This deposit contains the supporting records of analysis for 3D cytometry presented in, "An atlas of healthy and injured cell states and niches in the human kidney". Contents: 1) a collection of .zip files contains the 3D tissue cytometry files for tissue analyzed in the preprint doi: 10.1101/2021.07.28.454201. This collection includes the individual tissue specimens, XX-XXXX.zip, further described in detail in "Supplementary Table 2. 3D imaging and spatial transcriptomic experiments." 2) neighborhoods by specimen as indicated above and calculated by Volumetric Tissue Exploration and Analysis (VTEA) for a radius of 50 voxels(accounting for anisotropy of voxels) or ~25 um as described in the methods of the preprint, doi: 10.1101/2021.07.28.454201. 3) R environment file (.RData as a .zip file) for regenerating analysis from code at: https://github.com/KPMP/Cell-State-Atlas-2022 Contents of XX-XXXX.zip files: 1) maximum projections as used in the manuscript (all archived at kpmp.org) 2) .obx and a .tif file which includes the segmented objects and associated measurements for use by VTEA (https://vtea.wiki/) 3) .csv file including all the segmented objects and associated measurements 4) .csv file including the neighborhood analysis results also found in the combined .zip file 5) folder of ImageJ/FIJI folder which includes the expert ROIs and the pixel-wise consensus of ROIs drawn by experts used in cell classification strategy outlined in the methods 6) folder of VTEA gate files and images of gating .png files used to label objects and used in cell classification strategy outlined in the methods of doi: 10.1101/2021.07.28.454201 Please address any concerns or questions to the authors listed in the deposit or manuscript, doi: 10.1101/2021.07.28.454201.