顯微CT三維血管圖像定量分析的研究
發(fā)布時間：2018-09-09 14:24
【摘要】：CT成像技術(shù)自上世紀(jì)70年代問世以來取得了迅速的發(fā)展,在生物醫(yī)學(xué)領(lǐng)域獲得了廣泛而深入的應(yīng)用。同時,通過圖像定量分析的方法分析三維CT圖像中研究對象的形態(tài)和結(jié)構(gòu),也成為了生物醫(yī)學(xué)研究的重要手段。許多疾病的產(chǎn)生和發(fā)展都表現(xiàn)出了血管異常與畸變的現(xiàn)象,例如血栓、腫瘤和肝硬化等。利用三維圖像定量分析的方法分析血管結(jié)構(gòu)的形態(tài)和特征,提取血管分支數(shù)、血管管徑以及血管密度等定量參數(shù)研究醫(yī)學(xué)問題,已成為許多疾病早期檢測、診斷和研究治療方案的必要輔助方法。近年來,隨著X射線成像技術(shù)的不斷進(jìn)步,采集到的三維血管圖像具有越來越高的分辨率,血管細(xì)節(jié)信息更為豐富�；谕捷椛涞娘@微CT成像(Synchrotron radiation micro-computed tomography,SR-μCT)技術(shù),具有高分辨和可實現(xiàn)相襯成像(Phase Contrast Imaging,PCI)的特點。相比于傳統(tǒng)的X射線吸收成像,X射線相位襯度CT成像(Phase Contrast Computed Tomography)對低Z元素樣品具有更高的密度分辨能力。例如對生物樣品的成像中,由于不同生物軟組織間密度差異較小,吸收成像難以分辨出不同的軟組織;而通過相位襯度CT成像,利用相位信息分辨不同的軟組織,可以獲得較好襯度的三維圖像。利用X射線的吸收特性采集生物樣品的血管圖像時,為了在圖像中顯示清晰的血管,往往需要對血管填充造影材料。與之相比,相位襯度CT成像無需借助造影劑,減少了樣品制備的復(fù)雜性,并且對于采用吸收成像時因為造影劑顆粒太大而不能滲透的微小血管也能夠采集到清晰的圖像。采集到的三維血管圖像分辨率高、細(xì)節(jié)豐富和數(shù)據(jù)量大的新特點對圖像的定量分析方法也提出了更高的要求和新的挑戰(zhàn)。針對上海光源X射線成像及生物醫(yī)學(xué)應(yīng)用光束線站(BL13W)對于三維圖像定量分析的大量需求,本文開始了顯微CT三維血管圖像定量分析的研究,取得了一下幾個方面的成果:1.發(fā)展出了基于血管樹形結(jié)構(gòu)提取血管定量參數(shù)的三維圖像分析方法。該方法根據(jù)血管樹狀結(jié)構(gòu)的特點,從根部區(qū)域遍歷整個血管網(wǎng)絡(luò),提取血管分支、血管分叉點和血管長度等一系列定量參數(shù)。此外,與傳統(tǒng)提取血管定量參數(shù)的方法相比,還得到了血管關(guān)于樹形結(jié)構(gòu)的定量信息,如血管分支所位于的樹的層級和血管樹延伸的最高層級深度等,為定量描述三維血管的結(jié)構(gòu)和形態(tài)提供了更加豐富的分析手段。2.顯微CT三維血管圖像定量分析中,提取血管骨架(skeleton)是獲得整個血管網(wǎng)絡(luò)定量信息的關(guān)鍵步驟。通過血管骨架這種單像素寬度的線性結(jié)構(gòu),“簡化”表征血管圖形,能夠方便的提取出描述血管結(jié)構(gòu)和形狀的量化參數(shù),如長度和數(shù)目等。因此,提取的血管骨架是否足夠精確直接決定了后續(xù)定量分析的可靠性和準(zhǔn)確性。為了解決現(xiàn)有的骨架提取算法存在的過度細(xì)化、缺失分支和存在“毛刺”噪聲等問題,本文提出了基于血管末端的骨架細(xì)化提取算法,提取到的血管骨架具有幾何不變性。生成精確表征三維血管圖形的骨架,保證了血管定量分析結(jié)果的準(zhǔn)確性和可靠性。3.血管骨架的提取是一個極為耗費時間的運算過程,通過Open MP多線程技術(shù)實現(xiàn)血管骨架提取算法的并行化運算,使得提取血管骨架的時間縮短了一個數(shù)量級。對于1.95 GB大小的顯微CT三維血管圖像,使用16個線程進(jìn)行并行運算時,可將運算時間由176 min縮短到13 min,顯著的提高了提取血管骨架的時間效率。4.血管分析算法和骨架提取算法軟件工具的開發(fā)實現(xiàn),本文提出的算法作為軟件模塊集成在3D Slicer中運行。并簡單介紹了利用軟件工具分析CT血管圖像的流程。5.應(yīng)用本文三維血管圖像定量分析的算法對小鼠肝臟纖維化模型進(jìn)行研究。利用圖像分析的方法提出了新的定量分析指標(biāo)高層級血管率(HVR)用以評估不同小鼠肝臟的纖維化程度,圖像分析的結(jié)果與實際血管增生現(xiàn)象和肝臟纖維化程度關(guān)系相符合。
[Abstract]:CT imaging technology has made rapid progress since its appearance in the 1970s, and has been widely and deeply applied in the field of biomedicine. At the same time, it has become an important means of biomedical research to analyze the shape and structure of the object of study in three-dimensional CT images by image quantitative analysis. Vascular abnormalities and distortions, such as thrombus, tumor and cirrhosis, have been demonstrated. Quantitative analysis of the morphology and characteristics of vascular structures, extraction of quantitative parameters such as vessel branch number, vessel diameter and vessel density, has become an early detection, diagnosis and treatment of many diseases. In recent years, with the development of X-ray imaging technology, the three-dimensional vascular images acquired have higher and higher resolution and more detailed information of blood vessels. Synchrotron radiation micro-computed tomography (SR-uCT) technology has high resolution and realizable phase. Compared with conventional X-ray absorption imaging, Phase Contrast Computed Tomography (PCI) has higher density resolution for low Z element samples. For example, in