CosMx SMI Knowledge Base: Data Analysis

NanoString offers several support resources for CosMx SMI data analysis to aid researchers with different levels of expertise or access to computational biology resources. Analysis can be performed in the AtoMx Spatial Informatics Platform (SIP) or using open-source software. Determining which is the best way forward for your data is dependent on a few factors.

For researchers who want to analyze their own data but do not have computational biology resources such as coding support, we recommend working with the modules and pipelines provided in the AtoMx SIP. AtoMx SIP is a no-code informatics solution that allows researchers to analyze spatial multiomics data with NanoString-developed analysis modules. Learn more about working in AtoMx SIP from the AtoMx 101 course in NanoString University and documents such as the AtoMx SIP User Manual and CosMx SMI Data Analysis User Manual. The CosMx SMI Liver Dataset Vignette, though written for a coding audience, is another great resource as it explains the types of data that CosMx SMI generates, data organization and handling, and some theory of spatial biology data analysis.

For researchers with access to computational biology resources such as coding support, CosMx SMI data can be exported in various file formats (TileDB, Seurat, flat files) and processed outside of CosMx SMI or AtoMx SIP. In this case, there is practically no limit to the analysis pipelines that are possible through open-source software. These researchers may also find value in working in the AtoMx SIP, as it provides the flexibility to create custom analysis pipelines and scripts in addition to the pre-built modules and had built in data visualization. Recommended resources include the CosMx SMI Data Analysis User Manual and Data Export Guide, as well as the NanoString Biostats workspace in GitHub for custom scripts with user documentation.

For researchers who prefer to have NanoString experts analyze the data, we provide the Spatial Data Analysis Service (sDAS). Work with our team of computational biologists to find the answers to your research questions.

Yes! We have 4 CosMx SMI Datasets available for download on the NanoString website. These datasets include human pancreas (RNA; Whole Transcriptome), human liver (RNA; 1000-Plex Human Universal Cell Characterization Panel), human frontal cortex (RNA; 6K Human Discovery Panel), and mouse brain (RNA; 1000-Plex Mouse Neuroscience Panel).

We also have an archival non-small cell lung cancer dataset. This data set was obtained using a CosMx SMI prototype and does not reflect the quality of data generated on commercial instruments.