DOI: 10.5061/dryad.j3tx95xq7
title: Terrestrial Laser Scanning data of two intertidal oyster reefs in the Wadden Sea, Germany (2020-2022)

description: 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.
description: 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.
description: # Terrestrial Laser Scanning data of two intertidal oyster reefs in the
 Wadden Sea, Germany (2020-2022) [https://doi.org/10.5061/dryad.j3tx95xq7
 ](https://doi.org/10.5061/dryad.j3tx95xq7) ## Description of the data and
 file structure This dataset was collected as part of our study aimed at
 quantifying the vertical growth dynamics of two intertidal oyster reefs in
 the German Wadden Sea, built by the non-native Pacific oyster *Magallana
 gigas*. The data, gathered using terrestrial laser scanning (TLS), provide
 detailed 3D point cloud representations of the reefs over multiple seasons
 between 2020 and 2022. In addition to raw TLS point clouds, the dataset
 includes segmented point clouds of the oyster reef surface (excluding the
 surrounding sediment surface), a 5 cm subsampled version of the oyster
 reef surface, and multiscale model-to-model cloud comparison (M3C2)
 analysis, allowing for an in-depth investigation of spatial and temporal
 changes within the reefs. Additional information on the timing of the
 individual scan surveys and a file overview can be found in the file
 *metadata.csv*. ### Files and variables #### **File:
 KB\_raw\_scans\_2020A.zip** **Description:** Raw terrestrial laser scan
 (TLS) data collected at the Kaiserbalje reef during autumn 2020,
 containing unprocessed point cloud data of the reef in the FARO folder
 format `.fls`. #### **File: KB\_raw\_scans\_2020S.zip** **Description:**
 Raw terrestrial laser scan (TLS) data collected at the Kaiserbalje reef
 during spring 2020, containing unprocessed point cloud data of the reef in
 the FARO folder format `.fls`. #### **File: KB\_raw\_scans\_2021A.zip**
 **Description:** Raw terrestrial laser scan (TLS) data collected at the
 Kaiserbalje reef during autumn 2021, containing unprocessed point cloud
 data of the reef in the FARO folder format `.fls`. #### **File:
 KB\_raw\_scans\_2021S.zip** **Description:** Raw terrestrial laser scan
 (TLS) data collected at the Kaiserbalje reef during spring 2021,
 containing unprocessed point cloud data of the reef in the FARO folder
 format `.fls`. #### **File: KB\_raw\_scans\_2022S.zip** **Description:**\
 Raw terrestrial laser scan (TLS) data collected at the Kaiserbalje reef
 during spring 2022, containing unprocessed point cloud data of the reef in
 the FARO folder format `.fls`. #### **File: NL\_raw\_scans\_2020A.zip**
 **Description:** Raw terrestrial laser scan (TLS) data collected at the
 Nordland reef during autumn 2020, containing unprocessed point cloud data
 of the reef in the FARO folder format `.fls`. #### **File:
 NL\_raw\_scans\_2021A.zip** **Description:** Raw terrestrial laser scan
 (TLS) data collected at the Nordland reef during spring 2021, containing
 unprocessed point cloud data of the reef in the FARO folder format `.fls`.
