WT Arabidopsis ovule atlas: A 3D digital cell atlas of wild-type Arabidopsis ovule development with cellular and tissue resolution.

ABSTRACT: Here we present a canonical 3D digital atlas of Arabidopsis ovule development with cellular resolution. The atlas covers all stages from early primordium outgrowth to the mature pre-fertilization ovule. The atlas not only provides information about the number of cells and their relative positions but also about characteristics of cellular morphology, such as cell size and shape, for nearly all cells of the ovule. Database is organised according to the developmental stages of individual images captured. Each dataset is a 3D z-stack. 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 3D 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. The high-quality dataset includes 158 wild-type 3D digital ovules comprises across stage 1-I to 3-VI. The additional dataset contains another 85 early-stage 3D digital ovules with slightly higher number of segmentation errors. 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:  

PROVIDER: S-BSST475 | bioimages |

REPOSITORIES: bioimages