phenoptrExamples contains example code and extended data sets demonstrating the use of the phenoptr package to analyze data from multiple fields.

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

• Aggregating data from multiple fields demonstrates reading and processing cell seg data from multiple fields and samples.
• Aggregating touch counts shows how to count touching cells across multiple fields and aggregate the results per sample.

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)
• CD68+ (macrophage)
• FoxP3+ (regulatory T cell)
• CK+ (tumor)
• other

Four files are included for each image:

• Composite image in JPEG format (composite_image.jpg)
• Cell segmentation data (cell_seg_data.txt)
• Cell segmentation maps (binary_seg_maps.tif)
• Composite with tissue segmentation (image_with_tissue_seg.jpg)

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.

See the Tutorials and the full phenoptr documentation.