Minimal Inhibitory Concentration (MIC) Assay¶
Read the inputs, initialize the assay class¶
import rda_toolbox as rda
mic = rda.MIC(
"../data/raw/", # Folderpath for rawfiles
"../data/input/MIC_Input.xlsx", # Input excel table
"../data/input/DiS_MP_AsT_2024-12-02.txt", # Mapping file from Motherplates to AssayTransfer plates
"../data/input/AmA_AsT_AcD_20241204.txt", # Mapping file from AssayTransfer to ActivityDetermination plates
plate_type=384,
measurement_label="Raw Optical Density",
negative_controls="Organism + Medium", # Label of negative controls ('Bacteria + Medium', 'Fungi + Medium', 'Organism + Medium', 'Negative Controls' etc.)
precip_exclude_outlier=True, # Exclude outliers from the precipitation
precipitation_rawfilepath = "../data/raw/Precipitation_measurements/", # Folderpath for precipitation rawfiles
)
Save the results¶
mic.save_results(<tables path>, <figures path>, <processed data path>, figureformats=["svg, html"], tableformats=["xlsx", "csv"])
If everything went well you can stop now.
If errors occured you may inspect in-between results and debug from there.
(Check your inputs!)
In-between inspection:¶
View in-between results (e.g. in a notebook)¶
Its possible to inspect the assay object:
Show how plates are related to each other (hirarchical dictionary):