Edge-to-centre melanization profiles — colony

Melanization of a Z. tritici colony is not uniform: the growing margin consists of young, often lighter hyphae, while older central tissue is darker. Profiles as a function of distance from the colony edge (not from the centroid) follow this age gradient for irregular, lobed colonies too.

Usage

colony_profiles(
  result,
  ring_width_mm = 0.5,
  mode = c("absolute", "relative"),
  n_rings = 10L,
  n_boot = 200L,
  block_mm = 0.5,
  seed = 1L
)

Arguments

result: A funmel_result from analyze_plate(), or a plate processed by segment_colonies().
ring_width_mm: Ring width in absolute mode (mm).
mode: "absolute" or "relative".
n_rings: Number of rings in relative mode.
n_boot, block_mm, seed: Block-bootstrap settings.

Value

Data frame with one row per colony x ring.

Details

The Euclidean distance transform of each colony gives every pixel its distance to the nearest colony edge. Pixels are grouped into rings of width ring_width_mm (absolute mode, comparable between colonies of different size) or into n_rings rings of equal relative depth (relative mode, comparable in developmental stage).

Confidence intervals. Neighbouring pixels are strongly correlated (same hypha, JPEG blocks, smoothing in the camera), so a naive pixel bootstrap grossly overstates precision. FunMel uses a spatial block bootstrap (Künsch 1989; Lahiri 2003): the colony is divided into square blocks of block_mm, and whole blocks are resampled with replacement. Choose block_mm at least as large as the wrinkle / texture scale (default 0.5 mm).

Examples

sim <- simulate_plate(width = 300, height = 400, seed = 8, edge_lightening = 8)
res <- analyze_plate(sim$image, verbose = FALSE)
head(res$profiles)
#>   plate_id colony_id ring from_edge_mm to_edge_mm mid_mm  rel_depth n_pixels
#> 1    plate        TL    1          0.0        0.5   0.25 0.03966576      416
#> 2    plate        TL    2          0.5        1.0   0.75 0.11899727      384
#> 3    plate        TL    3          1.0        1.5   1.25 0.19832878      354
#> 4    plate        TL    4          1.5        2.0   1.75 0.27766029      283
#> 5    plate        TL    5          2.0        2.5   2.25 0.35699180      284
#> 6    plate        TL    6          2.5        3.0   2.75 0.43632331      256
#>   n_blocks   L_mean     L_sd  MI_mean    MI_lo    MI_hi
#> 1      151 57.74614 8.927770 42.25386 41.32626 43.20779
#> 2      139 56.55090 4.014191 43.44910 42.88760 44.09499
#> 3      131 53.02250 3.347690 46.97750 46.48161 47.56379
#> 4      104 51.81904 3.695064 48.18096 47.38680 48.83208
#> 5      108 51.14082 4.359298 48.85918 48.03981 49.76930
#> 6       96 49.91173 4.864773 50.08827 49.12574 51.09368