imaging biological samples, absorption imaging is difficult because of the small density difference between different biological soft tissues. In order to distinguish different soft tissues, three-dimensional images with better contrast can be obtained by phase contrast CT imaging, which uses phase information to distinguish different soft tissues. Compared with phase contrast CT imaging, phase contrast CT imaging does not require the use of contrast agents, which reduces the complexity of sample preparation, and can also capture clear images of small vessels that are too large to penetrate because of the size of contrast agents. Quantitative analysis methods also put forward higher requirements and new challenges. In view of the large demand for quantitative analysis of three-dimensional images by Shanghai Light Source X-ray Imaging and Biomedical Applied Beam Line Station (BL13W), this paper began the study of quantitative analysis of three-dimensional vascular images by micro-CT, and achieved the following results: 1. Based on the development of a new method of quantitative analysis of three-dimensional vascular images. According to the characteristics of vascular dendritic structure, this method traverses the whole vascular network from the root region, and extracts a series of quantitative parameters, such as vascular branches, vascular bifurcation points and vascular length. Quantitative information about the tree-like structure of the vessels, such as the hierarchy of the branches and the highest depth of the extension of the vascular tree, provides a more abundant analytical means for quantitative description of the structure and morphology of three-dimensional blood vessels. Quantitative parameters, such as length and number, can be extracted conveniently by simplifying the vascular skeleton, which is a linear structure with a single pixel width. Therefore, the reliability of subsequent quantitative analysis depends on whether the extracted vascular skeleton is accurate enough. In order to solve the problems of over-thinning, missing branches and "burr" noise in existing skeleton extraction algorithms, this paper proposes a skeleton thinning extraction algorithm based on the end of blood vessel. The skeleton extracted from the skeleton has geometric invariance. Accuracy and reliability of the analysis results. 3. Extraction of vascular skeleton is a time-consuming process. Parallel operation of the algorithm is realized by Open MP multithreading technology, which shortens the time of extracting vascular skeleton by an order of magnitude. For 3-D vascular images of 1.95 GB, 16 are used. The parallel operation of threads can shorten the operation time from 176 minutes to 13 minutes, which greatly improves the time efficiency of extracting vascular skeleton. The flow chart of CT angiography was analyzed. 5. The model of liver fibrosis in mice was studied by using the algorithm of quantitative analysis of three-dimensional angiography. A new quantitative analysis index, high-level vascular rate (HVR), was proposed to evaluate the degree of liver fibrosis in different mice, the results of image analysis and the actual proliferation of blood vessels. The phenomenon is consistent with the degree of liver fibrosis.
