Orthomosaic images of the Whale's Tail Marsh region, South San Francisco Bay, CA

Metadata also available as - [Questions & Answers] - [Parseable text] - [XML]

Metadata:

Identification_Information:
Citation:
Citation_Information:
Originator: Joshua B. Logan
Originator: Lukas T. Winklerprins
Originator: Jessica R. Lacy
Publication_Date: 20230508
Title:
Orthomosaic images of the Whale's Tail Marsh region, South San Francisco Bay, CA
Geospatial_Data_Presentation_Form: GeoTIFF
Series_Information:
Series_Name: data release
Issue_Identification: DOI:10.5066/P9L9R2VS
Publication_Information:
Publication_Place:
Pacific Coastal and Marine Science Center, Santa Cruz, California
Publisher: U.S. Geological Survey
Online_Linkage: https://doi.org/10.5066/P9L9R2VS
Online_Linkage: Larger_Work_Citation:
Citation_Information:
Originator: Joshua B. Logan
Originator: Lukas T. Winklerprins
Originator: Jessica R. Lacy
Publication_Date: 2023
Title:
Structure-from-motion derived orthomosaic imagery and digital surface models (DSMs) from the intertidal region at Whale's Tail Marsh, South San Francisco Bay, CA
Series_Information:
Series_Name: data release
Issue_Identification: DOI:10.5066/P9L9R2VS
Publication_Information:
Publication_Place: Pacific Coastal and Marine Science Center, Santa Cruz, CA
Publisher: U.S. Geological Survey
Other_Citation_Details:
Suggested Citation: Logan, J.B., Winklerprins, L.T., and Lacy, J.R., 2023, Structure-from-motion derived orthomosaic imagery and digital surface models (DSMs) from the intertidal region at Whale's Tail Marsh, South San Francisco Bay, CA: U.S. Geological Survey data release, https://doi.org/10.5066/P9L9R2VS.
Online_Linkage: https://doi.org/10.5066/P9L9R2VS
Description:
Abstract:
This portion of the data release presents orthomosaic images of the Whale's Tail Marsh region of South San Francisco Bay, CA. The orthomosaics have resolutions of 2.5 centimeters per pixel and were derived from structure-from-motion (SfM) processing of repeat aerial imagery collected from fixed-wing aircraft. The raw imagery used to create these elevation models was acquired from an approximate altitude of 427 meters (1,400 feet) above ground level (AGL), using a Hasselblad A6D-100c camera fitted with an HC 80 lens, resulting in a nominal ground-sample-distance (GSD) of 2.5 centimeters per pixel. The acquisition flight lines were designed to provide approximately 50 percent overlap between adjacent flight lines (sidelap), with approximately 70 percent overlap between sequential images along the flight line (forelap). Survey control was established using an onboard camera-synchronized dual-frequency GPS system as well as ground control points (GCPs) distributed throughout the survey area and measured using survey-grade post-processed kinematic (PPK) GPS. Both the data from the onboard GPS and from the GPS used to measure the GCPs were post-processed using a nearby Continuously Operating Reference Station (CORS) station operated by the National Geodetic Survey (NGS). Structure-from-motion processing of these data was conducted using a "4D" processing workflow in which imagery from each of the different acquisition dates were co-aligned in order to increase relative spatial precision between the final data products. The resulting orthomosaics have been formatted as cloud optimized GeoTIFFs with internal overviews and masks to facilitate cloud-based queries and display.
Purpose:
These data are intended to be used to characterize the seasonal patterns and rates of change in the position and morphology of the Whale's Tail marsh in South San Francisco Bay, in California.
