Create giotto polygons from mask file#

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Last Updated: Mar 11, 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#

maskfile

path to mask file

mask_method

how the mask file defines individual segmentation annotations

name

name for polygons

remove_background_polygon

try to remove background polygon (default: FALSE)

background_algo

algorithm to remove background polygon

fill_holes

fill holes within created polygons

poly_IDs

unique names for each polygon in the mask file

flip_vertical

flip mask figure in a vertical manner

shift_vertical_step

shift vertical (boolean or numerical)

flip_horizontal

flip mask figure in a horizontal manner

shift_horizontal_step

shift horizontal (boolean or numerical)

calc_centroids

calculate centroids for polygons

fix_multipart

try to split polygons with multiple parts (default: TRUE)

remove_unvalid_polygons

remove unvalid polygons (default: TRUE)

Value#

a giotto polygon object