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)

Arguments

map_path

Path to the map file or a cell seg data file in the same directory.

Value

A named list of images, one for each map in the source file.

Details

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.

See also

Other file readers: get_field_info, list_cell_seg_files, read_cell_seg_data, read_components

Examples

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"