【學(xué)位授予單位】：中國科學(xué)院研究生院(上海應(yīng)用物理研究所)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：TP391.41
本文編號：2232645
[Abstract]:CT imaging technology has made rapid progress since its appearance in the 1970s, and has been widely and deeply applied in the field of biomedicine. At the same time, it has become an important means of biomedical research to analyze the shape and structure of the object of study in three-dimensional CT images by image quantitative analysis. Vascular abnormalities and distortions, such as thrombus, tumor and cirrhosis, have been demonstrated. Quantitative analysis of the morphology and characteristics of vascular structures, extraction of quantitative parameters such as vessel branch number, vessel diameter and vessel density, has become an early detection, diagnosis and treatment of many diseases. In recent years, with the development of X-ray imaging technology, the three-dimensional vascular images acquired have higher and higher resolution and more detailed information of blood vessels. Synchrotron radiation micro-computed tomography (SR-uCT) technology has high resolution and realizable phase. Compared with conventional X-ray absorption imaging, Phase Contrast Computed Tomography (PCI) has higher density resolution for low Z element samples. For example, in imaging biological samples, absorption imaging is difficult because of the small density difference between different biological soft tissues. In order to distinguish different soft tissues, three-dimensional images with better contrast can be obtained by phase contrast CT imaging, which uses phase information to distinguish different soft tissues. Compared with phase contrast CT imaging, phase contrast CT imaging does not require the use of contrast agents, which reduces the complexity of sample preparation, and can also capture clear images of small vessels that are too large to penetrate because of the size of contrast agents. Quantitative analysis methods also put forward higher requirements and new challenges. In view of the large demand for quantitative analysis of three-dimensional images by Shanghai Light Source X-ray Imaging and Biomedical Applied Beam Line Station (BL13W), this paper began the study of quantitative analysis of three-dimensional vascular images by micro-CT, and achieved the following results: 1. Based on the development of a new method of quantitative analysis of three-dimensional vascular images. According to the characteristics of vascular dendritic structure, this method traverses the whole vascular network from the root region, and extracts a series of quantitative parameters, such as vascular branches, vascular bifurcation points and vascular length. Quantitative information about the tree-like structure of the vessels, such as the hierarchy of the branches and the highest depth of the extension of the vascular tree, provides a more abundant analytical means for quantitative description of the structure and morphology of three-dimensional blood vessels. Quantitative parameters, such as length and number, can be extracted conveniently by simplifying the vascular skeleton, which is a linear structure with a single pixel width. Therefore, the reliability of subsequent quantitative analysis depends on whether the extracted vascular skeleton is accurate enough. In order to solve the problems of over-thinning, missing branches and "burr" noise in existing skeleton extraction algorithms, this paper proposes a skeleton thinning extraction algorithm based on the end of blood vessel. The skeleton extracted from the skeleton has geometric invariance. Accuracy and reliability of the analysis results. 3. Extraction of vascular skeleton is a time-consuming process. Parallel operation of the algorithm is realized by Open MP multithreading technology, which shortens the time of extracting vascular skeleton by an order of magnitude. For 3-D vascular images of 1.95 GB, 16 are used. The parallel operation of threads can shorten the operation time from 176 minutes to 13 minutes, which greatly improves the time efficiency of extracting vascular skeleton. The flow chart of CT angiography was analyzed. 5. The model of liver fibrosis in mice was studied by using the algorithm of quantitative analysis of three-dimensional angiography. A new quantitative analysis index, high-level vascular rate (HVR), was proposed to evaluate the degree of liver fibrosis in different mice, the results of image analysis and the actual proliferation of blood vessels. The phenomenon is consistent with the degree of liver fibrosis.
【學(xué)位授予單位】：中國科學(xué)院研究生院(上海應(yīng)用物理研究所)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：TP391.41
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