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The PXL File Format​

The PXL file format (.pxl) is used to store data from both Molecular Pixelation Assay (MPX) and Proximity Network Assay (PNA), but the internal structure differs between the two technologies:

MPX (Molecular Pixelation Assay)​

  • File type: Zipped folder (.pxl)
  • Contents:
    • adata – AnnData file containing cell-by-cell count data, similar to other single-cell omics techniques.
    • polarization – Table with spatial protein polarity scores per detected cell.
    • colocalization – Table with spatial protein-protein colocalization scores per detected cell.
    • edgelist – Table listing edges in the graph components for each cell, used for visualization and spatial statistics.
    • metadata – JSON file with metadata such as original ID and Pixelator version.

PNA (Proximity Network Assay)​

  • File type: DuckDB database (.pxl)
  • Contents:
    • adata – AnnData file containing cell-by-cell count data.
    • proximity – Table with spatial protein-protein proximity scores per detected cell (replaces polarization and colocalization from MPX).
    • edgelist – Table listing edges in the graph components for each cell.
    • metadata – Metadata table with information such as original ID and Pixelator version.

The pixelatorR and pixelator libraries facilitate the creation of data structures from PXL files, directly compatible with the most commonly used single-cell omics analysis tools scanpy (Python) and Seurat (R). These data structures include protein abundance data for common analyses such as data-driven clustering and cell annotation, along with the technology-specific spatial and graph information.