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10x Genomics
Visium Spatial Gene Expression

Spatial Gene Expression Outputs

The spaceranger count pipeline for single-library analysis of fresh frozen (FF) and formalin-fixed paraffin embedded (FFPE) samples will each output the files described below in the outs/ directory. The file hierarchy of the subfolder outs/ will follow this structure:

├── analysis
│   ├── clustering
│   ├── diffexp
│   ├── pca
│   ├── tsne
│   └── umap
├── cloupe.cloupe
├── filtered_feature_bc_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── filtered_feature_bc_matrix.h5
├── metrics_summary.csv
├── molecule_info.h5
├── possorted_genome_bam.bam     --------|
├── possorted_genome_bam.bam.bai         | [Optional outputs, disabled using --no-bam argument]
├── possorted_genome_bam.bam.csi --------|
├── probe_set.csv  [For Visium FFPE samples only]
├── raw_feature_bc_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── raw_feature_bc_matrix.h5
├── spatial
│   ├── aligned_fiducials.jpg
│   ├── aligned_tissue_image.jpg  [CytAssist workflow only]
│   ├── barcode_fluorescence_intensity.csv  [For --darkimage fluorescence image input only]
│   ├── cytassist_image.tiff  [CytAssist workflow only]
│   ├── detected_tissue_image.jpg
│   ├── scalefactors_json.json
│   ├── spatial_enrichment.csv
│   ├── tissue_hires_image.png
│   ├── tissue_lowres_image.png
│   └── tissue_positions.csv
└── web_summary.html

Gene Expression library outputs

The table lists the output files within the outs/ subfolder indicating workflow specific files:

File NameDescription
web_summary.htmlRun summary metrics and plots in HTML format, described in Web Summary
cloupe.cloupeLoupe Browser visualization and analysis file
spatial/ Folder containing outputs that capture the spatiality of the data. Learn more
spatial/aligned_fiducials.jpgAligned fiducials QC image
spatial/aligned_tissue_image.jpgAligned CytAssist and Microscope QC image. Present only for CytAssist workflow
spatial/barcode_fluorescence_intensity.csvCSV file containing the mean and standard deviation of fluorescence intensity for each spot and each channel. Present for fluorescence image input specified by --darkimage
spatial/cytassist_image.tiffInput CytAssist image in original resolution that can be used to rerun the pipeline. Present only for CytAssist workflow
spatial/detected_tissue_image.jpgDetected tissue QC image
spatial/scalefactors_json.jsonScale conversion factors for spot diameter and coordinates at various image resolutions
spatial/spatial_enrichment.csvFeature spatial autocorrelation analysis using Moran's I in CSV format
spatial/tissue_hires_image.pngDownsampled full resolution image. The image dimensions depend on the input image and slide version.
spatial/tissue_lowres_image.pngFull resolution image downsampled to 600 pixels on the longest dimension
spatial/tissue_positions.csvCSV containing spot barcode, if the spot was called under (1) or out (0) of tissue, the array position, image pixel position x, and image pixel position y for the full resolution image
analysis/Folder containing secondary analysis data including graph-based clustering and K-means clustering 2-10; differential gene expression between clusters; and PCA, t-SNE, and UMAP dimensionality reduction. Learn more
metrics_summary.csvRun summary metrics in CSV format, described in Gene Expression Metrics page.
probe_set.csvCopy of the input probe set reference CSV file. Present only for Visium FFPE data
possorted_genome_bam.bamIndexed BAM file containing position-sorted reads aligned to the genome and transcriptome, annotated with barcode information
possorted_genome_bam.bam.baiIndex for possorted_genome_bam.bam
In cases where the reference transcriptome is generated from a genome with very long chromosomes (>512 Mbp), Space Ranger v2.0+ generates a possorted_genome_bam.bam.csi index file instead.
filtered_feature_bc_matrix/Contains only tissue-associated barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column), as described in the Feature-Barcode Matrix page. This file can be input into third-party packages and allows users to wrangle the barcode-feature matrix (e.g. to filter outlier spots, run dimensionality reduction, normalize gene expression).
filtered_feature_bc_matrix.h5Same information as filtered_feature_bc_matrix/ in HDF5 format.
raw_feature_bc_matrices/Contains all detected barcodes in MEX format. Each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column), as described in the Feature-Barcode Matrix page.
raw_feature_bc_matrix.h5Same information as raw_feature_bc_matrices/ in HDF5 format.
molecule_info.h5Contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or protein barcode. This file is required for additional analysis spaceranger pipelines including aggr, targeted-compare and targeted-depth. Learn more