Process root images by filling holes and optionally smoothing edges

Process root images by filling holes and optionally smoothing edges

Usage

clean_root_image(
  img,
  remove_small_particles = TRUE,
  min_size = 100,
  connectivity = 8,
  fill_holes = TRUE,
  min_hole_size = 1,
  max_hole_size = Inf,
  smooth_edges = FALSE,
  kernel_shape = "disk",
  kernel_size = 3,
  iterations = 1
)

Arguments

img

A binary image of root systems (imager cimg object)

remove_small_particles

Boolean indicating whether only big objects are retained

min_size

Minimum particle size (in pixel). Removing all patches below the minimal size

connectivity

Determines which connection type is used to assess whether pixel belong to the same patch: 4 or 8

fill_holes

Boolean indicating whether to fill holes

min_hole_size

Minimum size of holes to fill (in pixels)

max_hole_size

Maximum size of holes to fill (in pixels, Inf means no limit)

smooth_edges

Boolean indicating whether to smooth edges

kernel_shape

Shape of the kernel for edge smoothing: "square", "diamond", or "disk"

kernel_size

Size of the kernel for edge smoothing (odd integer)

iterations

Number of iterations for the smoothing process

Value

A processed binary image

See also

smooth_root_edges, fill_root_holes, remove_small_foreground_objects

Examples

data("seg_Oulanka2023_Session01_T067")
img <-  seg_Oulanka2023_Session01_T067
# Fill holes only
result1 <- clean_root_image(img, fill_holes = TRUE, smooth_edges = FALSE)
#> Warning: Assuming third dimension corresponds to colour
#> Warning: Assuming third dimension corresponds to time/depth
#> Error in `[.pixset`(hole_mask, nrow(hole_mask), ): object 'hole_mask' not found
# Fill holes and smooth edges
result2 <- clean_root_image(img, fill_holes = TRUE, smooth_edges = TRUE)
#> Warning: Assuming third dimension corresponds to colour
#> Warning: Assuming third dimension corresponds to time/depth
#> Error in `[.pixset`(hole_mask, nrow(hole_mask), ): object 'hole_mask' not found
plot(result2)
#> Error: object 'result2' not found