Joshua B. Logan Eric E. Grossman Nathan R. VanArendonk Avery F.G. Maverick 20210222 point cloud digital data data release DOI:10.5066/P94LH20J Pacific Coastal and Marine Science Center, Santa Cruz, California U.S. Geological Survey https://doi.org/10.5066/P94LH20J https://www.sciencebase.gov/catalog/item/5ef522a582ced62aaae6a015 Joshua B. Logan Eric E. Grossman Nathan R. VanArendonk Avery F.G. Maverick 2021 data release DOI:10.5066/P94LH20J Pacific Coastal and Marine Science Center, Santa Cruz, CA U.S. Geological Survey https://doi.org/10.5066/P94LH20J https://www.sciencebase.gov/catalog/item/5f2c568b82ceae4cb3c2cffc This portion of the data release presents topographic point clouds of the intertidal zone at Post Point, Bellingham Bay, WA. The point clouds were derived from structure-from-motion (SfM) processing of aerial imagery collected with an unmanned aerial system (UAS) on 2019-06-06. Two point clouds are presented with different resolutions: one point cloud (PostPoint_2019-06-06_pointcloud.zip) covers the entire survey area and has 145,653,2221 points with an average point density of 1,057 points per-square meter; the other point cloud (PostPointHighRes_2019-06-06_pointcloud.zip) has 139,427,055 points with an average point density of 3,487 points per-square meter and was derived from a lower-altitude flight covering an inset area within the main survey area. The point clouds are tiled to reduce individual files sizes and grouped within zip files for downloading. Each point in the point clouds contains an explicit horizontal and vertical coordinate, color, intensity, and classification. Water portions of the point cloud were classified using a polygon digitized from the orthomosaic imagery derived from these surveys (also available in this data release). No other classifications were performed. The raw imagery used to create these point clouds was acquired using a UAS fitted with a Ricoh GR II digital camera featuring a global shutter. The UAS was flown on pre-programmed autonomous flight lines spaced to provide approximately 70 percent overlap between images from adjacent lines. The camera was triggered at 1 Hz using a built-in intervalometer. For the main survey area point cloud, the UAS was flown at an approximate altitude of 70 meters above ground level (AGL), resulting in a nominal ground-sample-distance (GSD) of 1.8 centimeters per pixel. For the higher-resolution point cloud, the UAS was flown at an approximate altitude of 35 meters (AGL), resulting in a nominal ground-sample-distance (GSD) of 0.9 centimeters per pixel. The raw imagery was geotagged using positions from the UAS onboard single-frequency autonomous GPS. Nineteen temporary ground control points (GCPs) were distributed throughout each survey area to establish survey control. The GCPs consisted of a combination of small square tarps with black-and-white cross patterns and "X" marks placed on the ground using temporary chalk. The GCP positions were measured using post-processed kinematic (PPK) GPS, using corrections from a GPS base station located approximately 5 kilometers from the study area. The point clouds are formatted in LAZ format (LAS 1.2 specification). These data were collected to characterize the morphology, substrate composition and roughness of intertidal areas to support modeling of coastal storm and wave impacts with sea-level rise as part of the USGS Puget Sound Coastal Storm Modeling System (PS-CoSMoS). The data are also intended to be used to model and evaluate sediment transport and its effects on coastal habitats, a focus of the USGS Coastal Habitats in Puget Sound Project (CHIPS) and its partners to inform resource management and adaptive planning for our Nation's coasts. Additional information about the field activity from which these data were derived is available online at: http://cmgds.marine.usgs.gov/fan_info.php?fan=2019-623-FA Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. 20190606 ground condition at time data were collected Complete None planned -122.5201 -122.5156 48.7204 48.7113 ISO 19115 Topic Category elevation geoscientificInformation Data Categories for Marine Planning Bathymetry and Elevation USGS Thesaurus topography topographic maps remote sensing geomorphology aerial photography image mosaics geospatial datasets Marine Realms Information Bank (MRIB) keywords photography remote sensing aerial and satellite photography altimetry orthophotography coastal processes None U.S. Geological Survey USGS Coastal and Marine Hazards and Resources Program CHMRP Pacific Coastal and Marine Science Center PCMSC Unmanned aerial system UAS Structure-from-motion SfM USGS Metadata Identifier USGS:5ef522a582ced62aaae6a015 Geographic Names Information System (GNIS) State of Washington Whatcom County Bellingham South Bellingham Fairhaven Puget Sound Salish Sea Bellingham Bay Post Point None USGS-authored or produced data and information are in the public domain from the U.S. Government and are freely redistributable with proper metadata and source attribution. Please recognize and acknowledge the U.S. Geological Survey as the originator(s) of the dataset and in products derived from these data. This information is not intended for navigation purposes. U.S. Geological Survey, Pacific Coastal and Marine Science Center PCMSC Science Data Coordinator mailing and physical

