Terrestrial Laser Scanning data of two intertidal oyster reefs in the Wadden Sea, Germany (2020-2022)
Data files
Oct 09, 2024 version files 105.31 GB
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KB_2020S_sphere_positions_dGPS_utm32_mNHN.txt
578 B
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KB_M3C2_results.zip
266 MB
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KB_M3C3_point_clouds.zip
4.25 GB
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KB_raw_scans_2020A.zip
10.21 GB
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KB_raw_scans_2020S.zip
1.81 GB
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KB_raw_scans_2021A.zip
3.61 GB
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KB_raw_scans_2021S.zip
13.20 GB
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KB_raw_scans_2022S.zip
14.68 GB
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metadata.csv
9.15 KB
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NL_2021S_sphere_positions_dGPS_utm32_mNHN.txt
625 B
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NL_M3C2_results.zip
308.35 MB
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NL_M3C3_point_clouds.zip
4.38 GB
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NL_raw_scans_2020A.zip
13.10 GB
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NL_raw_scans_2021A.zip
4.08 GB
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NL_raw_scans_2021S.zip
20.41 GB
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NL_raw_scans_2022S.zip
15.01 GB
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README.md
11.93 KB
Abstract
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.
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:
- 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.e57represents the segmented point cloud data for the Kaiserbalje reef from the spring 2020 survey. - 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.e57represents 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:
- 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.e57represents the segmented point cloud data for the Nordland reef from the autumn 2020 survey. - 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.e57represents 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
Additionally, FARO Scene LT is freely available for viewing raw scan files and can be downloaded from the FARO website:
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:
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.
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.