Series of three-dimensional structured illumination microscopy (3D SIM) and deconvolution microscopy data of 3µm think tissue sections of Schlemm’s Canal in the chamber angle of mice’s eyes. Schlemm’s Canal endothelium was labeled with an anti-CD31 antibody and an AF647 secondary antibody, the slides were also treated with the nuclear stain DAPI. In addition, eye tissue has significant autofluorescence. The eyes are of either a CD1 mouse strain wildtype animal or of the same background but carrying a βB1-CTGF transgenic construct. CTGF is known to play a key role in mediating the effects of primary open angle glaucoma. The aim of the study was to test the feasibility of 3D SIM of eye tissue and especially in the examination of Schlemm’s Canal.