phenoptr
packageThe PerkinElmer Phenoptics team is now part of Akoya Biosciences.
For the latest version of phenoptrExamples
please visit https://akoyabio.github.io/phenoptrExamples/. For information about
the acquisition, see this
press release.
phenoptrExamples
contains
example code
and extended data sets demonstrating
the use of the phenoptr package to
analyze data from multiple fields.
phenoptr
documentation.phenoptr
contains functions that make it easier to read and analyze data tables
and images created by PerkinElmer's inForm® software.
phenoptr
and phenoptrExamples
are part of the PerkinElmer Phenoptics™
family of
Quantitative Pathology Research Solutions. For more information
visit the Phenoptics™
home page.
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("PerkinElmer/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)CD68+
(macrophage)FoxP3+
(regulatory T cell)CK+
(tumor)other
Four files are included for each image:
composite_image.jpg
)cell_seg_data.txt
)binary_seg_maps.tif
)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
See the Tutorials and the full phenoptr documentation.
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