Modular, Open-Sourced Multiplexing for Democratizing Spatial Multi-Omics

Spatial omics technologies have revolutionized the field of biology by enabling the visualization of biomolecules within their native tissue context. However, the high costs associated with proprietary instrumentation, specialized reagents, and complex workflows have limited the broad application of these techniques. In this study, we introduce Python-based Robotic Imaging and Staining for Modular Spatial omics (PRISMS), an open-sourced, automated multiplexing pipeline compatible with several sample types and Nikon NIS Elements Basic Research software. PRISMS utilizes a liquid handling robot with thermal control to enable rapid, automated staining of RNA and protein samples. The modular sample holders and Python control facilitate high-throughput, single-molecule fluorescence imaging on widefield and confocal microscopes.We successfully demonstrate the versatility of PRISMS by imaging tissue slides and adherent cells. We also show that PRISMS can be used to perform super-resolved imaging, such as super-resolution radial fluctuations (SRRF) 1. PRISMS is a powerful tool that can be used to democratize spatial omics by providing researchers with an accessible, reproducible, and cost-effective solution for multiplex imaging. Specifically, PRISMS is an open-sourced, automated multiplexing pipeline for spatial omics, is compatible with several sample types and Nikon NIS Elements Basic Research software, performs high-throughput, single-molecule fluorescence imaging on widefield and confocal microscopes, and can be used to perform super-resolved imaging, such as SRRF. Overall, PRISMS is a powerful tool that can be used to democratize spatial omics by providing researchers with an accessible, reproducible, and cost-effective solution for multiplex imaging. This open-source platform will enable researchers to push the boundaries of spatial biology and make groundbreaking discoveries.空间组学技术（Spatial omics technologies）通过实现生物分子在其原生组织环境中的可视化，革新了生物学领域。然而，专有仪器、专用试剂与复杂操作流程带来的高昂成本，限制了这类技术的广泛应用。本研究中，我们推出了基于Python的模块化空间组学自动化成像与染色系统（Python-based Robotic Imaging and Staining for Modular Spatial omics，PRISMS）——一款开源自动化多重分析流程，兼容多种样本类型与尼康NIS Elements Basic Research软件。PRISMS搭载带温控功能的液体处理机器人，可实现RNA与蛋白质样本的快速自动化染色。模块化样本架与Python控制系统可助力在宽场显微镜及共聚焦显微镜上实现高通量单分子荧光成像。我们通过对组织切片与贴壁细胞进行成像，成功验证了PRISMS的多功能性。此外我们证实，PRISMS可用于开展超分辨率成像，例如超分辨率径向波动成像（super-resolution radial fluctuations，SRRF）¹。PRISMS是一款强大工具，可通过为研究人员提供易用、可重复且高性价比的多重成像解决方案，推动空间组学的普及。具体而言，PRISMS作为面向空间组学的开源自动化多重分析流程，兼容多种样本类型与尼康NIS Elements Basic Research软件，可在宽场显微镜及共聚焦显微镜上实现高通量单分子荧光成像，同时支持开展包括SRRF在内的超分辨率成像。综上，PRISMS可通过为研究人员提供易用、可重复且高性价比的多重成像方案，助力空间组学的普及，是一款极具应用价值的工具。这一开源平台将助力研究人员突破空间生物学的研究边界，取得突破性科研成果。