| reference png | PNG image of the tissue section supplied as the Space Ranger alignment reference image, used to register the capture-area spot grid to the tissue for spatial gene expression analysis. | Not available |
| reference jpg | JPEG image of the tissue section supplied as the Space Ranger alignment reference image, used to register the capture-area spot grid to the tissue for spatial gene expression analysis. | Not available |
| json scale factors | JSON file output by Space Ranger (scalefactors_json.json) that records the scaling factors needed to relate spot positions to the full-resolution, high-resolution, and low-resolution tissue images. | Not available |
| probe dataset csv | CSV file listing the probe set used in a probe-based (e.g., FFPE) Visium assay, including probe IDs and the genes they target. | Not available |
| qc result html | HTML quality-control report summarizing metrics from Space Ranger processing of a Visium sample, such as sequencing, alignment, and spatial coverage statistics. | EDAM:data_3914 |
| filtered mex | Filtered feature-barcode expression matrix in Market Exchange (MEX) sparse-matrix format, containing only spots that Space Ranger called as being covered by tissue in a Visium sample. | NCIT:C184778 |
| unfiltered mex | Unfiltered feature-barcode expression matrix in Market Exchange (MEX) sparse-matrix format, containing all spots on the capture area regardless of tissue coverage, output by Space Ranger. | NCIT:C184778 |
| tissue_positions | Space Ranger output file (tissue_positions.csv/.parquet) that maps each spot barcode to its row/column array coordinates and pixel coordinates on the full-resolution tissue image, and indicates whether the spot overlaps tissue. | Not available |
| barcodes | Space Ranger output file (barcodes.tsv) listing the spot barcode sequences corresponding to the columns of the feature-barcode expression matrix. | Not available |
| features | Space Ranger output file (features.tsv) listing the gene/feature IDs and names corresponding to the rows of the feature-barcode expression matrix. | Not available |
| fiducial image png | PNG image showing the fiducial frame (alignment markers) printed on the Visium slide, used by Space Ranger/Loupe Browser to register the capture area to the tissue image. | Not available |
| fiducial image jpg | JPEG image showing the fiducial frame (alignment markers) printed on the Visium slide, used by Space Ranger/Loupe Browser to register the capture area to the tissue image. | Not available |
| detected image png | PNG image output by Space Ranger showing the tissue area and spots detected during the tissue-detection step, overlaid on the slide image. | Not available |
| detected jpg | JPEG image output by Space Ranger showing the tissue area and spots detected during the tissue-detection step, overlaid on the slide image. | Not available |
| high res image | High-resolution tissue microscopy image (tissue_hires_image.png) bundled in Space Ranger spatial output, used for detailed visualization of the tissue section with the overlaid spot grid. | Not available |
| low res image | Low-resolution, downsampled tissue microscopy image (tissue_lowres_image.png) bundled in Space Ranger spatial output, used for lightweight visualization of the tissue section with the overlaid spot grid. | Not available |
| json scale factors | JSON file output by Space Ranger (scalefactors_json.json) that records the scaling factors needed to relate spot positions to the full-resolution, high-resolution, and low-resolution tissue images. | Not available |
| probe dataset csv | CSV file listing the probe set used in a probe-based (e.g., FFPE) Visium assay, including probe IDs and the genes they target. | Not available |