 #### **File: NL\_raw\_scans\_2021S.zip** **Description:** Raw terrestrial
 laser scan (TLS) data collected at the Nordland reef during autumn 2021,
 containing unprocessed point cloud data of the reef in the FARO folder
 format `.fls`. #### **File: NL\_raw\_scans\_2022S.zip** **Description:**
 Raw terrestrial laser scan (TLS) data collected at the Nordland reef
 during spring 2022, containing unprocessed point cloud data of the reef in
 the FARO folder format `.fls`. #### File:
 KB\_2020S\_sphere\_positions\_dGPS\_utm32\_mNHN.txt **Description:**
 Contains the differential GPS (dGPS) data for the fixed reference
 positions used during the Kaiserbalje (KB) 2020 spring survey. The data is
 provided in the UTM Zone 32 coordinate system and referenced to the German
 standard datum for mean sea level (mNHN). ##### Variables: * **ID:**
 Identifier of the reference spheres. * **x:** Latitude in UTM Zone 32. *
 **y:** Longitude in UTM Zone 32. * **z:** Elevation above Normalhoehennull
 (mNHN). #### File: NL\_2021S\_sphere\_positions\_dGPS\_utm32\_mNHN.txt
 **Description:** Contains the differential GPS (dGPS) data for the fixed
 reference positions used during the Nordland (NL) 2021 spring survey. The
 data is provided in the UTM Zone 32 coordinate system and referenced to
 the German standard datum for mean sea level (mNHN). ##### Variables: *
 **ID:** Identifier of the reference spheres. * **x:** Latitude in UTM Zone
 32. * **y:** Longitude in UTM Zone 32. * **z:** Elevation above
 Normalhoehennull (mNHN). #### File: KB\_M3C3\_point\_clouds.zip
 **Description:** Contains processed point cloud data for the Kaiserbalje
 (KB) reef in an .e57 file format. The archive includes: 1. Segmented point
 cloud data representing only the oyster reef surface, excluding the
 surrounding sediment. The files follow a similar naming convention, with
 "_oyster_segmented" added to indicate segmentation. For example,
 `KB_20S_oyster_segmented.e57` represents the segmented point cloud data
 for the Kaiserbalje reef from the spring 2020 survey. 2. A 5 cm subsampled
 version of the segmented point cloud data for each survey. These files are
 named similarly, with "_oyster_segmented.subsampled" to indicate
 the subsampling. For example, `KB_20S_oyster_segmented.subsampled.e57`
 represents the 5 cm subsampled point cloud data for the Kaiserbalje reef
 from the spring 2020 survey. #### File: NL\_M3C3\_point\_clouds.zip
 **Description:** Contains processed point cloud data for the Nordland (NL)
 reef in an .e57 file format. The archive includes: 1. Segmented point
 cloud data representing only the oyster reef surface, excluding the
 surrounding sediment. The files follow a similar naming convention, with
 "_oyster_segmented" added to indicate segmentation. For example,
 `NL_20A_oyster_segmented.e57` represents the segmented point cloud data
 for the Nordland reef from the autumn 2020 survey. 2. A 5 cm subsampled
 version of the segmented point cloud data for each survey. These files are
 named similarly, with "_oyster_segmented.subsampled" to indicate
 the subsampling. For example, `NL_20A_oyster_segmented.subsampled.e57`
 represents the 5 cm subsampled point cloud data for the Nordland reef from
 the autumn 2020 survey. #### File: KB\_M3C2\_results.zip **Description:**
 Contains the results of the Multiscale Model to Model Cloud Comparison
 (M3C2) analysis for the Kaiserbalje (KB) oyster reef in `.txt` format.
 These files provide detailed vertical change measurements between
 successive surveys of the reef, allowing for analysis of vertical growth
 dynamics over time. The analysis was performed with a subsample scale of 5
 cm (0.05 m). The table format is as follows: * **X:** X-coordinate in the
 UTM Zone 32 coordinate system. * **Y:** Y-coordinate in the UTM Zone 32
 coordinate system. * **Z:** Z-coordinate (elevation) above
 Normalhoehennull (NHN), the German standard for mean sea level. *
 **Npoints_cloud1:** Number of points in the first point cloud within the
 specified radius. * **Npoints_cloud2:** Number of points in the second
 point cloud within the specified radius. * **STD_cloud1:** Standard
 deviation of the points in the first point cloud (m). * **STD_cloud2:**
 Standard deviation of the points in the second point cloud (m). *
 **Significant change:** Indicator of whether a significant change has been
 detected (m). * **Distance uncertainty:** Uncertainty of the calculated
 distance (m). * **M3C2 distance:** Calculated distance change between the
 two point clouds (m). #### File: NL\_M3C2\_results.zip **Description:**
 Contains the results of the Multiscale Model to Model Cloud Comparison
 (M3C2) analysis for the Nordland (NL) oyster reef in `.txt` format. These
 files provide detailed vertical change measurements between successive
 surveys of the reef, enabling the analysis of vertical growth dynamics
 over time. The analysis was performed with a subsample scale of 5 cm (0.05
 m). The table format is as follows: * **X:** X-coordinate in the UTM Zone
 32 coordinate system. * **Y:** Y-coordinate in the UTM Zone 32 coordinate
 system. * **Z:** Z-coordinate (elevation) above Normalhoehennull (NHN),
 the German standard for mean sea level. * **Npoints_cloud1:** Number of
 points in the first point cloud within the specified radius. *
 **Npoints_cloud2:** Number of points in the second point cloud within the
 specified radius. * **STD_cloud1:** Standard deviation of the points in
 the first point cloud (m). * **STD_cloud2:** Standard deviation of the
 points in the second point cloud (m). * **Significant change:** Indicator
 of whether a significant change has been detected (m). * **Distance
 uncertainty:** Uncertainty of the calculated distance (m). * **M3C2
 distance:** Calculated distance change between the two point clouds (m).
