Overview¶
Loading, transforming and fitting plate reader data.
from cdk.instruments.platereader import load_platereader_dataThe plate reader half of the CDK uses an immutable object API. Loading gives you an object that carries its own metadata, and each transform returns a new object, leaving the original unchanged. The transform history travels with the data, so a plot can label its own axes from the transforms that produced it.
| Module | Role |
|---|---|
loader / loaders | File → PlateReaderResult. Loaders self-register by extension; BioTek is currently the only one. |
result | PlateReaderResult and PlateReaderData — the core objects. |
transforms | The pure reference-application core behind blank and normalize. |
kinetics | Kinetics — per-group curve fits and their plots. |
standardcurve | StandardCurve — a fitted, invertible calibration curve. |
legacy | The pre-refactor function-based pipeline, preserved verbatim. |
Loading¶
load_platereader_data(data_file, platemap_file=None, platereader=None)
The data objects¶
PlateReaderResult — a sequence of read blocks.
PlateReaderResult.take(which=None, *, modality=None)
PlateReaderData — one read block: a long-form frame, a format, and a lineage.
Transforms¶
PlateReaderData.blank(blank_name="Blank", *, window=...)
PlateReaderData.normalize(standard_name, *, window=..., group_by=())
PlateReaderData.ratio(numerator_read, denominator_read, *, name=None)
PlateReaderData.standardize(curve)
Selecting rows¶
PlateReaderData.select(*, well=None, read=None, read_name=None, modality=None, name=None, type=None)
Fitting¶
PlateReaderData.fit_kinetics(data_column=None, fit_function_name="sigmoid_drift", group_by=..., completion_threshold=0.95)
PlateReaderData.fit_standard_curve(*, known, standard_name="Standard", model="linear", data_column=None)
Kinetics results¶
Kinetics.plot(...), Kinetics.plot_data(...), Kinetics.plot_summary(...), Kinetics.plot_response(x, y, ...)
Plotting data¶
PlateReaderData.plot(...), PlateReaderData.plot_plate(...)
Platemaps¶
load_platemap(path, sep=","), validate_platemap(df), merge_platemap(data, platemap)
Legacy API¶
cdk.instruments.platereader.legacy — DataFrame-in / DataFrame-out. Reach for it when you need the rolling-window steady-state analysis or the wider instrument set (Envision, Glomax) that the object API does not cover yet.