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’.
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)