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The PXL File Format

Molecular Pixelation (MPX) data comes in the form of the pxl file format (.pxl), which is especially made to be easily used by single cell omics analysis tools such as Scanpy and Seurat, while also containing the additional single cell spatial information gained from MPX. The pxl file is a zipped folder containing five elements:

  • adata - AnnData file containing the cell by cell count data, similarly to other single cell omics techniques.
  • polarization - A table containing the spatial protein polarity scores per each detected cell.
  • colocalization - A table containing the spatial protein-protein colocalization scores per each detected cell.
  • edgelist - A table containing the edgelist; a list of edges in the graph components which each correspond to a cell. This file is used to visualize individual cells, and has been used to calculate spatial statistics like polarizaty scores and colocalization scores.
  • metadata - a json file with metadata with information such as original ID and the version of Pixelator that generated the .pxl file.

The Edge List

The edge list is named as such as it contains the edges that constitute the MPX graph, where each graph component corresponds to a cell. Each row in the edge list is an edge, constituting a uniquely identified antibody molecule and is identified by a UMI, UPIA, and a UPIB. The UPIA is the unique identifier for the specific A pixel, while the UPIB is the unique identifier for the B pixel, and the edge (unique antibody molecule) represents a link between the UPIA and UPIB in a bipartite graph. This information can be used to build graphs for each individual cell and infer spatial relationships between antibody molecules to calculate spatial statistics and to visualize the cell.