面向生物多模态显微成像数据的大规模三维重建方法及应用 | |
刘家正![]() | |
2024-05-18 | |
页数 | 210 |
学位类型 | 博士 |
中文摘要 | 在微观尺度下重建生物组织对于深入理解组织结构、功能和疾病至关重要。传统的二维成像分析在捕捉组织的复杂三维结构方面存在局限性,而这对于阐明组织在健康和疾病中的作用至关重要。近年来,共聚焦显微镜、双光子显微镜、电子显微镜和组织透明化方法等微观组织重建技术的进步,使得研究人员能够以前所未有的分辨率和深度对组织进行三维重建和分析。这些技术为研究组织发育、形态发生和疾病发生机制提供了新的途径,同时也为药物发现和测试提供了便利。 本文基于微观成像技术和人工智能的大规模数据处理技术,在与细胞生物学、植物生物学、神经生物学及脑科学的交叉领域开展生物组织超微结构的自动重建分析方法研究。首先,针对细胞生物学中的不同品系细胞的三维结构差异,基于结构光照明显微镜和光片荧光显微镜探究了拟南芥叶片中不同生长阶段的内质网结构差异和不同品系杨树种子和油松茎尖分生组织的空间分布及三维形态;其次,针对植物生物学中细胞及亚细胞结构与功能的探究,使用连续切片自动收集系统和扫描电子显微镜,探究了不同发育时期和发育部位拟南芥雄蕊和根尖细胞的超微结构的变化;最后,针对神经生物学和脑科学的微观图谱构建,使用基于自动条带收集超薄切片机的高速电镜三维系统,重建了大鼠睾丸精细胞和斑马鱼幼鱼全脑微观连接组,为探索神经系统精细的功能调控提供了结构性的证据。论文的主要成果和贡献如下: 1. 面向植物样品的三维光学显微数据的快速重建算法及分析应用。针对光学显微镜拍摄图像在三维重建过程中遇到的光学畸变和像差等问题,本文基于深度学习设计了一套三维光学显微数据中超微结构的快速重建算法。首先将得到的三维序列光镜图像进行去噪、增强及反卷积处理后,通过改进基于transformer模型的识别网络,对不同类型的组织结构进行了重建。本研究将算法应用于使用结构光照明显微镜成像的不同生长阶段的拟南芥幼苗叶片细胞的内质网时空数据和光片荧光显微镜成像的不同品系杨树种子和油松茎尖分生组织三维数据,定量分析了不同生长阶段内结构的差异,统计和验证了内质网对环境胁迫的动态响应以及为植物组织内多细胞类型的精确空间排列和拓扑结构提供了宝贵的见解,可作为植物研究的数字化参考。 2. 面向植物样品的三维电子显微数据的密集重建算法及分析应用。本文提出了一套基于体电子显微镜序列图像的密集重建算法,对组织细胞内超过10种不同类型的细胞器进行了有效的识别和区分。该框架确保结果的端到端直接输出,包括拓扑网络和形态学分析。本研究将算法应用于使用连续切片自动收集系统和扫描电子显微镜成像的不同发育时期的拟南芥雄蕊数据和拟南芥根尖数据,重建结果的分析证明了细胞的多样性以及具有相似特征的细胞倾向于在特定区域聚集。同时为细胞发育提供了全面的3D视图,这将有助于理解植物细胞生长和分化背后的分子机制。 3. 超大体量三维电镜数据的分布式计算框架设计及斑马鱼全脑连接网络分析。针对大体量动物组织的重建面临的海量数据处理等问题,本文设计了一套应用于超大体量数据的大规模神经环路算法重建的计算框架。 |
英文摘要 | Reconstructing biological tissues at the microscopic scale is crucial for gaining a deep understanding of tissue structure, function, and disease. Traditional two-dimensional imaging analysis has limitations in capturing the complex three-dimensional structure of tissues, which is essential for elucidating the role of tissues in health and disease. In recent years, advances in microscopic tissue reconstruction techniques, such as confocal microscopy, two-photon microscopy, electron microscopy, and tissue clearing methods, have enabled researchers to reconstruct and analyze tissues in three dimensions with unprecedented resolution and depth. These techniques provide new avenues for studying tissue development, morphogenesis, and disease mechanisms, as well as facilitating drug discovery and testing. This paper focuses on the research of automatic reconstruction and analysis methods for ultra-microstructures of biological tissues at the intersection of cell biology, plant biology, neurobiology, and brain science, based on microscopic imaging techniques and large-scale data processing techniques using artificial intelligence. Firstly, to address the differences in three-dimensional structures of cells from different strains in cell biology, this study investigated the structural differences of the endoplasmic reticulum in Arabidopsis thaliana leaves at different growth stages and the spatial distribution and three-dimensional morphology of seed and stem apical meristem tissues of different poplar strains using structured illumination microscopy and light sheet fluorescence microscopy. Secondly, to explore the relationship between cellular and subcellular structures and functions in plant biology, this study used an automated tape-collecting ultramicrotome system and scanning electron microscopy to investigate the changes in ultrastructure of Arabidopsis anthers and root tip