Analyzing Highly Multiplexed and Multi-Modal Spatial-Omics ChipCytometry™ Datasets

ChipCytometry™ is a technique for collecting and analyzing highly multiplexed spatial cytometry data that has been established since 2009, and commercialized since 2016 with the ZellScannerOne™ instrument. Introduction of the CellScape™ instrument in the Spring of 2022 now affords ChipCytometry users high capacity, higher resolution, and full automation. Here, we will explore the utility of the ChipCytometry dataset through a set of sample analysis pipelines. First, the pipeline native to the CellScape and ZellScannerOne is a generalized image analysis and cytometry method providing immediate access to highly multiplexed spatial datasets for novice users and those ancillary to image analysis. Second, a custom and sophisticated pipeline with extremely high spatial fidelity that additionally incorporates both transcriptomics and proteomics data highlights both the versatility of the platform and easy compatibility with common open-source analysis tools. Finally, we will highlight recent advancements to the ChipCytometry on-board data analysis architecture, where simple and fast expansion of the spatial analysis capabilities of the pipeline increase spatial analysis fidelity while maintaining base cytometry functionality. These three examples illustrate the flexibility of the ChipCytometry platform as well as the versatility of the dataset itself, which is unique in the multiplexing arena as a scheme that is all at once highly agnostic to detection scheme, exceptionally accurate through HDR image capture and subcellular spatial resolution, and now scalable with high sample throughput and automation.

 

Learning Objectives