Measure colonies: size, shape, melanization and interaction metrics

Usage

measure_colonies(
  plate,
  edge_exclude_mm = 0.1,
  dark_L = NULL,
  n_boot = 200L,
  block_mm = 0.5,
  seed = 1L
)

Arguments

plate

A plate processed by segment_colonies().

edge_exclude_mm

Width of the colony margin excluded from colour statistics (mm).

dark_L

Optional \(L^*\) threshold for dark_fraction.

n_boot

Bootstrap replicates for confidence intervals.

block_mm

Side of the square spatial blocks for the bootstrap (mm).

seed

RNG seed for the bootstrap.

The clearer alias radial_asymmetry_pct equals the legacy growth_inhibition_pct. Both describe toward/away radial asymmetry, not inhibition referenced to a separate control plate.

Value

Data frame with one row per expected colony.

Details

Melanization readouts

All colour statistics use unsmoothed, flat-field-corrected pixels of the colony interior: a rim of edge_exclude_mm is removed (mixed colony/agar pixels, "partial-volume" effect) and specular highlights (\(L^* > 97\) or a saturated channel) are excluded.

L_mean, L_median, L_sd, L_q05...L_q95: CIE lightness \(L^*\) (0 black - 100 white). An approximately perceptual lightness coordinate; it is not a direct pigment concentration.
MI_mean, MI_median: Melanization index \(MI = 100 - L^*\). Higher = darker; attribution to melanin requires validation. Linear in \(L^*\), so MI differences are comparable across the whole range.
MI_min, MI_max: Observed minimum and maximum eligible-pixel MI; these are noise-sensitive extrema, not confidence limits.
MI_lo, MI_hi: Nominal 95 % spatial block-bootstrap interval of MI_mean, conditional on image and segmentation; this does not represent variation between biological replicate plates.
gray_imagej: Mean of (R + G + B) / 3 on the 0-255 scale, an unweighted RGB channel average (ImageJ conversion depends on its weighting settings), for comparison with earlier Z. tritici melanization studies that report mean grey values.
a_mean, b_mean, chroma_mean, hue_deg: Chromatic components; DHN-melanin is dark brown-black, so strongly melanized colonies drift towards low \(L^*\) with slightly positive \(a^*, b^*\) (brown), whereas "grey" colonies are nearly neutral.
dark_fraction: Fraction of interior pixels with \(L^* <\) dark_L (only if dark_L is given). Choose dark_L from control plates, e.g. the 10th percentile of control colonies.

Interaction readouts

The interaction direction of a colony is the vector from its centroid to the centroid of the central partner (confrontations), or to the dish centre (controls, so that the same metrics give the null expectation).

MI_facing, MI_away, delta_MI_facing: MI of the colony half facing the central partner (angle < 90 deg to the interaction direction) and of the opposite half, and their difference. A localized melanization response towards the central partner gives delta_MI_facing > 0.
R_toward_mm, R_away_mm, growth_inhibition_pct: Colony radius from the centroid towards / away from the central partner (maximum radius in a +/- 20 deg sector), and the percent inhibition of radial growth 100 (R_away - R_toward) / R_away, a within-colony radial asymmetry index. Despite the legacy column name, this is not control-referenced percent inhibition of radial growth.
gap_bacteria_mm, gap_hyphae_mm: Shortest edge-to-edge distance from the colony to the central partner and its peripheral hyphal extent (0 = contact).

Examples

sim <- simulate_plate(width = 300, height = 400, seed = 7)
res <- analyze_plate(sim$image, verbose = FALSE)
res$colonies[, c("colony_id", "area_mm2", "L_mean", "MI_mean")]
#>   colony_id area_mm2   L_mean  MI_mean
#> 1        TL 154.4311 52.30603 47.69397
#> 2        TR 154.9466 46.53839 53.46161
#> 3        BR 154.5456 41.47310 58.52690
#> 4        BL 154.8893 58.45871 41.54129