phenoptr contains functions that make it easier to read and analyze data tables and images created by Akoya Biosciences' inForm software.
phenoptr is part of the Akoya Biosciences Phenoptics family of Quantitative Pathology Research Solutions. For more information visit the Phenoptics™ home page.
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).
Useful links: