MTX Files

Matrix Market (.mtx) file outputs for raw, grid-binned, cell-binned, and nuclei-binned data.

• The following outputs are produced for each sample:

  • Raw or un-binned matrix files
  • Grid-binned matrix files
  • Cell-binned matrix files
  • (Optional) Nuclei-binned matrix files

The following three files provide per-bin or per-cell gene expression information in the commonly used Matrix Market (*.mtx) format:

• matrix.mtx.gz

  • Count of unique molecules for each cell and gene pair, in sparse matrix format.
• barcodes.tsv.gz

  • Raw matrix files format: SBC:Y:X
  • Grid-binned format: bin10:Y:X
  • Cell-binned format: cellid:Y:X
  • NOTES:

    • All X and Y positions are reported in microns using the global substrate position.
    • Cell-binned and grid-binned data report the X:Y position of the center of the cell or bin.
• features.tsv.gz

  • Gene name and ID for each gene in the matrix.

What are Matrix Market Files?

Matrix Market (.mtx) files are a standard sparse matrix format used in single-cell and spatial transcriptomics to efficiently store large gene expression matrices. The format is particularly efficient because spatial transcriptomics data is sparse (most genes are not expressed in most cells/bins).

File Structure

A typical Matrix Market output consists of three files:

1. matrix.mtx.gz - The sparse expression matrix

   • Contains only non-zero values
   • Format: row_index column_index value
2. features.tsv.gz - Gene/feature information

   • One gene per line
   • Typically: gene_id gene_name feature_type
3. barcodes.tsv.gz - Cell, bin, or spatial barcode identifiers

   • One barcode per line
   • Can be spatial barcodes, cell IDs, or spatial bin identifiers

Matrix Market File Format Example

matrix.mtx header:

%%MatrixMarket matrix coordinate integer general
%
30000 5000 1500000
1 1 5
1 234 3
2 1 12
...

• Line 1: Format specification.
• Line 2: Comment line.
• Line 3: n_genes n_barcodes n_nonzero_entries.
• Following lines: gene_index barcode_index count.

For help using these files with third-party tools, see Third Party Tools.