Correcting nuisance variation using Wasserstein distance.

Profiling cellular phenotypes from microscopic imaging can provide meaningful biological information resulting from various factors affecting the cells. One motivating application is drug development: morphological cell features can be captured from images, from which similarities between different drug compounds applied at different doses can be quantified. The general approach is to find a function mapping the images to an embedding space of manageable dimensionality whose geometry captures relevant features of the input images.