2885 Mission Street

Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov https://www.sciencebase.gov/catalog/file/get/5ef522a582ced62aaae6a015?name=PostPoint_2019-06-06_pointcloud_browse.jpg Perspective view of the Post Point topographic point cloud from the 2019-06-06 UAS survey. JPEG Microsoft Windows 10, Agisoft PhotoScan version 1.4.4 through Agisoft Metashape 1.5.3, ESRI ArcGIS 10.6 through 10.7, Exiftool, Geosetter 3.4.16, QGIS 3.04 through 3.12, and LAStools ver. 190417. No formal attribute accuracy tests were conducted. No formal logical accuracy tests were conducted. Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details. Horizontal accuracy was estimated by comparing SfM-derived ground control point (GCP) positions to PPK GPS measurements. Due to the time-intensive process of placing GCPs in the field, all available GCPs were used for registration and camera optimization in the SfM processing workflow during the creation of the final point clouds. To evaluate the horizontal positional accuracy of the point clouds after processing was completed, a subset of GCPs was disabled one-at-a-time using a python script to create 'temporary check points'. With a single GCP temporarily disabled, camera optimization was performed with all lens parameters fixed, and all other GCPs enabled. The residual errors of the check point relative to its GPS-measured position were recorded. After all temporary check point iterations were complete, the root-mean-square error (RMSE) and mean-absolute error (MAE) were calculated. For the main survey area point cloud (files contained in PostPoint_2019-06-06_pointcloud.zip), the resulting horizontal RMSE was 0.018 meters (MAE 0.015 meters), and for the high-resolution Post Point point cloud (files contained in PostPointHighRes_2019-06-06_pointcloud.zip), the resulting horizontal RMSE was 0.030 meters (MAE 0.027 meters). The addition of the estimated horizontal GPS uncertainty (0.020 meters) in quadrature results in a total accuracy estimate of 0.027 meters for the main resolution point cloud, and 0.036 meters for the high-resolution point cloud. It should be noted that this error estimate is for areas of bare ground or low vegetation where GCPs were placed. Additional sources of error such as poor image-to-image point matching due to vegetation or uniform substrate texture (such as sand) resulting in poor surface reconstruction may cause localized errors in some portions of the point clouds to exceed this estimate. Vertical accuracy was estimated by comparing SfM-derived ground control point (GCP) positions to PPK GPS measurements. These 'check points' consisted of GCPs which were temporarily disabled after the completion of the SfM processing workflow. Due to the time-intensive process of placing GCPs in the field, all available GCPs were used for registration and camera optimization in the SfM processing workflow during the creation of the final point cloud. To evaluate the vertical positional accuracy of the point cloud, a subset of GCPs was disabled one-at-a-time using a python script to create 'temporary check points'. With a single GCP temporarily disabled, camera optimization was performed with all lens parameters fixed, and all other GCPs enabled. The residual errors of the check point relative to its GPS-measured position were recorded. After all temporary check point iterations were complete, the root-mean-square error (RMSE) and mean-absolute error (MAE) were calculated. For the main survey area point cloud (files contained in PostPoint_2019-06-06_pointcloud.zip), the resulting vertical RMSE was 0.040 meters (MAE 0.030 meters), and for the high-resolution Post Point point cloud (files contained in PostPointHighRes_2019-06-06_pointcloud.zip), the resulting vertical RMSE was 0.042 meters (MAE 0.034 meters). The addition of the estimated vertical GPS uncertainty (0.030 meters) in quadrature results in a total accuracy estimate of 0.050 meters for the main resolution point cloud, and 0.052 meters for the high-resolution point cloud. It should be noted that this error estimate is for areas of bare ground or low vegetation where GCPs were placed. Additional sources of error such as poor image-to-image point matching due to vegetation or uniform substrate texture (such as sand) resulting in poor surface reconstruction may cause localized errors in some portions of the point clouds to exceed this estimate. Aerial imagery was collected using a Department of Interior-owned 3DR Solo quadcopter fitted with a Ricoh GR II digital camera featuring a global shutter. The camera was mounted using a fixed mount on the bottom of the UAS and oriented in an approximately nadir orientation. The UAS was flown on pre-programmed autonomous flight lines. Flights F01, F02, and F03 were flown at an approximate altitude of 70 meters above ground level (AGL); flights F04 and F05 were flown at an approximate altitude of 35 meters AGL. The flight lines were oriented roughly shore-parallel and were spaced to provide approximately 70 percent overlap between images from adjacent lines. After the flight lines were completed some additional imagery was collected in manual flight mode to fill in additional areas and to collect redundant imagery with the camera sensor at different orientations to improve lens-model reconstruction. The camera was triggered at 1 Hz using a built-in intervalometer and was programmed to simultaneously acquire imagery in both JPG and camera raw (Adobe DNG) formats. Before each flight, the camera’s digital ISO, aperture and shutter speed were manually set to adjust for ambient light conditions. Although these settings were changed between flights, they were not permitted to change during a flight; thus, the images from each flight were acquired with consistent camera settings. 20190606 Joshua Logan U.S. Geological Survey, Pacific Coastal and Marine Science Center Physical Scientist mailing address

