phenoptrExamples - Extended examples for use with the phenoptr package

<style type="text/css"> img { border: none; } table { width: auto !important; } </style>

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.

• 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.

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.