Space Ranger v4.0 includes support for cell and nucleus segmentation in the spaceranger count pipeline for Visium HD and Visium HD 3' data. When this feature is enabled, most of the following output files and directories are provided in the segmented_outputs folder.
The barcode_mappings.parquet file efficiently stores spatial mapping information, essentially functioning as a CSV that tracks key relationships within your Visium HD data. It details which 2 µm barcodes (Square_002um) correspond to larger 8 µm bins (Square_008um) and 16 µm bins (Square_016um), and which inferred cells (Cell_id) they belong to. Additionally, it indicates whether a given barcode falls within a nucleus (In_nucleus) and/or a cell (In_cell).
To convert this file to a more human-readable CSV format, you can use the parquet-tools utility with the following command:
parquet-tools cat -l 3 -f csv path/to/outs/barcode_mappings.parquet
Here is an example of the file's structure once converted to CSV:
Square_002um,Square_008um,Square_016um,Cell_id,In_nucleus,In_cell
s_002um_00000_00000,s_008um_00000_00000,s_016um_00000_00000,cellid_000000000,false,false
s_002um_00000_00001,s_008um_00000_00000,s_016um_00000_00000,cellid_000000000,false,false
S_002um_00000_00002,s_008um_00000_00000,s_016um_00000_00000,cellid_000199028,false,true
The analysis/ folder contains results of the clustering, differential expression, PCA, and UMAP analyses performed downstream of cell segmentation. For more information, see the Secondary Analysis page.
Space Ranger generates cell (cell_segmentations.geojson) and nucleus (nucleus_segmentations.geojson) segmentation masks in GeoJSON format, which can also be provided as input to the spaceranger count pipeline. For advanced analysis, annotated versions of these masks, incorporating graph-based clustering results, are also output as graphclust_annotated_cell_segmentations.geojson and graphclust_annotated_nucleus_segmentations.geojson.
The cloupe.cloupe contains segmented cells. Open this file in Loupe Browser v9.0 or later to interactively visualize and analyze your Visium data.
The filtered feature-cell matrix, which contains only tissue-associated barcodes, is provided in both MEX and H5 formats.
The raw feature-cell matrix, which includes both background and tissue-associated barcodes, is provided in both MEX and H5 formats.