Obtain and add files to the project

There are 5 data files needed for CosMx data import: polygons.csv.gz, exprMat_file.csv.gz, fov_positions_file.csv.gz, metadata_file.csv.gz, tx_file.csv.gz. The last file (tx_file.csv.gz) contains the transcript information and is not required when importing protein data. Additionally the user will need an image folder, called either CellComposite or CellOverlay (please ensure the images in this folder are not blank before uploading them to Flow). This image folder contains one image per FOV and will be used for the visualisation of the spatial data.

Transfer the data to your Flow server before moving onto the import step.

Data import

• Create a new project and click the 'Add data' button in the Analyses tab  
• Select Single cell > Spatial > NanoString CosMx and click Next