Package index • FunMel

All functions

analyze_plate(): Analyse one plate photograph
analyze_plates(): Analyse many plates
annotate_plate(): Interactively annotate training regions
assess_experiment(): Assess matched treatment effects within and across control sets
calibrate_color(): Colour / exposure calibration against a reference patch
classify_pixels(): Classify target colonies and central fungal growth
colony_profiles(): Edge-to-centre melanization profiles
compare_melanization(): Compare colony measurements while accounting for plates
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_experiment(): Reproducible synthetic matched-set experiment for learning the workflow
example_plate(): Paths to the example plate photographs shipped with FunMel
extract_training_pixels(): Extract annotated training pixels
finalize_analysis(): Finalize saved measurements after reviewing metadata and image masks
finish_experiment(): Finalize a prepared experiment after plate review
is_funmel_plate(): Test for a FunMel plate object
is_mycohalo_plate(): Check a plate object (compatibility name from MycoHalo)
lab_chroma_hue(): Chroma and hue angle from a* and b*
lab_to_srgb(): Convert CIE Lab* to sRGB
layout_by_treatment(): Choose a segmentation layout from one metadata row
load_experiment(): Open an existing experiment in its current folder
make_metadata(): Create a metadata template for matched treatment-control sets
measure_colonies(): Measure colonies: size, shape, melanization and interaction metrics
melanization_coefficient(): Calculate the treatment-to-control melanization coefficient
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
plot_treatment_comparison(): Plot plate-level darkness and matched melanization coefficients
prepare_experiment(): Prepare photographs as an experiment project
prepare_photo_archive(): Extract and locate the photographs required by metadata
print(<funmel_result>) print(<funmel_classifier>) print(<funmel_layout>) print(<funmel_plate>): Print a FunMel object summary
read_experiment(): Read saved experiment tables
read_plate(): Read a plate photograph
run_experiment(): Analyze all photographs in a prepared experiment
sample_colony_spots(): Sample a chosen number of circular spots within each target colony
segment_colonies(): Separate Zymoseptoria targets and the central fungal colony
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
validate_metadata(): Validate the plate-to-set metadata used for matched controls