Merge nuclear and cell body masks

Combines a nuclear segmentation mask with a cell body segmentation mask to produce paired nuclear-cell assignments.

Usage

sg_merge_masks(nuclear_mask, cell_mask, method = c("assign", "expand"))

Arguments

nuclear_mask

An sg_mask object for nuclei.

cell_mask

An sg_mask object for cell bodies.

method

Character. "assign" (default) assigns nuclei to overlapping cells; "expand" expands nuclear labels outward to fill cell boundaries.

Value

A list with elements $nuclear and $cell, both sg_mask objects with matched cell IDs.

Examples

nuc_labels <- matrix(0L, nrow = 20, ncol = 20)
nuc_labels[5:7, 5:7] <- 1L
nuc_labels[14:16, 14:16] <- 2L
cell_labels <- matrix(0L, nrow = 20, ncol = 20)
cell_labels[3:9, 3:9] <- 1L
cell_labels[12:18, 12:18] <- 2L
nuc_mask <- new_sg_mask(nuc_labels)
cell_mask <- new_sg_mask(cell_labels)
merged <- sg_merge_masks(nuc_mask, cell_mask)
#> ✔ Merged nuclear (2 nuclei) and cell (2 cells) masks.
#> ℹ Method: "assign"
print(merged$nuclear)
#> <sg_mask>: 20 x 20, 2 cells