基于非線性形變模型的雙向凝膠圖像校正
發(fā)布時間：2018-08-15 16:29
【摘要】：在生物化學(xué)和生命科學(xué)等領(lǐng)域,隨著現(xiàn)代科學(xué)水平的進(jìn)步,蛋白質(zhì)組學(xué)已經(jīng)成為前沿的研究領(lǐng)域。在蛋白質(zhì)的鑒定及生理病理學(xué)中的蛋白質(zhì)功能測定中,首先利用雙向凝膠電泳技術(shù)對復(fù)雜的蛋白質(zhì)組織進(jìn)行分離,掃描存檔,完成雙向凝膠電泳圖像的采集。凝膠圖像中含有大量蛋白點(diǎn),需要利用計算機(jī)軟件進(jìn)行分析。分析同一樣本在不同時期凝膠圖像中對應(yīng)蛋白點(diǎn)對的變化,從而提取出感興趣蛋白點(diǎn)對進(jìn)行研究。在獲取凝膠圖像的過程中,由于蛋白點(diǎn)的移動變形、外部環(huán)境的變化、儀器的多樣性和儀器產(chǎn)生的噪聲等問題可能造成同一樣本的凝膠之間出現(xiàn)圖像失真。為了更好地進(jìn)行蛋白質(zhì)組的分析,必須在凝膠圖像的預(yù)處理階段消除失真,完成圖像的校正,以便更好地實現(xiàn)凝膠圖像的匹配。凝膠圖像的校正,就是消除幾何失真對圖像產(chǎn)生的影響。本論文以凝膠圖像的幾何失真校正為研究重點(diǎn),基于多種形變方法,完成凝膠圖像的校正。主要研究內(nèi)容如下:(1)本論文研究了基于薄板樣條函數(shù)(Thin Plate Spline,TPS)的形變,通過手動標(biāo)記控制點(diǎn),找到一個通過部分控制點(diǎn)的彎曲能量最小的光滑曲面。實驗結(jié)果表明,對于凝膠圖像的非線性幾何失真,校正效果比較明顯,但手動選點(diǎn)會存在一定的誤差,而標(biāo)記點(diǎn)的位置偏移,會導(dǎo)致圖像的校正偏差;(2)基于B樣條函數(shù)的形變,同樣是非線性形變方法的一種,用自由形變模型的網(wǎng)格點(diǎn)作為圖像的控制點(diǎn),根據(jù)控制點(diǎn)局部控制性和計算效率考慮,構(gòu)建三次均勻B樣條形變模型。通過改變網(wǎng)格間距的大小,網(wǎng)格控制點(diǎn)周圍的點(diǎn)隨之改變,其校正效果也有明顯的變化,必須根據(jù)失真程度選擇合適的網(wǎng)格大小。仿真結(jié)果表明,較TPS形變校正來講,校正效果有所改善。但在失真程度比較嚴(yán)重、網(wǎng)格間距較大時,部分控制點(diǎn)形變效果欠佳;(3)由于凝膠圖像失真的中心拉伸特點(diǎn),“笑臉”形變模型可以對圖像進(jìn)行整體的形變,消除這種微笑失真。本論文將“笑臉”形變模型和B樣條形變模型有效的融合在一起,提出一種新的校正算法,充分利用“笑臉”全局形變和B樣條函數(shù)局部形變的特點(diǎn)。仿真實驗結(jié)果表明,這種方法和其他形變校正方法相比,形變校正效果更佳。剛性變換、仿射變換等線性變化,算法簡單,運(yùn)算速度快,但是只適合圖像的平移、旋轉(zhuǎn)等線性幾何失真的校正,對非線性的幾何失真效果甚微。本論文將幾種典型的非線性形變方法用在凝膠圖像的失真校正上,對比分析校正效果得出,本論文所提出的形變校正方法,能將失真圖像的細(xì)節(jié)信息和先驗知識進(jìn)行有效結(jié)合,在保證形變平滑性的同時又能得到良好的校正效果,并具有較高的計算效率,適合實際研究中使用。
[Abstract]:With the progress of modern science, proteomics has become a frontier research field in biochemistry and life sciences. In the identification of proteins and the determination of protein function in physiology and pathology, two-dimensional gel electrophoresis was used to separate the complex protein tissues, scan and archive, and complete the collection of two-dimensional gel electrophoresis images. Gel images contain a large number of protein spots, which need to be analyzed by computer software. The changes of protein point pairs corresponding to the same sample in different periods of gel images were analyzed, and the interested protein point pairs were extracted for study. In the process of obtaining gel images, the distortion of the gel images of the same sample may occur due to the movement and deformation of the protein points, the change of the external environment, the diversity of the instruments and the noise generated by the instruments. In order to better analyze the proteome, the distortion must be eliminated in the pre-processing stage of the gel image, and the correction of the image should be completed, so that the matching of the gel image can be realized better. The correction of gel image is to eliminate the effect of geometric distortion on the image. In this paper, we focus on geometric distortion correction of gel image, and complete the correction of gel image based on various deformation methods. The main research contents are as follows: (1) the deformation based on thin plate spline function (Thin Plate splines is studied in this paper. By manually marking control points, a smooth surface with minimum bending energy through partial control points is found. The experimental results show that the correction effect is obvious for the nonlinear geometric distortion of the gel image, but there will be some errors in the manual selection of the point, and the deviation of the position of the mark point will lead to the correction deviation of the image. (2) based on the deformation of B-spline function, It is also one of the nonlinear deformation methods. The mesh points of the free deformation model are used as the control points of the image, and the cubic uniform B-spline deformation model is constructed according to the local control and computational efficiency of the control points. By changing the size of the mesh spacing, the points around the grid control point will change, and the correction effect will also change obviously. The appropriate mesh size must be selected according to the distortion degree. The simulation results show that the correction effect is better than that of TPS deformation correction. However, when the distortion degree is serious and the mesh spacing is large, the deformation effect of some control points is not good. (3) because of the central stretching characteristics of gel image distortion, the "smiling face" deformation model can deform the image as a whole and eliminate the smile distortion. In this paper, the "smiling face" deformation model and the B-spline deformation model are effectively fused together, and a new correction algorithm is proposed to make full use of the global deformation of "smiling face" and the local deformation of B-spline function. The simulation results show that this method is more effective than other deformation correction methods. The linear changes such as rigid transformation and affine transformation are simple and fast, but they are only suitable for the correction of linear geometric distortion, such as translation and rotation, and have little effect on nonlinear geometric distortion. In this paper, several typical nonlinear deformation methods are applied to the distortion correction of gel images. By comparing and analyzing the correction results, it is concluded that the distortion correction method proposed in this paper can effectively combine the details of distorted images with prior knowledge. It can ensure the smoothness of deformation at the same time get a good correction effect, and has a higher calculation efficiency, which is suitable for practical research.