2885 Mission Street

Santa Cruz CA 95060 US 831-460-7519 831-427-4748 jlogan@usgs.gov Ground control was established using ground control points (GCPs) consisting of small square tarps with black-and-white cross patterns and temporary chalk 'X' marks placed on the ground surface throughout the survey area. The GCP positions were measured using survey-grade GPS receivers operating in post-processed-kinematic (PPK) mode. The GPS receivers were placed on short fixed-height tripods and set to occupy each GCP for a minimum occupation time of one minute. The PPK corrections were referenced to a Continuously Operating Reference (CORS) GPS base station ('BELI') located approximately 5 kilometers from the study area operated by the Washington State Reference Network (WSRN). 20190606 Joshua Logan U.S. Geological Survey, Pacific Coastal and Marine Science Center mailing and physical

2885 Mission Street

Santa Cruz CA 95060 831-460-7519 jlogan@usgs.gov The image files were renamed using a custom python script. The file names were formed using the following pattern Fx-YYYYMMDDThhmmssZ_Ryz.*, where: - Fx = Flight number - YYYYMMDDThhmmssZ = date and time in the ISO 8601 standard, where 'T' separates the date from the time, and 'Z' denotes UTC ('Zulu') time. - Ry = RA or RB to distinguish camera 'RicohA' from 'RicohB' - z = original image name assigned by camera during acquisition - * = file extension (JPG or DNG) The approximate image acquisition coordinates were added to the image metadata (EXIF) ('geotagged') using the image timestamp and the telemetry logs from the UAS onboard single-frequency 1-Hz autonomous GPS. The geotagging process was done using a custom Python script which processes the GPS data from the UAS telemetry log and calls the command-line 'exiftool' software. To improve timestamp accuracy, the image acquisition times were adjusted to true ('corrected') UTC time by comparing the image timestamps with several images taken of a smartphone app ('Emerald Time') showing accurate time from Network Time Protocol (NTP) servers. For this survey, +00:00:02 (2 seconds) were added to the image timestamp to synchronize with corrected UTC time. The positions stored in the EXIF are in geographic coordinates referenced to the WGS84(G1150) coordinate reference system (EPSG:7660), with elevation in meters relative to the WGS84 ellipsoid. Additional information was added to the EXIF using the command-line 'exiftool' software with the following command: exiftool ^ -P ^ -Copyright="Public Domain. Please credit U.S. Geological Survey." ^ -CopyrightNotice="Public Domain. Please credit U.S. Geological Survey." ^ -ImageDescription="Low-altitude aerial image of the intertidal zone at Post Point, Bellingham Bay, Bellingham, Washington, USA, from USGS survey 2019-623-FA." ^ -Caption-Abstract="Intertidal zone at Post Point, Bellingham Bay, Bellingham, Washington, USA, from USGS survey 2019-623-FA." ^ -Caption="Aerial image of the intertidal zone at Post Point, Bellingham Bay, Bellingham, Washington, USA, from USGS survey 2019-623-FA." ^ -sep ", " ^ -keywords="Marine Nearshore Intertidal, Post Point, Bellingham Bay, Bellingham, Washington, 2019-623-FA, Unmanned Aircraft System, UAS, drone, aerial imagery, U.S. Geological Survey, USGS, Pacific Coastal and Marine Science Center" ^ -comment="Low-altitude aerial image from USGS Unmanned Aircraft System (UAS) survey 2019-623-FA." ^ -Credit="U.S. Geological Survey" ^ -Contact="pcmsc_data@usgs.gov" ^ -Artist="U.S. Geological Survey, Pacific Coastal and Marine Science Center" 2019 Joshua Logan U.S. Geological Survey, Pacific Coastal and Marine Science Center mailing and physical

