Marker-controlled watershed segmentation

Segments cells using a marker-controlled watershed algorithm. Seeds (markers) are detected automatically via distance-transform peaks or h-minima, and the watershed flood fills from these seeds.

Usage

sg_segment_watershed(
  image,
  channel = 1L,
  seed_method = c("h_minima", "distance", "markers"),
  h = 0.05,
  min_distance = 10L,
  expand_method = c("voronoi", "dilation"),
  expand_pixels = 3L,
  membrane_channel = NULL
)

Arguments

image

An sg_image object.

channel

Integer index of the image channel used for segmentation. Default is 1L.

seed_method

Character string specifying how seeds are generated. One of "h_minima" (default), "distance", or "markers".

h

Numeric; height parameter for h-minima or distance threshold fraction for seed detection. Default is 0.05.

min_distance

Integer; minimum pixel distance between seeds. Default is 10L.

expand_method

Character string specifying how seed regions are expanded. One of "voronoi" (default) or "dilation".

expand_pixels

Integer; number of pixels to expand beyond the initial watershed regions. Default is 3L.

membrane_channel

Integer or NULL. If provided, this channel is used as the topographic surface for watershed flooding. If NULL, the inverted channel image is used.

Value

An sg_mask object with labelled cell regions.

Examples

set.seed(42)
pixels <- matrix(runif(400), nrow = 20, ncol = 20)
img <- new_sg_image(pixels)
mask <- sg_segment_watershed(img, seed_method = "distance", h = 0.3)
#> ℹ Generated 1 seed via "distance".
#> ✔ Watershed segmented 1 object.
print(mask)
#> <sg_mask>: 20 x 20, 1 cell
#> Method: watershed