phenoptr contains functions that make it easier to read and analyze data tables and images created by Akoya Biosciences' inForm software.

Details

phenoptr is part of the Akoya Biosciences Phenoptics family of Quantitative Pathology Research Solutions. For more information visit the Phenoptics™ home page.

Package options

read_cell_seg_data converts pixel measurements to microns. Several other functions also implicitly convert pixels to microns. The default conversion is given by getOption('phenoptr.pixels.per.micron'), which has a default value of 2 pixels/micron, i.e. pixels are 0.5 micron square (the resolution of 20x MSI fields taken on Vectra Polaris and Vectra 3). To use a different value, either pass a pixels_per_micron parameter to functions which take one, or set options(phenoptr.pixels.per.micron=<new value>).

Several distance functions will use a fast implementation based on the rtree package if it is available. To disable this and use the simpler distance matrix-based implementations, set options(use.rtree.if.available=FALSE).

See also