The effectiveness and robustness of the proposed fully automatic hierarchical registration framework is validated using two datasets, including a dual staining breast cancer dataset with 43 H&E slides and 43 IHC CK(AE1/AE3) slides and a triple staining prostate cancer dataset with 30 H&E slides, 30 IHC CK18 slides, and 30 IHC HMCK slides. The gene discussed is KRT18; the disease is prostate carcinoma.