Supplemental_Information:
Additional information about the field activity from which these data were derived is available online at:
https://cmgds.marine.usgs.gov/fan_info.php?fan=2021-624-FA
Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
Time_Period_of_Content:
Time_Period_Information:
Multiple_Dates/Times:
Single_Date/Time:
Calendar_Date: 20210530
Single_Date/Time:
Calendar_Date: 20210909
Single_Date/Time:
Calendar_Date: 20211114
Single_Date/Time:
Calendar_Date: 20220210
Single_Date/Time:
Calendar_Date: 20220519
Currentness_Reference: ground condition at time data were collected
Status:
Progress: Complete
Maintenance_and_Update_Frequency: None planned
Spatial_Domain:
Bounding_Coordinates:
West_Bounding_Coordinate: -122.15222
East_Bounding_Coordinate: -122.11319
North_Bounding_Coordinate: 37.61345
South_Bounding_Coordinate: 37.57572
Keywords:
Theme:
Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: geoscientificInformation
Theme:
Theme_Keyword_Thesaurus: Data Categories for Marine Planning
Theme_Keyword: Bathymetry and Elevation
Theme:
Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: remote sensing
Theme_Keyword: geomorphology
Theme_Keyword: aerial photography
Theme_Keyword: image mosaics
Theme_Keyword: geospatial datasets
Theme_Keyword: structure from motion
Theme:
Theme_Keyword_Thesaurus: Marine Realms Information Bank (MRIB) keywords
Theme_Keyword: photography
Theme_Keyword: remote sensing
Theme_Keyword: aerial and satellite photography
Theme_Keyword: altimetry
Theme_Keyword: orthophotography
Theme:
Theme_Keyword_Thesaurus: None
Theme_Keyword: U.S. Geological Survey
Theme_Keyword: USGS
Theme_Keyword: Coastal and Marine Hazards and Resources Program
Theme_Keyword: CHMRP
Theme_Keyword: Pacific Coastal and Marine Science Center
Theme_Keyword: PCMSC
Theme_Keyword: Structure-from-motion
Theme_Keyword: SfM
Theme:
Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:63080760d34e3b967a8c15ce
Place:
Place_Keyword_Thesaurus: Geographic Names Information System (GNIS)
Place_Keyword: State of California
Place_Keyword: Alameda County
Place_Keyword: San Francisco Bay
Place_Keyword: Alameda Creek
Place_Keyword: Mount Eden Creek
Access_Constraints: None
Use_Constraints:
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.
Point_of_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Person: PCMSC Science Data Coordinator
Contact_Address:
Address_Type: mailing and physical
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Contact_Voice_Telephone: 831-427-4747
Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov
Browse_Graphic:
Browse_Graphic_File_Name: Browse_Graphic_File_Description: Orthomosaic image of south Whale's Tail Marsh (2021-09-09)
Browse_Graphic_File_Type: JPEG
Native_Data_Set_Environment:
Microsoft Windows 10, Agisoft PhotoScan version 1.4 through Agisoft Metashape 1.7, ESRI ArcGIS 10.6 through 10.7, Exiftool, Geosetter 3.4.16, QGIS 3.26, and GDAL 3.5.1
Cross_Reference:
Citation_Information:
Originator: Logan, J.B.
Originator: Wernette, P.A.
Originator: Ritchie, A.C.
Publication_Date: 2022
Title:
Agisoft Metashape/Photoscan Automated Image Alignment and Error Reduction version 2.0
Other_Citation_Details:
Logan, J.B., Wernette, P.A., and Ritchie, A.C., 2022, Agisoft Metashape/Photoscan Automated Image Alignment and Error Reduction version 2.0: U.S. Geological Survey code repository, U.S. Geological Survey software release, python package, Reston, Va., (https://doi.org/10.5066/P9DGS5B9).
Online_Linkage: https://doi.org/10.5066/P9DGS5B9
Cross_Reference:
Citation_Information:
Originator: Federal Geographic Data Committee
Publication_Date: 1998
Title:
Geospatial Positioning Accuracy Standards Part 3: National Standard for Spatial Data Accuracy
Other_Citation_Details: FGDC-STD-007.3-1998
Online_Linkage:
Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report: No formal attribute accuracy tests were conducted.
Logical_Consistency_Report: No formal logical accuracy tests were conducted.
Completeness_Report:
Dataset is considered complete for the information presented, as described in the abstract.
