merquaco.experiment.Experiment.run_full_pixel_classification

Experiment.run_full_pixel_classification(save_metrics: bool = True, force_mask=True)

Runs entire pixel classification workflow:

• generates binary masks for transcripts, DAPI, gel lifting, ventricles, and damage

• resizes and aligns masks

• calculates pixel percentages over “ideal” tissue area

Attributes Set

pixel_areasnp.ndarray

Array of pixel classification area designations in microns: [damage, tissue, gel lifting, ventricles]

pixel_percentagesnp.ndarray

Array of pixel classification area designations as percentage of “ideal” tissue area [damage, tissue, gel lifting, ventricles]

ideal_tissue_areafloat

Sum of all non-off-tissue pixels