Joshua B. Logan Andrew W. Stevens Cordell D. Johnson Jessica R. Lacy 20200817 GeoTIFF data release DOI:10.5066/P9GF8R1M Pacific Coastal and Marine Science Center, Santa Cruz, California U.S. Geological Survey https://doi.org/10.5066/P9GF8R1M https://www.sciencebase.gov/catalog/item/5eb2105a82cefae35a29c456 Joshua B. Logan Andrew W. Stevens Cordell D. Johnson Jessica R. Lacy 2020 data release DOI:10.5066/P9GF8R1M Pacific Coastal and Marine Science Center, Santa Cruz, CA U.S. Geological Survey https://doi.org/10.5066/P9GF8R1M https://www.sciencebase.gov/catalog/item/5dcdc9fce4b069579760b11b This portion of the data release presents a digital surface model (DSM) and hillshade of the Liberty Island Conservation Bank Wildlands restoration site in the Sacramento-San Joaquin Delta. The DSM has a resolution of 10 centimeters per-pixel and was derived from structure-from-motion (SfM) processing of aerial imagery collected with an Unmanned Aerial System (UAS) on 2018-10-23. Unlike a digital elevation model (DEM), the DSM represents the elevation of the highest object within the bounds of a cell. Vegetation, buildings and other objects have not been removed from the data. In addition, data artifacts resulting from noise in the original imagery have not been removed. The raw imagery used to create this DSM was acquired using two UAS fitted with Ricoh GR II digital cameras global shutters. The UAS were flown on pre-programmed autonomous flight lines at an approximate altitude of 120 meters above-ground-level. The flight lines were oriented roughly east-west and were spaced to provide approximately 66 percent overlap between images from adjacent lines. The cameras were triggered at 1 Hz using a built-in intervalometer. The imagery was geotagged using positions from the UAS onboard single-frequency autonomous GPS. Ground control was established using twenty-four ground control points (GCPs) consisting of small square tarps with black-and-white cross patterns distributed throughout the mapping area. The GCP positions were measured using RTK GPS, with real-time corrections from a GPS base station located approximately 3 kilometers south of the study area. The DSM and hillshade have been formatted as cloud optimized GeoTIFFs with internal overviews and masks to facilitate cloud-based queries and display. These data were collected in support of ongoing field experiments and numerical modeling by the USGS and others, with funding from the U.S. Bureau of Reclamation, to improve our understanding of habitat quality, the influence on various landscape features on ecosystem function, and the effects of restoration actions in the Sacramento–San Joaquin Delta. These data are intended for science researchers, students, policy makers, and the general public. The DSM can be used with geographic information systems (GIS) software for research purposes. 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=2018-676-FA Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. 20181023 ground condition at time data were collected Complete None planned -121.6769 -121.6657 38.3370 38.3247 USGS Metadata Identifier USGS:5eb2105a82cefae35a29c456 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 fragile ecosystems altimetry wetland restoration None U.S. Geological Survey USGS Coastal and Marine Hazards and Resources Program CHMRP Pacific Coastal and Marine Science Center PCMSC UAS Unmanned aerial system Structure-from-motion Geographic Names Information System (GNIS) Liberty Island Cache Slough State of California Sacramento River San Joaquin River Sacramento-San Joaquin Delta Sacramento River Deep Water Ship Channel 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/5eb2105a82cefae35a29c456?name=Wildlands_2018-10-23_DSM_browse.png Color shaded relief map of 2018-10-23 DSM. PNG 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 GDAL 3.1.0. Theresa A. Fregoso Andrew W. Stevens Rueen-Fang Wang Thomas Handley Peter Dartnell Jessica R. Lacy Eli Ateljevich Evan T. Dailey 2020 dataset Pacific Coastal and Marine Science Center, Santa Cruz, California U.S. Geological Survey https://doi.org/10.5066/p9aqsrvh https://www.sciencebase.gov/catalog/item/5d702b8ae4b0c4f70cfa990f 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. All available GCPs were used in the SfM processing workflow. To evaluate horizontal positional accuracy a python script was used in Agisoft to iteratively disable selected GCPs one-at-a-time to create temporary 'check points'. With the check point disabled, a camera optimization was performed with all lens parameters fixed, and all other GCPs enabled. The residual errors of each 'check point' relative to its measured position were logged. After all iterations were complete, the root-mean-square error (RMSE) of all residuals was calculated. For this analysis a subset of eight interior GCPs (GCPs which were within the convex hull of all GCPs) were used, resulting in a horizontal RMSE of 0.076 meters. It should be noted that this estimate is for areas of low vegetation where GCPs