Data Exploration and Visualization Tools for HuBMAP and a Human Reference Atlas

为了实现人类生物分子图谱计划(HuBMAP)联合体的生产阶段，我们 将开发几个新的和改进的空间单细胞和生物成像数据可视化 功能。其中包括对结合了2D的大容量3D数据的Vitessce支持 地图、通过HuBMAP数据门户用户界面和Vitessce以2D地图形式进行的空间查询、用户工作空间 通过支持社区和HuBMAP数据的联合分析，外部数据的“数据中心” 可以在人类参考地图集和HuBMAP数据的上下文中显示，新的文件格式 3D空间数据，在HuBMAP数据中部署通用的“cell x gene”矩阵格式 门户、存储和共享使用分析工作区进行的数据分析的能力， 将Vitessce与通用坐标框架导航工具、用户界面增强功能相集成 扩展以适应不断增长的HuBMAP数据(在数据量和丰富性方面，以及 分析结果)，不断发展的人类参考图集用户界面和数据之间的无缝集成 门户用户界面。此外，我们还将研究(1)HuBMAP无缝导航的解决方案 以及通过可视化界面集成社区数据，该界面将数据门户用户界面、 参考图集用户界面和交互式可视化工具，如Vitessce。(2)VITESSCE的延期 通过网络和路径支持功能单细胞和组织数据的解释 支持2D和3D空间信息的可视化。(3)推出“数据枢纽”，即格式 以及可在上下文中查看的空间单细胞和组织数据的注记标准 人类参考地图集(类似于基因组浏览器的“跟踪中心”)。(4)基于用户界面 分析工作区以组装用于数据处理和可视化的执行管道。

To enable the Human BioMolecular Atlas Program (HuBMAP) Consortium production phase, we will develop several new and improved spatial single cell and bioimaging data visualization features. These include Vitessce support for large volume 3D data combined with 2D maps, spatial queries in 2D maps via HuBMAP Data Portal UI and Vitessce, user workspaces with support for co-analysis of community and HuBMAP data, “datahubs” for external data that can be displayed in context of Human Reference Atlas and HuBMAP data, new file formats for 3D spatial data, deployment of generalized “cell x gene” matrix format across HuBMAP Data Portal, ability to store and share analyses of data conducted with analysis workspaces, integration of Vitessce with Common Coordinate Framework navigation tools, UI enhancements to scale to growing body of HuBMAP data (both in terms of volume and richness of the data and analysis results), seamless integration between evolving Human Reference Atlas UI and Data Portal UI. Furthermore, we will research solutions for (1) Seamless navigation through HuBMAP and integrated community data through visual interfaces that combine data portal UI, human reference atlas UI, and interactive visualization tools, e.g., Vitessce. (2) Extension of Vitessce to support interpretation of functional single-cell and tissue data through network and pathway visualizations that support 2D and 3D spatial information. (3) Rollout of “data hubs”, i.e., formats and annotation standards for spatial single-cell and tissue data that can be viewed in the context of the Human Reference Atlas (similar to “track hubs” for genome browsers). (4) UI-based analysis workspaces to assemble execution pipelines for data processing and visualization.