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

## Details

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).