Arabidopsis ovule primordium stages 0-I to 2-II, wild-type Col_0, Ws-4 and botero (bot1-7) mutant
Baroux, Célia; Mendocilla-Sato, Ethel; Autran, Daphné (2021), Arabidopsis ovule primordium stages 0-I to 2-II, wild-type Col_0, Ws-4 and botero (bot1-7) mutant, Dryad, Dataset, https://doi.org/10.5061/dryad.02v6wwq2c
This image resource describes the development of ovule primordia from stages 0-I to 2-I in 3D and at cellular resolution. The images were segmented using ImarisCell (BitplaneAG) and annotated as described in the associated manuscript Hernandez-Lagana et al. https://www.biorxiv.org/content/10.1101/2020.07.30.226670v3
Imaging of ovule primordia stained in whole-mount for cell boundary was done as described (Mendocilla-Sato, 2017) using a laser scanning confocal microscope Leica LCS SP8 equipped with a 63X glycerol immersion objective and HyD detectors.
3D imaging and image processing (segmentation and labeling).
Entire carpels were stained using the pseudo-Schiff propidium iodide (PS-PI) cell wall staining procedure providing excellent optical transparency for 3D imaging in depth in whole-mount. We described previously the manipulation, staining, mounting of the flower carpels and imaging procedures (Mendocilla-Sato, 2017). Cell-boundary based image segmentation was done using ImarisCell (Bitplane) as described in details previously (Mendocilla-Sato, 2017). Each ovule was manually labelled in Imaris using customized Cell Labels for the different cell types and domains colored as shown in Figure 1. We defined the labels as follows:
- SMC (Spore Mother Cell): most apical central enlarged L2 cell. At stage 0-I, as enlargement is not always detected visually, the most apical L2 cell was then selected as candidate SMC (cSMC).
- L1: epidermal cells
- L1 dome: most apical cells in contact with SMC
- L2/L3: cells below the epidermis. L2 and L3 were not distinguished originally.
- Apical domain: group of cells at the apex of the primordium and encompassing the SMC and direct neighbor cells.
- Basal domain: group of cells at the basis of the primordium below the apical domain and until, but not including cells of the placental surface. At stages 0-I and 0-II only an apical domain is defined. A basal domain appears only starting stage 0-III.
- CC (Companion Cell): L2 cells in apical domain in contact with the SMC with an elongated shape (as judged in ovule longitudinal median section using the “clipping plane” IMARIS tool).
- SMC contact: cells in contact with the SMC.
Semi-automated segmentation requiring user input and manual labelling can be error prone. To reduce the error rate, the 92 images were segmented and labeled by one author, but verified and curated by two others.
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: 310030L_170167
Agence Nationale de la Recherche, Award: 16-CE93-0002