3D gene expression atlas of WUSCHEL in Arabidopsis ovules with cellular, nuclear and tissue resolution.

ABSTRACT: Here we present a canonical 3D digital atlas of Arabidopsis ovules expressing a WUSCHEL reporter (pWUS::2xVENUS:NLS::tWUS). The dataset consists of 69 3D digital ovules covering stages 1-I to 2-III. The database is organized according to the individual ovule identity code used in the study. Each dataset contains the 3D z-stack and the associated 3D mesh file. The dataset includes raw cell boundaries from confocal microscopy, neural network based cell boundary predictions from PlantSeg (https://github.com/hci-unihd/plant-seg), nuclei stack, 3D segmented cells from the boundary predictions as well as the annotated 3D cell meshes and the associated attribute files in csv format. The WUSCHEL reporter and the associated blob mesh is also available as a resource. The 3D cell mesh and blob mesh files can be opened in the open source software MorphoGraphX (MGX) (www.morphographx.org), the mesh file can be reconverted to obj, stl, ply or any other format of interest in MGX. Nomenclature of early ovule IDs A few image stacks comprise multiple ovules attached to the same pistil fragment. In such instances the format "ID_6x" represents an image stack with 6 ovules attached to the same pistil fragment. For further analysis with the mesh, individual ovules were classified as "ID_A", "ID_B", "ID_C" etc. For example, the dataset "396_6x" encompasses 6 ovules attached to the same pistil fragment. Ovules "396_A", "396_B" etc represent the individual ovules. One can open the ID_6x mesh and enable the parents to display the labels annotated to the cells in the mesh. The labels are integer values that represent tissue IDs. In general, we follow a pattern of 1-10 tissue labels representing "ID_A" or ovule "A", "11-20" representing "ID_B" and so on. Download of latest version of MorphoGraphX To obtain the latest version of MorphoGraphX please visit the MorphoGraphX website (www.mpipz.mpg.de/MorphoGraphX) or contact Richard Smith by email ([e-mail]).

ORGANISM(S): Arabidopsis thaliana (thale cress)

SUBMITTER: Kay Schneitz 

PROVIDER: S-BSST498 | bioimages |

REPOSITORIES: bioimages