Fits a layout-initialized mixture to colour and texture features relative to agar. Expected target positions seed one component; the centre seeds the dense partner core and an adjacent region seeds peripheral central growth. For a fungal partner this peripheral growth represents candidate hyphal tissue, not inhibition or a diffusible pigment boundary. All image classes require visual review; the photograph does not identify species or resolve individual microscopic hyphae. Similar colours or overlapping cultures may remain ambiguous. Seeded segmentation separates the target colonies later.
Usage
classify_pixels(
plate,
layout = plate_layout(),
classifier = NULL,
posterior_smooth_mm = 0.15,
context_mm = 0.5,
max_em_pixels = 60000L
)Arguments
- plate
A plate processed by
model_background().- layout
- classifier
Optional
funmel_classifierfromtrain_classifier().- posterior_smooth_mm
Smoothing of class posteriors for confident pixels (mm).
- context_mm
Neighbourhood (mm) from which low-confidence (faint) pixels borrow their class.
- max_em_pixels
Maximum number of pixels used to fit the mixture.
Value
The plate with element classes: an integer matrix
(0 agar/outside, 1 target-like tissue, 2 central core, 3 peripheral central growth, 4 other) and the fitted
model.
Details
The internal labels fungus and bacteria denote target-like and central-core components; the biological partner identity comes from the layout.
Examples
sim <- simulate_plate(width = 300, height = 400, seed = 4)
p <- read_plate(sim$image) |> detect_plate() |> model_background()
p <- classify_pixels(p, plate_layout())
table(p$classes$map)
#>
#> 0 1 2 3 4
#> 91861 12415 1749 13869 106