BCTMA dataset

Dataset associated with manuscript titled "Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms".

Descriptions of column names are below.

source: name of TMA

scene: unique core id for particular TMA

cell: unique cell id for particular source and scene

centroid_<x,y>: physical location of cell (0.325um/pixel)

<marker>_<compartment>: mean intensity for the given compartment, e.g. pHH3_Nuclei, Ecad_Ring. Here "Ring" means mean intensity from area defined by the full cell segmentation mask minus the nuclear segmentation mask, i.e. a 2D approximation of the cytoplasm.

Enorm_scene_<marker>_<compartment>: Same as above, but used RESTORE normalization for each core for each marker.

40_neighbor: PhenoGraph cluster label (we set k=40 when building the k-nearest neighbor graph)

metacluster: aggregated PhenoGraph cluster labels, based on hierarchical clustering to group cells in similar non-functional epigenetic/proliferative/stress states and to preserve known biological differences.

metacluster_name: semantic label for metacluster based on marker expression.