Threshold-based cell segmentation

Segments cells in an sg_image by applying a global or local intensity threshold, followed by morphological cleanup and connected-component labelling with size filtering.

Usage

sg_segment_threshold(
  image,
  channel = 1L,
  method = c("otsu", "adaptive", "triangle"),
  block_size = 51L,
  offset = 0.05,
  morphology = list(open = 5L, fill_holes = TRUE),
  min_area = 50L,
  max_area = 5000L
)

Arguments

image

An sg_image object.

channel

Integer index of the image channel to threshold. Default is 1L.

method

Character string specifying the thresholding method. One of "otsu" (default), "adaptive", or "triangle".

block_size

Integer block size for adaptive thresholding. Must be a positive odd integer. Only used when method = "adaptive". Default is 51L.

offset

Numeric offset subtracted from the local mean in adaptive thresholding. Default is 0.05.

morphology

A named list controlling morphological cleanup:

open

Integer; structuring element size for opening (erosion then dilation). Set to 0L to skip. Default 5L.

fill_holes

Logical; whether to fill holes inside objects. Default TRUE.

min_area

Integer; minimum object area in pixels. Objects smaller than this are removed. Default is 50L.

max_area

Integer; maximum object area in pixels. Objects larger than this are removed. Default is 5000L.

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_threshold(img, method = "otsu")
#> ℹ Threshold applied using "otsu" method.
#> ✔ Segmented 0 objects via threshold (otsu).
print(mask)
#> <sg_mask>: 20 x 20, 0 cells
#> Method: threshold:otsu