Zellige example dataset: Drosophila pupal wing and abdomen

Drosophila pupa imaged at around 24h after puparium formation.

The z-stack image encompasses a distal portion of the wing and a portion of the abdomen. The four distinct surfaces are the abdomen cuticle, the abdomen epithelium, the wing cuticle and the wing epithelium. The z-stack was acquired with a spinning disk confocal microscope (Yokogawa W1) equipped with a Nikon Plan-Apochromat 60x lens (NA=1.4). Pixel size 0.183 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:

\(T_{A}=6, T_{otsu}=1, S_{min}=5, \sigma_{xy}=5, \sigma_{z}=1, T_{OSE1}=0.7, R_{1}=10, C_{1}=0.8, T_{OSE2}=0.1, R_{2}=5, C_{2}=0.9.\)

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