获得一个大致准确的校正结果,基于这个结果判断出各个谱峰的特性,即将谱图中的谱峰区分为正峰、负峰和畸变峰。然后利用最小化自定义的负值惩罚函数进行细调,从而获得更准确的自动相位校正结果。最后,通过实验验证出新的自动相位校正方法不仅适用于各种NMR谱图,而且几乎不受信噪比、基线失真等因素的影响。表明此方法不仅普适性强,而且具有很好的鲁棒性以及准确性。新的自动基线校正方法的基础是改进的基线识别算法和迭代的基线模型构建算法。其中,改进的基线识别算法不仅结合了三种常用的基线识别算法,而且还利用谱峰轮廓拟合的方法来准确地识别出谱图中的宽峰信号。而在迭代的基线模型构建算法中,我们不仅利用了识别出的基线区间,还在迭代的过程中自动地寻出谱图中谱峰重叠非常严重区间中的“准基线点”,利用这些“准基线点”我们可以构建出更符合实际情况的基线模型,从而得到更好的基线校正结果。实验证明这种新的自动基线校正方法能够更有效地处理谱峰密集和基线失真严重的复杂NMR谱图。
Nuclear Magnetic Resonance technology has been developing rapidly since1945and has become one of the most successful analytical techniques. High resolution is the basis of the fact that the NMR spectra can provide the information of chemical structure and dynamics. In recent years, the rapid development of NMR in the field of metabolomics has raised a question of how to get the spectra automatically, which is an important challenge and opportunity for NMR spectrometer manufacturers.
In this thesis, the question of how to get the high resolution spectra automatically is discussed through both experiment and data processing. A variety of methods of automatic shimming and automatic data processing methods are implemented in the spectrometer with independent intellectual property rights.
The research of automatic shimming includes shimming based on search algorithm, gradient shimming and gradient shimming with lineshape optimization. In the gradient shimming, an improved pulse sequence is utilized to make three dimensional gradients shimming available in the probe without XY gradient coils. Moreover, some improvements are also made to address two issues of gradient shimming:One is that the shimming current will be out of range, and the other one is that a long time is needed in three dimensional automated shimming.
In the research of automatic data processing, a robust automatic phase correction method and a new automatic baseline correction method are proposed. In the automatic phase correction method, a new strategy combining'coarse tuning' with 'fine tuning' is introduced to correct various spectra accurately. In the'coarse tuning' procedure, the preliminary phased spectra are obtained by minimizing the objective function based on the height difference of'critical signal points'in peaks'tails. After that, the peaks in the preliminary corrected spectra can be categorized into three classes:positive, negative, and distorted. Based on the classification result, a new custom negative penalty function used in the step of 'fine tuning' is constructed to avoid the negative points in the spectra excluded in the negative peaks and distorted peaks. Finally, the fine phased spectra can be obtained by minimizing the custom negative penalty function. This automatic method is proven to be very robust for it is tolerant to low signal-to-noise ratio, large baseline distortion and independent of the starting search points of phasing parameters. The new baseline correction method is based on an improved baseline recognition method and a new iterative baseline modeling method. The presented baseline recognition method takes advantages of three baseline recognition algorithms in order to recognize all signals in spectra. While in the iterative baseline modeling method, except for the well-recognized baseline points in signal-free regions, the 'quasi-baseline points' in the signal-crowded regions are also identified and then utilized to improve robustness by preventing the negative regions. The experimental results on both simulated data and real metabolomics spectra with over-crowded peaks show the efficiency of this automatic method.
引文
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