2885 Mission Street

Santa Cruz CA 95060 831-460-7519 jlogan@usgs.gov Structure-from-motion (SfM) processing techniques were used to create the point clouds in the Agisoft Photoscan/Metashape software package using the following workflow: 1. Initial image alignment was performed with the following parameters - Accuracy: 'high'; Pair selection: 'reference', 'generic'; Key point limit: 0 (unlimited); Tie point limit: 0 (unlimited). 2. Sparse point cloud error reduction was performed using an iterative gradual selection and camera optimization process with the following parameters: Reconstruction Uncertainty: 10; Projection Accuracy: 3. Lens calibration parameters f, cx, cy, k1, k2, k3, p1, and p2 were included in the optimization. Additional sparse points obviously above or below the true surface were manually deleted after the last error reduction iteration. 3. Ground control points (GCPs) were automatically detected using the 'Cross (non-coded)' option. False matches were manually removed, and all markers were visually checked and manually placed or adjusted if needed. Markers were manually placed for GCPs that consisted of chalk 'X' marks. 4. Additional sparse point cloud error reduction was performed using an iterative gradual selection and camera optimization process with the following parameters: Reconstruction Error: 0.3. Lens calibration parameters f, cx, cy, k1, k2, k3, p1, and p2 were initially included in the optimization, but additional parameters k4, b1, b2, p3, and p4 were included once Reconstruction Error was reduced below 1 pixel. Additional sparse points obviously above or below the true surface were manually deleted after the last error reduction iteration, and a final optimization was performed. 5. A dense point cloud was created using the 'high' accuracy setting, with 'aggressive' depth filtering. 6. A Digital Surface Model (DSM) with a native resolution of 3.57 centimeters per pixel was created using all points in the dense point cloud for the main DSM. For the high-resolution data a DSM with a native resolution of 1.78 centimeters per pixel was created using all points in the high-resolution dense point cloud. 7. An RGB orthomosaic with a native resolution of 1.84 centimeters per pixel was created using the main DSM as the orthorectification surface. For the high-resolution data an RGB orthomosaic with a native resolution of 0.92 centimeters per pixel was created using the high-resolution DSM as the orthorectification surface. 8. An exterior boundary was digitized using the orthomosaics as a reference and was used as a clipping mask to exclude areas of water, obvious edge artifacts, and large areas of interpolation. 9. The point clouds were exported in LAZ format. 10. LAStools 'lasclip' was used to set the classification of all points falling within the horizontal bounds of the water clipping mask shapefile as Class 9 ('water'). 2019 Joshua Logan U.S. Geological Survey, Pacific Coastal and Marine Science Center Physical Scientist mailing address