Positional_Accuracy:
Horizontal_Positional_Accuracy:
Horizontal_Positional_Accuracy_Report:
Horizontal accuracy was estimated by comparing ground control point (GCP) positions measured with PPK GPS measurements to their SfM-estimated positions. For each data set (images from a single acquisition date), five or more GCP positions were used as GCP check points. These positions were marked in the imagery, but they were left disabled (unchecked) during image alignment and sparse point cloud error reduction. The residual errors of the SfM-estimated positions of the check points relative to their GPS-measured position were used to calculate the root-mean-square error (RMSE), mean-absolute error (MAE), and mean error (bias). Following the Federal Geographic Data Committee National Standard for Spatial Data Accuracy (1998) guidelines, we use the RMSE to calculate the horizontal positional accuracy at the 95 percent confidence level. To account for additional uncertainty in the GPS-measured positions of the GCPs (0.030 meters) we include this as an additional error term through summation in quadrature to arrive at an estimate of total positional horizontal accuracy. The error statistics and horizontal accuracy estimates for each of the orthomosaics are below:
WhaleTailMarsh_2021-05-30_orthomosaic_25mm.tif: Horizontal RMSE (m): 0.034 Horizontal MAE (m): 0.028 Mean error, north (m): 0.015 Mean error, east (m): 0.003 Horizontal accuracy at the 95 percent confidence level (m): 0.058 Total horizontal accuracy estimate at the 95 percent confidence level, including GPS uncertainty (m): 0.062
WhaleTailMarsh_2021-09-09_orthomosaic_25mm.tif: Horizontal RMSE (m): 0.039 Horizontal MAE (m): 0.035 Mean error, north (m): 0.013 Mean error, east (m): 0.012 Horizontal accuracy at the 95 percent confidence level (m): 0.067 Total horizontal accuracy estimate at the 95 percent confidence level, including GPS uncertainty (m): 0.070
WhaleTailMarsh_2021-11-14_orthomosaic_25mm.tif: Horizontal RMSE (m): 0.046 Horizontal MAE (m): 0.043 Mean error, north (m): 0.010 Mean error, east (m): 0.008 Horizontal accuracy at the 95 percent confidence level (m): 0.079 Total horizontal accuracy estimate at the 95 percent confidence level, including GPS uncertainty (m): 0.081
WhaleTailMarsh_2022-02-10_orthomosaic_25mm.tif: Horizontal RMSE (m): 0.036 Horizontal MAE (m): 0.032 Mean error, north (m): 0.025 Mean error, east (m): 0.010 Horizontal accuracy at the 95 percent confidence level (m): 0.062 Total horizontal accuracy estimate at the 95 percent confidence level, including GPS uncertainty (m): 0.065
WhaleTailMarsh_2022-05-19_orthomosaic_25mm.tif:: Horizontal RMSE (m): 0.039 Horizontal MAE (m): 0.036 Mean error, north (m): 0.029 Mean error, east (m): 0.007 Horizontal accuracy at the 95 percent confidence level (m): 0.067 Total horizontal accuracy estimate at the 95 percent confidence level, including GPS uncertainty (m): 0.070
It should be noted that these accuracy estimates are for areas of bare ground or low vegetation in the locations where GCPs were placed. Although the GPS control on the image positions (from the post-processed camera-synchronized GPS) can reduce the need for on-the-ground control points, the overall accuracy of the final DSM may vary as a function of the distance to a measured ground control point. Areas where no ground control points were placed (Whale's Tail marsh north of Alameda Creek and any areas east of the unbreached north-south levy on the eastern edge of the marsh, as well as some areas along the marsh edge may have accuracies lower than these estimates. Additional sources of error such as poor image-to-image point matching due to vegetation or uniform substrate texture (such as mud) resulting in poor surface reconstruction may also cause additional localized errors in some portions of the orthomosaics which exceed these estimates.
Vertical_Positional_Accuracy:
Vertical_Positional_Accuracy_Report:
Vertical positional accuracy was not evaluated for this data product as no elevation data are presented.
Lineage:
Process_Step:
Process_Description:
Aerial imagery was acquired by the 111th Group, Inc. from a fixed-wing aircraft. Acquisition times were planned in advance to coincide with low tide to maximize the extent of the subaerially exposed portions of the marsh and mud-flats. The imagery was acquired from an approximate altitude of 427 meters (1,400 feet) above ground level (AGL) using a Hasselblad A6D-100c camera with an HC 80 lens mounted in a nadir orientation, resulting in a nominal ground-sample-distance (GSD) of 2.5 centimeters per pixel. The acquisition flight lines were designed to provide approximately 50 percent overlap between adjacent flight lines (sidelap), with approximately 70 percent overlap between sequential images along the flight line (forelap). A camera-synchronized onboard dual-frequency GPS receiver was used to record the precise shutter time and position of each image. The acquisition dates and times were as follows: 2021-05-30 18:12 - 18:38 (UTC) 2021-09-09 16:10 - 16:38 (UTC) 2021-11-14 22:19 - 22:42 (UTC) 2022-02-10 23:02 - 23:27 (UTC) 2022-05-19 17:46 - 18:46 (UTC)
Process_Date: 20220519
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Patrick Belanger
Contact_Organization: The 111th Group Inc
Contact_Address:
Address_Type: mailing and physical
Address: 13025 Murphy Ave. Suite 100
City: San Martin
State_or_Province: CA
Postal_Code: 95046
Contact_Voice_Telephone: 408-683-9111
Contact_Electronic_Mail_Address: pat@the111th.com
Process_Step:
Process_Description:
The raw aerial images were converted from 3FR to FFF images using the Hasselblad Phocus software package. The software lens corrections were performed for vignetting and chromatic aberration, but they were not performed for lens distortion. Exposure adjustments of up to +1.0 EV were performed on the images from some of the image acquisitions to increase the overall exposure on the imagery. Final images were exported using the JPG Max setting to create high-quality JPG images with low compression artifacts.
