Supporting data and analysis for," A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease", main figures PART 1

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