Dataset for annotation and analysis of complex 3D plant organs using 3DCoordX

ABSTRACT: Here we present the ensemble of 3D digital images which are part of the publication Vijayan et al., 2022, The annotation and analysis of complex 3D plant organs using 3DCoordX, Plant Physiology, 2022;, kiac145, https://doi.org/10.1093/plphys/kiac145 The dataset includes an exclusive example dataset of Arabidopsis ovules for the 3DCoordX user manual. Additionally, the 3D meshes used for different figures from other plant organs (Utricularia gibba, Marchantia polymorpha) in the manuscript are included in this dataset. Each dataset is derived from a 3D z-stack which are further processed and 3D instance cell segmented. The example dataset used in the 3DCoordX user manual can be found under "User_manual_example_dataset" directory. This includes raw cell boundaries from confocal microscopy, neural network-based cell boundary predictions using PlantSeg (https://github.com/hci-unihd/plant-seg), 3D instance segmented cells from the boundary predictions as well as the 3DCoordX annotated 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. To obtain the latest version of MorphoGraphX with 3DCoordX package, please visit the MorphoGraphX website (www.morphographx.org) or contact Richard Smith by email ([e-mail])

ORGANISM(S): Arabidopsis thaliana (thale cress)

SUBMITTER:  

PROVIDER: S-BSST734 | bioimages |

REPOSITORIES: bioimages