Zellige example dataset: synthetic image dataset

<strong>Phantom 3D image containing three distinct and superimposed synthetic surfaces. </strong> It models a typical stack of confocal images of epithelial and non-epithelial structures.The surfaces generated are of two types: “solid” surfaces, presenting a homogeneous signal over the entire surface, or surfaces presenting a signal restricted to a polygonal mesh mimicking the mesh of apical cellular junctions of an epithelium observed at its surface. This dataset contains both the ground-truth height maps and the height maps generated with Zellige. The Zellige parameters used are: \(T_{A}=16, T_{otsu}=12, S_{min}=5, \sigma_{xy}=4, \sigma_{z}=2, T_{OSE1}=0.9, R_{1}=5, C_{1}=0.1, T_{OSE2}=0.1, R_{2}=10, C_{2}=0.8.\) Nota: the ground-truth height maps can be directly compared to Zellige height maps by subtraction. See the accompanying paper: Extracting multiple surfaces from 3D microscopy images in complex biological tissues with the Zellige software tool. Trébeau <em>et al.</em> 2022: https://doi.org/10.1101/2022.04.05.485876