Zellige example dataset: primary culture of human bronchial cells infected by SARS-CoV-2

A human bronchial epithelium was infected by SARS-CoV-2. The specimen was imaged four days post-infection. The z-stack image encompasses the very irregular epithelium surface. It was acquired with a point scanning microscope (Zeiss LSM700) equipped with Zeiss Plan-Apochromat 63x lens (NA=1.4). Pixel size 0.110µm, z step 0.4µm. This dataset contains both the ground-truth height map and the height map generated with Zellige. The Zellige parameters used are: \(T_{A}=23, T_{otsu}=16, S_{min}=5, \sigma_{xy}=4, \sigma_{z}=1, T_{OSE1}=0.9, R_{1}=5, C_{1}=0.9, T_{OSE2}=0.1, R_{2}=5, C_{2}=0.8.\).

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 related paper:
https://hal-pasteur.archives-ouvertes.fr/pasteur-03319522

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