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
)
Cytation 10 readout table header¶
In the Cytation C10 reader software you can define things like table headers.
To detect the result matrix and be flexible in naming this table, the keyword cyt10_matrixheader_mapping was introduced.
The default value for this keyword is cyt10_matrixheader_mapping = {"Results": "Raw Optical Density"} (Usually its better to leave out the "Raw").
import rda_toolbox as rda
mic = rda.MIC(
rawfiles_folderpath="../data/raw/24 h/",
inputfile_path="../data/input/MIC_Input.xlsx",
mp_ast_mapping_filepath="../data/input/DiS_MP_AsT_2024-12-02.txt",
ast_acd_mapping_filepath="../data/input/AmA_AsT_AcD_20260317.txt",
precipitation_rawfilepath="../data/raw/Precipitation/",
cyt10_matrixheader_mapping={"Read 1:554,593": "Fluorescence", "Read 2:450": "Optical Density"},
negative_controls="Organism + Medium",
)
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):