The PXL File Format

Proximity Network Assay and Molecular Pixelation Assay data in PXL files (.pxl), 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. 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.