Xu Xintian, Su Jimeng, Zhu Rongyi, Li Kailong, Zhao Xiaolu, Fan Jibiao, Mao Fengbiao
Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China.
Cancer Center, Peking University Third Hospital, Beijing, China.
Mol Cancer. 2025 Mar 3;24(1):63. doi: 10.1186/s12943-025-02240-x.
High-resolution three-dimensional (3D) tissue analysis has emerged as a transformative innovation in the life sciences, providing detailed insights into the spatial organization and molecular composition of biological tissues. This review begins by tracing the historical milestones that have shaped the development of high-resolution 3D histology, highlighting key breakthroughs that have facilitated the advancement of current technologies. We then systematically categorize the various families of high-resolution 3D histology techniques, discussing their core principles, capabilities, and inherent limitations. These 3D histology techniques include microscopy imaging, tomographic approaches, single-cell and spatial omics, computational methods and 3D tissue reconstruction (e.g. 3D cultures and spheroids). Additionally, we explore a wide range of applications for single-cell 3D histology, demonstrating how single-cell and spatial technologies are being utilized in the fields such as oncology, cardiology, neuroscience, immunology, developmental biology and regenerative medicine. Despite the remarkable progress made in recent years, the field still faces significant challenges, including high barriers to entry, issues with data robustness, ambiguous best practices for experimental design, and a lack of standardization across methodologies. This review offers a thorough analysis of these challenges and presents recommendations to surmount them, with the overarching goal of nurturing ongoing innovation and broader integration of cellular 3D tissue analysis in both biology research and clinical practice.
高分辨率三维（3D）组织分析已成为生命科学领域一项变革性的创新技术，能够深入洞察生物组织的空间结构和分子组成。本综述首先追溯了塑造高分辨率3D组织学发展的历史里程碑，着重介绍了推动当前技术进步的关键突破。接着，我们系统地对高分辨率3D组织学技术的各个类别进行了分类，讨论了它们的核心原理、功能及固有局限性。这些3D组织学技术包括显微镜成像、断层扫描方法、单细胞和空间组学、计算方法以及3D组织重建（如3D培养和球体）。此外，我们还探讨了单细胞3D组织学的广泛应用，展示了单细胞和空间技术在肿瘤学、心脏病学、神经科学、免疫学、发育生物学和再生医学等领域的应用情况。尽管近年来取得了显著进展，但该领域仍面临重大挑战，包括进入门槛高、数据稳健性问题、实验设计最佳实践不明确以及方法缺乏标准化等。本综述对这些挑战进行了全面分析，并提出了克服这些挑战的建议，总体目标是推动细胞3D组织分析在生物学研究和临床实践中的持续创新与更广泛整合。
