Terrestrial Laser Scanning data of two intertidal oyster reefs in the Wadden Sea, Germany (2020-2022)

Terrestrial laser scanning was used to quantify the vertical growth of two intertidal oyster reefs, built by the non-native Pacific oyster Magallana gigas, in the German Wadden Sea. This dataset includes point cloud surveys of the Kaiserbalje reef (53.6470116° N, 008.2664760° E) and the Nordland reef (53.6424960° N, 008.9411970° E), collected semi-annually from 2020 to 2022. In addition to the raw TLS point cloud data, the dataset includes results from further analyses conducted to assess the spatial and temporal changes in reef structure. The data capture detailed 3D representations of the reefs across multiple seasons, providing valuable insights into the spatial and vertical dynamics of oyster reefs, supporting research on reef growth and morphology in intertidal environments.

Methods
The dataset was generated using terrestrial laser scanning (TLS) to capture detailed 3D point cloud data of the Kaiserbalje and Nordland reefs, with scans collected semi-annually between 2020 and 2022. Each survey involved approximately 20 individual scans per site, conducted during low-tide periods. The scans were captured using FARO Focus3D models (X130, S120, and Splus150), achieving an accuracy of ±2 mm at a distance of 25 m, with a point spacing of 3–6 mm at 10 m. The spatial analysis concentrated on representative areas approximately 80 × 80 m, covering both central and marginal parts of the reefs.

To ensure precise registration of the individual scan point clouds during post-processing, 15 to 17 movable reference spheres (Ø145 mm) were randomly distributed within the survey area. Additionally, 13 to 15 reference spheres were placed on permanently fixed iron rods (900 × 10 mm), embedded in the sediment, to establish a consistent local coordinate system. The positions of the fixed reference spheres were determined using a Stonex-9000-dGPS system with Real Time Kinematic (RTK) corrections and a local geoid model (GCG2016NW), achieving a horizontal accuracy of 8 mm and a vertical accuracy of 15 mm.

During post-processing, individual scans were registered into a single ScanScene using the positions of both movable and fixed reference spheres, with each scan clipped to a maximum extent of 30 meters. The registration was performed using the software FARO Scene. The first ScanScene from each series was designated as a reference, with subsequent ScanScenes spatially aligned based on the positions of the fixed reference spheres.

Further analysis of the dataset included multiscale model-to-model cloud comparison (M3C2) using 5 cm subsampled clouds from the initial scans as core points. This method, performed with the open-source software CloudCompare, enabled a detailed analysis of the vertical dynamics of the oyster reefs throughout the study period.