cells at different developmental stages and locations. Finally, to construct microscopic atlases in neurobiology and brain science, this study used a high-speed electron microscopy 3D system based on an automated tape-collecting ultramicrotome to reconstruct the microscopic connectome of rat testicular spermatogenic cells and the whole brain of zebrafish larvae, providing structural evidence for exploring the precise functional regulation of the nervous system. The main achievements and contributions of this paper are as follows: 1. Fast Reconstruction Algorithm and Analytical Application for 3D Optical Microscopy Data of Plant Samples. To address the issues of optical distortion and aberration encountered during the 3D reconstruction process of optical microscope images, this paper designs a set of fast reconstruction algorithms for ultra-microstructures in 3D optical microscopy data based on deep learning. First, the obtained 3D sequence of optical microscope images undergoes denoising, enhancement, and deconvolution processing. Then, different types of tissue structures are reconstructed through an improved recognition network based on the transformer model. this study applied the algorithm to the spatiotemporal data of the endoplasmic reticulum in Arabidopsis thaliana seedling leaf cells at different growth stages imaged by structured illumination microscopy, and the 3D data of seed and stem apical meristem tissues of different poplar strains imaged by light sheet fluorescence microscopy. This study quantitatively analyzed the differences in structures at different growth stages, statistically validated the dynamic response of the endoplasmic reticulum to environmental stresses, and provided valuable insights into the precise spatial arrangement and topological structure of multiple cell types within plant tissues. This can serve as a digital reference for plant research. 2. Dense Reconstruction Algorithm and Analytical Application for 3D Electron Microscopy Data of Plant Samples. This paper proposes a set of dense reconstruction algorithms based on serial block-face scanning electron microscopy images, which effectively identifies and distinguishes more than 10 different types of organelles within tissue cells. The framework ensures end-to-end direct output of results, including topological networks and morphological analysis. This study applied the algorithm to data from Arabidopsis thaliana anthers at different developmental stages and Arabidopsis root tips, which were imaged using an automated tape-collecting ultramicrotome system and scanning electron microscopy. The analysis of the reconstruction results demonstrated the diversity of cells and the tendency of cells with similar characteristics to cluster in specific regions. At the same time, it provided a comprehensive 3D view of cell development, which will help understand the molecular mechanisms behind plant cell growth and differentiation.
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关键词 | 光学显微镜,体电子显微镜,多模态成像,三维重建,自动分割算法 |
语种 | 中文 |
文献类型 | 学位论文 |
条目标识符 | http://ir.ia.ac.cn/handle/173211/57219 |
专题 | 毕业生_博士学位论文 |
推荐引用方式 GB/T 7714 | 刘家正. 面向生物多模态显微成像数据的大规模三维重建方法及应用[D],2024. |
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