were placed. Additional sources of error such as poor image-to-image point matching due to dense vegetation and resulting poor surface reconstruction may cause additional errors in some portions of the DSM which may exceed this uncertainty estimate. All available GCPs were used in the SfM processing workflow. To evaluate horizontal positional accuracy a python script was used in Agisoft to iteratively disable selected GCPs one-at-a-time to create temporary 'check points'. With the check point disabled, a camera optimization was performed with all lens parameters fixed, and all other GCPs enabled. The residual errors of each 'check point' relative to its measured position were logged. After all iterations were complete, the root-mean-square error (RMSE) of all residuals was calculated. For this analysis a subset of eight interior GCPs (GCPs which were within the convex hull of all GCPs) were used, resulting in a vertical RMSE of 0.107 meters. It should be noted that this estimate is for the vertical position of the vegetation canopy at the time of the survey only and not for the bare ground. Due to the dense vegetation in the survey area, the ground surface is not visible in much of the imagery and therefore not represented in the SfM reconstruction. Additional sources of error such as poor image-to-image point matching due to dense vegetation and resulting poor surface reconstruction may cause additional errors in some portions of the DSM which may exceed this uncertainty estimate. Aerial imagery was collected using two Department of Interior owned 3DR Solo quadcopters fitted with Ricoh GR II digital cameras featuring global shutters. The cameras were mounted on a fixed mount on the bottom of the UAS and oriented in a roughly nadir orientation. The UAS were flown on pre-programmed autonomous flight lines at an approximate altitude of 120 meters above-ground-level. The flight lines were oriented roughly east-west and were spaced to provide approximately 66 percent overlap between images from adjacent lines. The cameras were triggered at 1 Hz using a built in intervalometer, and were programmed to simultaneously acquire imagery in both JPG and camera raw (Adobe DNG) formats. Due to the limited UAS battery life, a total of 8 flights were required to achieve full coverage of the study area. The flights were conducted on 2018-10-23 between 18:21 and 20:35 Universal Coordinated Time (UTC) (11:21 and 13:35 Pacific Daylight Time (PDT)). Before each flight, the camera 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 individual flight were acquired with consistent camera settings. 20181023 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 twenty-four ground control points (GCPs) consisting of small square tarps with black-and-white cross patterns placed on the ground surface throughout the survey area. The GCP positions were measured using survey-grade GPS receivers operating in real-time-kinematic (RTK) 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 RTK corrections were referenced to a static GPS base station operating on a benchmark approximately 3 kilometers south of the survey area. The position of the benchmark was previously established using the average of three static GPS occupations (2017-06-26 to 2017-06-28) with durations between 4 and 8 hours, processed using the National Geodetic Survey (NGS) Online Positioning User Service (OPUS). 20181023 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 GeoSetter 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 RicohA no image time adjustment was needed; for RicohB, +00:00:02 (2 seconds) were added to the image time 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 Liberty Island Conservation Bank Wildlands restoration site, Cache Slough Complex, Sacramento-San Joaquin Delta, California, USA, from USGS survey 2018-676-FA" ^ -Caption-Abstract="Liberty Island Conservation Bank Wildlands restoration site, Cache Slough Complex, Sacramento-San Joaquin Delta, California, USA, from USGS survey 2018-676-FA" ^ -Caption="Liberty Island Conservation Bank Wildlands restoration site, Cache Slough Complex, Sacramento-San Joaquin Delta, California, USA, from survey 2018-676-FA" ^ -sep ", " ^ -keywords="Liberty Island, Liberty Island Conservation Bank, Wildlands restoration site, Cache Slough Complex, Sacramento-San Joaquin Delta, California, 2018-676-FA, Unmanned Aircraft System, UAS, aerial imagery, USGS, Pacific Coastal and Marine Science Center" ^ -comment="Low-altitude aerial image from USGS Unmanned Aircraft System (UAS) survey 2018-676-FA" ^ -Credit="U.S. Geological Survey" ^ -Contact="pcmsc_data@usgs.gov" ^ -Artist="Pacific Coastal and Marine Science Center" 2018 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 Digital Surface Model (DSM) 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. 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. Low-noise points were identified using the 'Classify Ground Points' tool in Agisoft with the following parameters: Max. Angle: 15 degrees; Max. Distance: 0.5 meters; Cell Size: 5 meters. Due to the prevalence of water, vegetation and tree cover some areas, it is not expected that this step identified all noise. 