CLARITY processed tissues can be incorporated for retrospective analysis of FFPE tissues. (a) A general workflow diagram of deparaffinization and subsequent tissue clearing and immunostaining utilized for archived FFPE blocks (b) Deparaffinized FFPE tumors #6, #7, and #8 (Indiana breast cancer core biopsy tissue) were re-embedded into an A4B4P0 HM solution followed by lipid clearing. The images show the tissues both before and five days after lipid clearing. (c) Confocal images of tumor #7 at 25X (Blue: DAPI, Green: pan-CK, Yellow: Ki67, Red: CD3). Top row: 3D volumetric images viewed from both the XY axes and XZ axes. Bottom row: Individual 2D optical section from the 3D view from increasing depths. In certain optical sections, the Ki67 positive epithelial cells and infiltrating CD3 positive T cells can be observed, denoted by arrows. (d) A comparison of Ki67 positive ratio (Ki67 positive epithelial cells/total epithelial cells) scores between respective converted FFPE to HM and FFPE thin sections (unpaired t test, p-value as listed).