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10x Genomics
Visium Spatial Gene Expression

Image Outputs

The pipeline output contains a subdirectory named spatial which stores imaging related files. These files are useful to confirm fiducdial alignment and tissue detection. However, the user supplied original full resolution images are used for visualization in Loupe Browser. The imaging files include the following:

aligned fiducials detected tissue

The spots are arranged using a orange crate packing to maximize packing density. Further explanation of this arrangement can be found in this article.

Note that the tissue_positions_list.csv contains the same information about the barcode whitelist and their slide coordinates as that contained in the barcodes folder that comes bundled with Space Ranger (spaceranger-x.y.z/lib/python/cellranger/barcodes where x.y.z represent the version number).