This is a data repository for the raw and processed images used for a 3D Digital Tissue Atlas of *[Arabidopsis thaliana][1]*. The component subpages contain the data associated with each tissue. 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 nodes) Cell annotation: .TXT (provided as integers and explained in the README file) Cell annotations are described in the README file together with the region used for topological analyses and mis-segmented cells. Cell identity annotation: .CSV (corresponding cell labels are retained in the MorphoGraphX mesh file format and TIFF segmented stack) If you wish to visualize or modify meshes, you can import the .OBJ format into other software including MeshLab (http://www.meshlab.net/). If you have any questions or requests please contact George Bassel: gbassel@gmail.com, http://www.georgebassellab.com/. [1]: https://en.wikipedia.org/wiki/Arabidopsis