2885 Mission Street

Santa Cruz CA 95060 US 831-460-7519 831-427-4748 jlogan@usgs.gov Point Universal Transverse Mercator 10 0.9996 -123.0 0.0 500000.0 0.0 coordinate pair 0.001 0.001 meters NAD83 (National Spatial Reference System 2011) (EPSG:1116) GRS 1980 (EPSG:7019) 6378137.0 298.257222101 North American Vertical Datum of 1988 (EPSG:5703), derived using GEOID12B 0.001 meters Explicit elevation coordinate included with horizontal coordinates The attribute information associated with point cloud follows the LAZ file standard. Attributes include location (northing, easting, and elevation in the NAD83(2011)/UTM zone 10N (EPSG:6339) horizontal and NAVD88 vertical coordinate systems), color (red, blue, and green components), intensity, and classification. All points are classified as 0 (unclassified) or 9 (water). American Society for Photogrammetry and Remote Sensing (ASPRS; 2013, https://www.asprs.org/committee-general/laser-las-file-format-exchange-activities.html) and Isenburg (2013, https://doi.org/10.14358/PERS.79.2.209) U.S. Geological Survey - ScienceBase mailing address

Denver Federal Center, Building 810, Mail Stop 302

Denver CO 80225 United States 1-888-275-8747 sciencebase@usgs.gov The topographic point clouds are available as LAZ files. Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. LAZ LAS 1.2 These zip files contain point cloud data in LAZ format (LAS 1.2 specification). Zip 1180 https://www.sciencebase.gov/catalog/file/get/5ef522a582ced62aaae6a015?name=PostPoint_2019-06-06_pointcloud.zip https://www.sciencebase.gov/catalog/item/5ef522a582ced62aaae6a015 https://doi.org/10.5066/P94LH20J Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to a zip file containing the main survey area point clouds in LAZ format. The second link points to a landing page with the point cloud, metadata, and browse image. The third link points to the landing page for the entire data release, including links to pages of the various data files. LAZ LAS 1.2 These zip files contain point cloud data in LAZ format (LAS 1.2 specification). Zip 1120 https://www.sciencebase.gov/catalog/file/get/5ef522a582ced62aaae6a015?name=PostPointHighRes_2019-06-06_pointcloud.zip https://www.sciencebase.gov/catalog/item/5ef522a582ced62aaae6a015 https://doi.org/10.5066/P94LH20J Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to a zip file containing the high-resolution point clouds in LAZ format. The second link points to a landing page with the point cloud, metadata, and browse image. The third link points to the landing page for the entire data release, including links to pages of the various data files. None. This zip file contains point cloud data in LAZ format (LAS 1.2 specification). The user must have software capable of uncompressing the .zip compressed file and displaying or processing the .laz format file. 20210222 U.S. Geological Survey, Pacific Coastal and Marine Science Center PCMSC Science Data Coordinator mailing and physical

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Santa Cruz CA 95060 831-427-4747 pcmsc_data@usgs.gov Content Standard for Digital Geospatial Metadata FGDC-STD-001-1998