Filter cells by morphological criteria — sg_filter

Removes cells from a segmentation mask that fall outside specified morphological thresholds. Useful for quality control after initial segmentation.

Usage

sg_filter_cells(
  mask,
  min_area = 50L,
  max_area = 5000L,
  min_circularity = 0.3,
  max_eccentricity = 0.95,
  border_cells = c("keep", "remove", "flag")
)

Arguments

mask: An sg_mask object.
min_area: Integer. Minimum cell area in pixels. Default 50L.
max_area: Integer. Maximum cell area in pixels. Default 5000L.
min_circularity: Numeric in [0, 1]. Minimum circularity (4 * pi * area / perimeter^2). Default 0.3.
max_eccentricity: Numeric in [0, 1]. Maximum eccentricity. Default 0.95.
border_cells: Character. How to handle cells touching the image border: "keep" (default), "remove", or "flag".

Value

A filtered sg_mask object. When border_cells = "flag", the returned mask has an additional border_cell_ids element.

Examples

labels <- matrix(0L, nrow = 20, ncol = 20)
labels[3:8, 3:8] <- 1L
labels[12:18, 12:18] <- 2L
mask <- new_sg_mask(labels)
filtered <- sg_filter_cells(mask, min_area = 10L, max_area = 100L)
#> ✔ Kept 2 of 2 cells.
#> ℹ Removed 0 cells by morphological filtering.
print(filtered)
#> <sg_mask>: 20 x 20, 2 cells