Create giotto polygons from mask file#
Last Updated: Oct 02, 2023
Description#
Creates Giotto polygon object from a mask file (e.g. segmentation results)
Usage#
createGiottoPolygonsFromMask(
maskfile,
mask_method = c("guess", "single", "multiple"),
name = "cell",
remove_background_polygon = FALSE,
background_algo = c("range"),
fill_holes = TRUE,
poly_IDs = NULL,
flip_vertical = TRUE,
shift_vertical_step = TRUE,
flip_horizontal = TRUE,
shift_horizontal_step = TRUE,
calc_centroids = FALSE,
fix_multipart = TRUE,
remove_unvalid_polygons = TRUE
)
Arguments#
|
path to mask file |
|
how the mask file defines individual segmentation annotations |
|
name for polygons |
|
try to remove background polygon (default: FALSE) |
|
algorithm to remove background polygon |
|
fill holes within created polygons |
|
unique names for each polygon in the mask file |
|
flip mask figure in a vertical manner |
|
shift vertical (boolean or numerical) |
|
flip mask figure in a horizontal manner |
|
shift horizontal (boolean or numerical) |
|
calculate centroids for polygons |
|
try to split polygons with multiple parts (default: TRUE) |
|
remove unvalid polygons (default: TRUE) |
Value#
a giotto polygon object