This deposit contains the supporting records of analysis for 3D cytometry 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 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 figure 6 analyses. 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). 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