【學(xué)位授予單位】：山東師范大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2017
【分類號】：TP391.41
本文編號：2184768
[Abstract]:With the progress of modern science, proteomics has become a frontier research field in biochemistry and life sciences. In the identification of proteins and the determination of protein function in physiology and pathology, two-dimensional gel electrophoresis was used to separate the complex protein tissues, scan and archive, and complete the collection of two-dimensional gel electrophoresis images. Gel images contain a large number of protein spots, which need to be analyzed by computer software. The changes of protein point pairs corresponding to the same sample in different periods of gel images were analyzed, and the interested protein point pairs were extracted for study. In the process of obtaining gel images, the distortion of the gel images of the same sample may occur due to the movement and deformation of the protein points, the change of the external environment, the diversity of the instruments and the noise generated by the instruments. In order to better analyze the proteome, the distortion must be eliminated in the pre-processing stage of the gel image, and the correction of the image should be completed, so that the matching of the gel image can be realized better. The correction of gel image is to eliminate the effect of geometric distortion on the image. In this paper, we focus on geometric distortion correction of gel image, and complete the correction of gel image based on various deformation methods. The main research contents are as follows: (1) the deformation based on thin plate spline function (Thin Plate splines is studied in this paper. By manually marking control points, a smooth surface with minimum bending energy through partial control points is found. The experimental results show that the correction effect is obvious for the nonlinear geometric distortion of the gel image, but there will be some errors in the manual selection of the point, and the deviation of the position of the mark point will lead to the correction deviation of the image. (2) based on the deformation of B-spline function, It is also one of the nonlinear deformation methods. The mesh points of the free deformation model are used as the control points of the image, and the cubic uniform B-spline deformation model is constructed according to the local control and computational efficiency of the control points. By changing the size of the mesh spacing, the points around the grid control point will change, and the correction effect will also change obviously. The appropriate mesh size must be selected according to the distortion degree. The simulation results show that the correction effect is better than that of TPS deformation correction. However, when the distortion degree is serious and the mesh spacing is large, the deformation effect of some control points is not good. (3) because of the central stretching characteristics of gel image distortion, the "smiling face" deformation model can deform the image as a whole and eliminate the smile distortion. In this paper, the "smiling face" deformation model and the B-spline deformation model are effectively fused together, and a new correction algorithm is proposed to make full use of the global deformation of "smiling face" and the local deformation of B-spline function. The simulation results show that this method is more effective than other deformation correction methods. The linear changes such as rigid transformation and affine transformation are simple and fast, but they are only suitable for the correction of linear geometric distortion, such as translation and rotation, and have little effect on nonlinear geometric distortion. In this paper, several typical nonlinear deformation methods are applied to the distortion correction of gel images. By comparing and analyzing the correction results, it is concluded that the distortion correction method proposed in this paper can effectively combine the details of distorted images with prior knowledge. It can ensure the smoothness of deformation at the same time get a good correction effect, and has a higher calculation efficiency, which is suitable for practical research.
【學(xué)位授予單位】：山東師范大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2017
【分類號】：TP391.41
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