(A) Overview of the MSIreg framework. (B–G) Case Study 1, tissue with elastic deformations. (B) Representative H&E image, (C) representative MS image, (D) overlay of the image pair before coregistration, (E) overlay of the image pair after coregistration, (F) overlay of the tissue masks before coregistration, and (G) overlay of the tissue masks after coregistration. (H–L) Case Study 2, TMA cores with dilated outlines. (H) H&E image before coregistration with a region of interest highlighted (rectangular area), (I) overlay of the image pair of the highlighted region before coregistration, (J) overlay of the image pair of the highlighted region after coregistration, (K) overlay of one tissue core before coregistration, and (L) overlay of one tissue core after coregistration.