This dataset includes 3-D images that have been generated by co-registration of CyCIF images from 58 sequential sections obtained from a frozen human kidney block that were interrogated with a panel of 12 validated antibodies and a lectin designed to evaluate glomerular and glomerulus-associated structures in the human kidney. We have attached an excel file (Supplemental Table 3) that includes all of the experimental and (de-identified) patient metadata associated with these images, with information and comments about each of the channel images, information aboiut each of the tissue sections stained, including documention of instances where tissues were folded, cycles were out of focus, or the tissues had been damaged during the CyCIF cycles, as well as the antibodies used, and the cell types and extracellular matrix compartments identified with these combinations of antibodies. GIF images were generated using four antibody channels (a-SMA, CD31, NaK-ATPase, and Podocalyxin) from the panel of 13 markers to best visualize 3-D glomerular, tubular (TAL), and vascular segmentation of the human kidney (Figures 34 and 35).