Obtain and add files to the project

There are 5 data files needed for CosMx data import: polygons.csv, exprMat_file.csv, fov_positions_file.csv, metadata_file.csv, tx_file.csv. The last file (tx_file.csv) 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.

Create a folder per sample, the folder will contain the 5 files and the image folder.

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  

• Click Add sample, name it and select the sample folder.
• The importer will automatically select the image folder. If you have uploaded more than one image folder, select the one you want to use for the project.
• Select the appropriate annotation files (in this case we'll use hg38 - Ensembl Transcripts release 109)
• Leave the rest of the settings as default and click Finish

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