ISAT DEMO

In ISAT: Extract Cell Density and Nearest Distance Based on 'PerkinElmer InForm' Software Output

Reading the dataset

This is a DEMO example, based on one image. The 20x images were acquired on the Vectra system of PerkinElmer and analyzed in inForm (>=2.2.0). There are seven different phenotypes present in this example: 'Melanoma','CD8 + T cell','CD4+ T cell','T regulatory cell','PDL1+ cell','CD3+ T cell' and 'other'.

require("knitr")
opts_knit$set(root.dir = ".")

library(ISAT)

      filename =c("DEMO_cell_seg_data.txt")
      cell_names = c( 'Melanoma','CD8 + T cell', 'CD4+ T cell', 'T regulatory cell','PDL1+ cell', 'CD3+ T cell','other')
#calculate distance result for the file
      distance_result = findNNs(filename,cell_names)


#calculate density result for the file
      density_result=getFileCount(filename)

ISAT documentation built on May 2, 2019, 9:12 a.m.