phenoptr contains functions that make it easier to read and analyze data tables and images created by Akoya Biosciences’ inForm® software.
phenoptrExamples are part of the Akoya Biosciences Phenoptics™ family of Quantitative Pathology Research Solutions.
Installation is from GitHub. Note: this package includes many large files. The entire package contains over 150 MB of data files.
# install.packages("devtools") devtools::install_github("akoyabio/phenoptrExamples", build_vignettes=TRUE)
The Tutorials demonstrate aggregation of data across multiple fields and slides.
phenoptrExamples contains selected inForm output from nine images taken from three samples of lung cancer tissue.
The tissue was stained with DAPI counterstain and Opal™ stains and imaged on a Vectra® Polaris™ Automated Quantitative Pathology Imaging System. The MSI images were unmixed to components, segmented and classified with inForm® image analysis software.
The sample cell data includes these phenotypes:
CD8+(cytotoxic T cell)
FoxP3+(regulatory T cell)
Four files are included for each image:
To see a full list of all included files, use the command
list.files(system.file("extdata", "samples", package = "phenoptrExamples")).
This table shows the stains used, the epitopes they were bound to, and the colors used to show the stains in the composite and phenotype views.