This is a data repository for the raw and processed images used for a 3D Digital Tissue Atlas of *Arabidopsis thaliana*. This folder contains all files describing the 3D cellular anatomy of the **[Root][1]**. The software MorphoGraphX was used to perform image analyses, and can be downloaded at the following URL : www.MorphoGraphX.org Files provided and their formats are as follows: Original confocal stack: .TIFF Cellular segmentation: .TIFF Tissue Mesh: .MGXM (MorphoGraphX format) Tissue Mesh: .OBJ (Wavefront format) Cellular connectivity network: .TXT (edge list using cell identity labels as node identifiers) Cell annotations are described in the README file together with the region used for topological analyses and mis-segmented cells. Cell annotation: .TXT (provided as integers and explained in the README file) Cell identity annotation: .CSV (corresponding cell labels are retained in the MorphoGraphX mesh file format and TIFF segmented stack) If you have any questions or requests please contact George Bassel: gbassel@gmail.com. [1]: http://msb.embopress.org/content/9/1/688