7. An exterior boundary was digitized and used as a clipping mask to exclude obvious edge artifacts and large areas of interpolation. 8. An initial Digital Surface Model (DSM) with a native resolution of 6.3 centimeters per-pixel was created using all points in the dense point cloud, except those classified as 'low-noise'. The DSM was exported to a GeoTIFF format with a 10-centimeter pixel resolution. 9. A water clipping mask was developed in ArcGIS by filtering elevation values below 1.6 meters and combining those with large areas of interpolation in the DSM (representing large areas of the original point cloud which had been classified as noise). The clipping mask was applied to the DSM to produce a final DSM with 'NoData' values for water areas. 10. The DSM was converted to a cloud optimized GeoTIFF format for compatibility with cloud storage services using the GDAL software package. The DSM was compressed using the lossless Deflate compression method, and 'NoData' value set to -32767. A hillshade of the DSM was created in cloud optimized GeoTIFF format using GDAL. 2018 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 A link was added to the Network Resource section of the metadata for accessing the cloud-optimized GeoTIFFs on cloud-based storage. This link can be used for cloud-based queries or viewing of the data directly from the cloud without having to download it. No data were changed. Users are advised to compare the metadata date of this file to any similar file to ensure they are using the most recent version. 20200918 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 Edited metadata to add keywords section with USGS persistent identifier as theme keyword. No data were changed. 20201019 U.S. Geological Survey VeeAnn A. Cross Marine Geologist Mailing and Physical

384 Woods Hole Road

Woods Hole MA 02543-1598 508-548-8700 x2251 508-457-2310 vatnipp@usgs.gov Raster Grid Cell 13470 9630 1 Universal Transverse Mercator 10 0.9996 -123.0 0.0 500000.0 0.0 row and column 0.100 0.100 meters NAD83_National_Spatial_Reference_System_2011 GRS 1980 6378137.0 298.257222101 North American Vertical Datum of 1988 0.001 meters Explicit elevation coordinate included with horizontal coordinates GeoTIFF GeoTIFF containing elevation values. Producer defined N/A Elevation relative to the North American vertical datum of 1988 (NAVD88) Producer defined 1.6000 26.048 meters 0.001 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 DSM (Wildlands_2018-10-23_DSM_10cm.tif) and hillshade (Wildlands_2018-10-23_DSM_10cm_hll.tif) are available as Cloud Optimized GeoTIFF 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. GeoTIFF GDAL 3.1.0dev Cloud Optimized GeoTIFF contains Digital Surface Model (DSM) with single-precision floating-point values compressed using the Deflate lossless compression method. No data value is -32767. none 706 https://www.sciencebase.gov/catalog/file/get/5eb2105a82cefae35a29c456?name=Wildlands_2018-10-23_DSM_10cm.tif https://prod-is-usgs-sb-prod-publish.s3.amazonaws.com/5eb2105a82cefae35a29c456/Wildlands_2018-10-23_DSM_10cm.tif https://www.sciencebase.gov/catalog/item/5eb2105a82cefae35a29c456 https://doi.org/10.5066/P9GF8R1M Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to download the 10 cm DSM. The second link is for accessing the DSM on cloud-based storage, and can be used for cloud-based queries or viewing. The third link points to a landing page with the DSM and a hillshade, metadata, and browse image. The fourth link points to the landing page for the entire data release, including links to pages of the various data files. GeoTIFF GDAL 3.1.0dev Cloud Optimized GeoTIFF contains hillshade of Digital Surface Model (DSM) with 8-bit unsigned integer values compressed using the Deflate lossless compression method. No data value is 0. none 99 https://www.sciencebase.gov/catalog/file/get/5eb2105a82cefae35a29c456?name=Wildlands_2018-10-23_DSM_10cm_hll.tif https://prod-is-usgs-sb-prod-publish.s3.amazonaws.com/5eb2105a82cefae35a29c456/Wildlands_2018-10-23_DSM_10cm_hll.tif https://www.sciencebase.gov/catalog/item/5eb2105a82cefae35a29c456 https://doi.org/10.5066/P9GF8R1M Data can be downloaded using the Network_Resource_Name links. The first link is a direct link to download hillshade version of the 10 cm DSM. The second link is for accessing the hillshade on cloud-based storage, and can be used for cloud-based queries or viewing. The third link points to a landing page with the hillshade, DSM, metadata, and browse image. The fourth link points to the landing page for the entire data release, including links to pages of the various data files. None. These data can be viewed with GIS software or other software capable of displaying geospatial raster data. 20201019 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 Content Standard for Digital Geospatial Metadata FGDC-STD-001-1998