phenoptrExamples - Extended examples for use with the phenoptr package

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

For introductory examples, please see the Tutorials included in the phenoptr documentation.

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

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)

Getting started

The Tutorials demonstrate aggregation of data across multiple fields and slides.

Sample data

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.

Stain Epitope Composite Phenotype
DAPI Nucleus Blue N/A
Opal520 PDL1 Red N/A
Opal540 CD8 Yellow Yellow
Opal570 FoxP3 Orange Orange
Opal620 CD68 Magenta Magenta
Opal650 PD1 Green N/A
Opal690 CK Cyan Cyan

Full documentation

See the Tutorials and the full phenoptr documentation.