This deposit contains the supporting records of images and image analysis presented in, " A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease". doi: https://doi.org/10.1101/2022.06.22.497218 Associated Zenodo repositories: Description DOI Main figures PART 1, Figure 1,2,3,5 10.5281/zenodo.7653239 Main figures PART 2, Figure 6 10.5281/zenodo.7900973 Supplemental 3DTC figures: S1, S4, S5, S7, S8, S9 10.5281/zenodo.7894632 Contents:1) a collection of .zip files contains the 3D tissue cytometry files for tissue analyzed in the manuscript doi: https://doi.org/10.1101/2022.06.22.497218. This collection includes the individual analyses for figures 2, 3 and 5. Figure 6 analyses are included in a compansion repository: 10.5281/zenodo.7900973. Contents of zip files by figure contain at a minimum the .obx and a .tif file which includes the segmented objects and associated measurements for use by VTEA (https://vtea.wiki/). Additional files may include gate files (.vtg) or max projections (.tif). 2) a collection of zip files containing the RNAScope image files shown in: Figure 1 P,Q. The supplemental figure data for RNAScope. Figures S1,S4 and S5 are found in: 10.5281/zenodo.7894633. Please address any concerns or questions to the authors listed in the deposit or manuscript, doi: https://doi.org/10.1101/2022.06.22.497218

5/12/23-Supplemental figure doi updated. One file missing in v1.