Embodiments disclosed herein provide methods and systems for delineating cell nuclei and classifying regions of histopathology or microanatomy while remaining invariant to batch effects. These systems and methods can include providing a plurality of reference images of histology sections. A first set of basis functions can then be determined from the reference images. Then, the histopathology or microanatomy of the histology sections can be classified by reference to the first set of basis functions, or reference to human engineered features. A second set of basis functions can then be calculated for delineating cell nuclei from the reference images and delineating the nuclear regions of the histology sections based on the second set of basis functions.
STATEMENT REGARDING FEDERALLY SPONSORED R&D
 This invention was made with government support under Contract No. DE-ACO2-05CH11231 awarded by the U.S. Department of Energy and under Grant Nos. CA1437991 and CA140663 awarded by the National Institutes of Health. The government has certain rights in the invention.