 #### File: metadata.csv **Description:** This file contains metadata for
 all survey campaigns, including the type of data, file names, locations,
 and timing information for each scan. ##### Variables: * **type:** Type of
 data (e.g., raw scan, processed point cloud). * **compressed archive:**
 Name of the compressed archive. * **file name:** Name of the individual
 file. * **file type:** File format. * **location:** Site of data
 collection (Kaiserbalje (KB)/Nordland (NL)). * **timing:** Seasonal timing
 of the survey (Spring (S)/Autumn (A)). * **date start (dd.mm.yyyy):**
 Start date of the survey. * **date end (dd.mm.yyyy):** End date of the
 survey. * **Latitude_Decimal degree (WGS84):** Latitude in decimal
 degrees. * **Longitude_Decimal degree (WGS84):** Longitude in decimal
 degrees. * **E_UTM 32U:** Easting in the UTM 32U zone. * **N_UTM 32U:**
 Northing in the UTM 32U zone. * **Method:** Data collection or processing
 method. * **Device:** Equipment used (e.g., FARO Focus3D). ##
 Code/software ### FARO Scene (Version: 2019.01 – 2023.01) **Description:**
 FARO Scene was used for processing raw terrestrial laser scan (TLS) data
 in the FARO format (.fls). It was used for the initial registration and
 co-registration of individual 3D scan point clouds from each survey
 campaign, resulting in a unified ScanScene. FARO Scene is available as a
 time-limited trial version, which can be accessed at:
 [https://www.faro.com/en/Products/Software/SCENE-Software](https://www.faro.com/en/Products/Software/SCENE-Software) Additionally, FARO Scene LT is freely available for viewing raw scan files and can be downloaded from the FARO website: [https://knowledge.faro.com/Software/FARO_SCENE/SCENE/Software_Download_Installation_and_Release_Notes_for_SCENE_LT](https://knowledge.faro.com/Software/FARO_SCENE/SCENE/Software_Download_Installation_and_Release_Notes_for_SCENE_LT) **Workflow:** * Movable and fixed reference spheres were used for accurate registration of individual scan point clouds, with each scan clipped to a maximum extent of 30 m. * The ScanScene from the first survey was designated as the Reference-ScanScene, and subsequent ScanScenes were spatially aligned using all suitable fixed reference sphere positions to ensure overall optimal alignment. * Global positioning of the survey areas was facilitated using differential GPS (dGPS) coordinates in UTM Zone 32. * Registered point clouds were then exported in .e57 format for further analysis. ### CloudCompare (Version: 2.13) **Description:** CloudCompare is an open-source 3D point cloud processing software used for additional post-processing and analysis of the registered ScanScenes. This software was used for segmentation, subsampling, and the Multiscale Model to Model Cloud Comparison (M3C2) analysis. CloudCompare is freely available and can be downloaded at: [https://www.danielgm.net/cc/](https://www.danielgm.net/cc/) **Workflow:** * After the point clouds were exported from FARO Scene, further post-processing such as segmentation of the oyster reef surface and removal of surrounding sediment was performed in CloudCompare. * For the M3C2 analysis, the point cloud from the first ScanScene in each pair was subsampled to a resolution of 50 mm and used as Corepoints. The M3C2 algorithm was then applied to calculate vertical differences between successive ScanScenes.