Imports a plate image (JPEG, PNG, TIFF, HEIC ... anything ImageMagick reads), applies the EXIF orientation, optionally down-samples it to a working resolution and converts it to CIELAB.
Arguments
- path
Path to an image file, or a numeric H x W x 3 array with sRGB values in [0, 1] (e.g. from
simulate_plate()).- max_dim
Maximum size (px) of the longest image side used for analysis. Default 2000.
- id
Optional plate identifier; defaults to the file name without extension.
Value
An object of class funmel_plate: a list with
- rgb
H x W x 3 array of sRGB values in [0, 1].
- lab
H x W x 3 array of CIELAB values.
- id, path
Identifier and source path.
- original_dim
Width and height of the file (px).
- resize_factor
Working px per original px.
- clipped_fraction
Fraction of pixels with a channel at 255.
Details
Working resolution. Segmentation and colour statistics are computed on
an image whose longest side is at most max_dim pixels. For a 90 mm dish
photographed so that it fills the frame, max_dim = 2000 gives roughly
0.05 mm per pixel. Resolution affects segmentation, boundaries and colour
summaries; evaluate stability across resolutions for the actual images.
Down-sampling can reduce fine texture and JPEG artefacts, but does not
guarantee unbiased colony means or a particular measurement precision.
Use max_dim = Inf to keep the native resolution.
Clipping. Pixels with a channel at 255 may be clipped in the encoded
image; this does not by itself establish sensor saturation. Their fraction is stored and
analyze_plate() warns if colonies contain clipped pixels. Photograph
with manual exposure so that the brightest bacterial growth stays below
~ 245.
Examples
sim <- simulate_plate(width = 300, height = 400, seed = 1)
plate <- read_plate(sim$image, id = "sim1")
plate
#> <funmel_plate> "sim1"
#> • Working size: 300 x 400 px (resize factor 1)
#> • Source: NA
#> • Over-exposed pixels: 0 %
#> • Colour calibration: none