Zellige example dataset: mouse embryonic cochlea stained for F-actin

Mouse embryonic cochlea stained for F-actin at embryonic stage E16.5.

The z-stack image encompasses an epithelial surface and a thick mesh of mesenchymal cells. It was acquired with a swept-field confocal microscope (Bruker OpterraII) equipped with a Nikon Plan-Apochromat 60x lens (NA=1.4). Pixel size 0.133 µm, z step <1 µm. This dataset contains both the ground-truth height map and the height map generated with Zellige, along with the parameters used to generate the latter one. The Zellige parameters used are:

\(T_{A}=1, T_{otsu}=1, S_{min}=5, \sigma_{xy}=4, \sigma_{z}=1, T_{OSE1}=0.1, R_{1}=5, C_{1}=0.7, T_{OSE2}=0.1, R_{2}=10, C_{2}=0.8.\)

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