Analyse one plate photograph — analyze

Runs the complete MycoHalo pipeline: import, dish detection and scale, optional colour calibration, flat-field correction, colour/texture pixel classification, seeded colony separation, measurement and QC.

analyze_plate(
  path,
  layout = plate_layout(),
  id = NULL,
  dish_diameter_mm = 90,
  agar_fraction = 0.88,
  dish = NULL,
  mm_per_px = NULL,
  reference = NULL,
  reference_lab = c(50, 0, 0),
  max_dim = 2000,
  flat_field = TRUE,
  classifier = NULL,
  min_delta_e = 3,
  min_area_mm2 = 0.5,
  min_core_mm = 0.4,
  morph_mm = 0.08,
  edge_criterion = 0.5,
  edge_exclude_mm = 0.1,
  dark_L = NULL,
  n_boot = 200L,
  block_mm = 0.5,
  ring_width_mm = 0.5,
  profile_mode = c("absolute", "relative"),
  n_rings = 10L,
  qc_file = NULL,
  keep_images = TRUE,
  verbose = TRUE
)

Arguments

path: Image file or H x W x 3 sRGB array.
layout: A plate_layout(). Use plate_layout(centre = "none") for control plates without bacteria.
id: Plate identifier (default: file name).
dish_diameter_mm: Outer diameter of the dish (mm); sets the scale.
agar_fraction: Fraction of the dish radius that is analysed.
dish: Optional manual dish circle c(x, y, r) in working pixels.
mm_per_px: Optional known scale (mm per working-image pixel); overrides dish_diameter_mm.
reference: Optional exposure / white-balance reference: a grey-card region c(x, y, r) in relative image coordinates, or "agar"; see model_background().
reference_lab: Known CIELAB of the reference.
max_dim: Working resolution (longest side, px).
flat_field: Apply illumination correction (recommended).
classifier: Optional supervised classifier (train_classifier()).
min_delta_e: Minimum colour difference from agar for objects.
min_area_mm2, min_core_mm, morph_mm, edge_criterion: Segmentation settings, see segment_colonies().
edge_exclude_mm, dark_L, n_boot, block_mm: Measurement settings, see measure_colonies().
ring_width_mm, profile_mode, n_rings: Profile settings, see colony_profiles().
qc_file: Optional path of a PNG quality-control figure.
keep_images: Keep image arrays in the result (needed for plot_qc() later; set FALSE in large batches to save memory).
verbose: Print progress.

Value

An object of class mycohalo_result, a list with

colonies: One row per expected colony (measure_colonies()).
profiles: Edge-to-centre profiles (colony_profiles()).
plate_summary: One row of plate-level measures and QC.
plate: The processed plate (images and masks) if keep_images = TRUE.
params, warnings: Settings used and QC warnings.

Examples

sim <- simulate_plate(width = 300, height = 400, seed = 10)
res <- analyze_plate(sim$image, id = "sim10", verbose = FALSE)
res
#> <mycohalo_result> plate "sim10"
#> • Scale: 0.2393 mm/px; agar L* = 22.2
#> • Colonies detected: 4 / 4; satellites: 1
#> • Bacterium r = 6.36 mm; halo outer r = 17.01 mm
#>  colony_id area_mm2 L_mean MI_mean MI_lo MI_hi delta_MI_facing
#>         TL      155   51.2    48.8  48.4  49.1            2.29
#>         TR      156   46.9    53.1  52.7  53.4            2.51
#>         BR      155   40.0    60.0  59.6  60.4            2.73
#>         BL      156   57.7    42.3  42.0  42.6           -2.54
#>  growth_inhibition_pct
#>                  2.450
#>                  0.270
#>                 -0.152
#>                 -7.634
res$colonies[, c("colony_id", "MI_mean", "delta_MI_facing")]
#>    colony_id  MI_mean delta_MI_facing
#> x         TL 48.75743        2.293812
#> x1        TR 53.05115        2.514062
#> x2        BR 59.99747        2.729403
#> x3        BL 42.27137       -2.539792
if (FALSE) { # \dontrun{
res <- analyze_plate("plates/2026_05_26_20.JPG", layout = plate_layout())
plot_qc(res)
ctrl <- analyze_plate("plates/2026_05_26_37.JPG",
                      layout = plate_layout(centre = "none"))
} # }