Cell3D 数据库发布，支持单细胞与空间组学的 3D 交互可视化和 crosstalk 分析
Cell3D: a comprehensive database for interactive 3D visualization and crosstalk analysis of single-cell and spatial omics
Cell3D 是一个可免费访问的交互式数据库，用于单细胞与空间转录组数据的整合探索、3D 可视化和 crosstalk 分析。它收录 898 个公开数据集，其中单细胞 397 个、空间转录组 501 个，覆盖 11 个物种、105 种疾病、756 种细胞类型和 83 个器官/组织，共 2 924 646 个单细胞和空间 spot。数据库整合 12 个主流功能注释系统，用户可从基因表达、细胞聚类到通路活性和临床表型多个层级查看数据。
来源：Nucleic Acids Research · doi.org
Single-cell and spatial transcriptomics yield large-scale, high-dimensional datasets. However, cross-feature integrative exploration is constrained, since most current platforms support a single data type and lack interactive visualization for multi-feature analysis. To address this unmet need, we developed Cell3D, an accessible and versatile interactive platform designed to advance integrative multi-level feature analysis. Cell3D curates 898 publicly available datasets, comprising 397 single-cell and 501 spatial transcriptomic datasets, encompassing 2 924 646 single cells and spatial spots across 105 diseases, 756 cell types, and 83 organs/tissues from 11 species. The database integrates twelve mainstream functional annotation systems, providing a comprehensive landscape for dissecting molecular features across spatial and cellular dimensions. Users can explore data at multiple levels, from gene expression and cell clusters to pathway activities and clinical phenotypes. Cell3D offers a suite of user-friendly functionalities, including customizable 2D/3D interactive visualization for dynamic multi-level feature projection, flexible data integration with automatic recognition, quantitative crosstalk analysis, and microenvironment-focused integrative analysis supporting disease research and biomarker discovery. Collectively, Cell3D enables exploration of tissue microenvironments at both cellular and spatial resolutions, bridging molecular perturbations and tissue architecture in health and disease. The database is freely accessible at https://bio-bigdata.hrbmu.edu.cn/Cell3D.