Zellige example dataset: inner ear organoid epithelium

Inner ear organoid at day 14 of culture.

The z-stack image encompasses half of the spherical organoid including two distinct and superimposed surfaces that correspond to the basal side of the epithelium and the apical junctional network. It was acquired with a confocal microscope (Nikon A1HD25) equipped with a Nikon Plan-Apochromat 25x lens (NA=1.05). Pixel size 0.690 µm, z step >1 µm.  This dataset contains both the ground-truth height maps and the height maps generated with Zellige. The Zellige parameters used are:

\(T_{A}=5, T_{otsu}=12, S_{min}=5, \sigma_{xy}=2, \sigma_{z}=1, T_{OSE1}=0.9, R_{1}=5, C_{1}=0.8, T_{OSE2}=0.1, R_{2}=10, C_{2}=0.8.\)

Nota: to compare the ground truth height map with the Zellige height map, one first needs to substrat 1 to all values of the Zellige height map.

See the accompanying paper: Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool. Trébeau et al. 2022: https://doi.org/10.1101/2022.04.05.485876