Reads an inForm `binary_seg_maps.tif`` file and returns a named list of images. The names reflect the content of the individual images. Possible names are Nucleus, Cytoplasm, Membrane, Object, TissueClassMap, and ProcessRegionImage; not every image file will include all names.
read_maps(map_path)Path to the map file or a cell seg data file in the same directory.
A named list of images, one for each map in the source file.
Images are oriented to match the coordinates in a cell seg data file, i.e. (0, 0) at the top left and the row corresponding to Y and column corresponding to X.
Other file readers:
get_field_info(),
list_cell_seg_files(),
read_cell_seg_data(),
read_components()
path <- system.file("extdata", "sample",
"Set4_1-6plex_[16142,55840]_binary_seg_maps.tif",
package = "phenoptr")
maps <- read_maps(path)
names(maps)
#> [1] "Nucleus" "Cytoplasm" "Membrane" "Tissue"