Package index • MycoHalo

All functions
`analyze_plate()`	Analyse one plate photograph
`analyze_plates()`	Analyse many plates
`annotate_plate()`	Interactively annotate training regions
`calibrate_color()`	Colour / exposure calibration against a reference patch
`classify_pixels()`	Classify non-agar pixels into fungus, bacteria and halo
`colony_profiles()`	Edge-to-centre melanization profiles
`compare_melanization()`	Compare melanization between treatments, respecting plate structure
`correct_facing_bias()`	Remove position-specific lighting bias from side-specific metrics
`delta_e76()`	Colour difference CIE76 (Euclidean distance in Lab*)
`detect_plate()`	Detect the Petri dish and set the spatial scale
`example_plate()`	Paths to the example plate photographs shipped with MycoHalo
`extract_training_pixels()`	Extract annotated training pixels
`is_mycohalo_plate()`	Test for a MycoHalo plate object
`lab_chroma_hue()`	Chroma and hue angle from a* and b*
`lab_to_srgb()`	Convert CIE Lab* to sRGB
`layout_by_treatment()`	Layout chooser for a metadata row
`make_metadata()`	Create a plate metadata sheet for a folder of photos
`measure_colonies()`	Measure colonies: size, shape, melanization and interaction metrics
`model_background()`	Model the agar background and correct uneven illumination
`plate_layout()`	Describe the inoculation layout of a plate
`plot_melanization_map()`	Melanization landscape: 3D shaded surface and 2D map of a plate
`plot_profiles()`	Plot edge-to-centre melanization profiles
`plot_qc()`	Quality-control figure
`read_plate()`	Read a plate photograph
`segment_colonies()`	Separate individual colonies, the bacterium and its halo
`simulate_plate()`	Simulate a plate photograph with known ground truth
`srgb_to_lab()`	Convert sRGB values to CIE 1976 Lab*
`train_classifier()`	Train a supervised pixel classifier

Reference

All functions