Process_Date: 2022
Process_Step:
Process_Description:
The onboard camera-synchronized GPS data were post-processed using kinematic post-processing (PPK) using the Novatel Waypoint Grafnav software package. The P222 continuously operating reference station (CORS) operated by the National Geodetic Survey (NGS) approximately 7 kilometers southeast of the survey area was used for post-processing. After PPK processing, the precise position of each image was interpolated along the GPS trajectory using GPS-synchronized camera-shutter event marks in Grafnav. The precise positions of each image were then exported to a csv file for use in structure from motion processing software.
Process_Date: 2022
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Joshua Logan
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Contact_Voice_Telephone: 831-460-7519
Contact_Electronic_Mail_Address: jlogan@usgs.gov
Process_Step:
Process_Description:
Ground control was established using ground control points (GCPs) consisting of small square tarps with black-and-white cross patterns placed on the ground surface throughout the survey area, as well as painted "X" marks on objects such as rocks or large logs, which were expected to be stable during the course of the project. The GCP positions were measured using survey-grade GPS receivers placed on fixed height tripods, using a static occupation time of 1 minute. The GPS positions were post-processed using kinematic post-processing (PPK) using the P222 continuously operating reference station (CORS) operated by the National Geodetic Survey (NGS) approximately 7 kilometers southeast of the survey area. The GCPs were periodically maintained and re-visited throughout the course of the project to ensure stability and visibility in the imagery. The dates of the GCP surveys were: 2021-05-19, 2021-07-28, 2021-11-01, 2022-02-04, 2022-05-18, and 2022-10-05.
Process_Date: 20221005
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Joshua Logan
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Address:
Address_Type: mailing and physical
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Contact_Voice_Telephone: 831-460-7519
Contact_Electronic_Mail_Address: jlogan@usgs.gov
Process_Step:
Process_Description:
Structure-from-motion (SfM) processing techniques were used to create point clouds, DSMs, and orthomosaic images in the Agisoft Metashape software package using the following workflow: 1. Imagery from each acquisition date was imported into a single processing group (also known as a chunk in Agisoft), and separated into different camera (sensor) groups. Precise positions from the onboard PPK GPS data were imported to provide precise camera positions for each image. Accuracy for the camera positions was set to 0.250 m. 2. Image alignment was performed using the 4D technique, in which all imagery in project are co-aligned to improve relative precision between the images from each acquisition date. The following alignment parameters were used: Accuracy: 'high'; Pair selection: 'reference', 'generic'; Key point limit: 0 (unlimited); Tie point limit: 0 (unlimited). 3. Ground control point (GCPs) positions were imported and manually placed on all imagery; accuracy for GCP markers was set to 0.050 meters. 4. Sparse point cloud error reduction was conducted using an automated script to perform iterative gradual selection and camera optimization (Logan and others, 2022). Lens calibration parameters f, cx, cy, k1, k2, k3, p1, and p2 were included in the optimization. 5. The aligned imagery from each acquisition date was divided into single-date groups (chunks) for product generation. 6. Dense point clouds were created for each acquisition date using the 'high' accuracy setting, with 'aggressive' depth filtering. 7. Digital Surface Models (DSM) were created for each acquisition date using the dense point clouds, and were exported to GeoTIFF files with 5-centimeter pixel resolutions. 8. RGB orthomosaic images were created using the DSMs as the orthorectification surfaces, and were exported to GeoTIFF files with 2.5-centimeter pixel resolutions. 9. The orthomosaic images were converted to cloud optimized GeoTIFF format with JPEG image compression (quality 90 percent) for compatibility with cloud storage services using the gdal_translate utility in the GDAL software package.
Process_Date: 2022
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Joshua Logan
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Position: Physical Scientist
Contact_Address:
Address_Type: mailing address
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Country: US
Contact_Voice_Telephone: 831-460-7519
Contact_Facsimile_Telephone: 831-427-4748
Contact_Electronic_Mail_Address: jlogan@usgs.gov
Spatial_Data_Organization_Information:
Direct_Spatial_Reference_Method: Raster
Raster_Object_Information:
Raster_Object_Type: Grid Cell
Spatial_Reference_Information:
Horizontal_Coordinate_System_Definition:
Planar:
Grid_Coordinate_System:
Grid_Coordinate_System_Name: Universal Transverse Mercator
Universal_Transverse_Mercator:
UTM_Zone_Number: 10
Transverse_Mercator:
Scale_Factor_at_Central_Meridian: 0.9996
Longitude_of_Central_Meridian: -123.0
Latitude_of_Projection_Origin: 0.0
False_Easting: 500000.0
False_Northing: 0.0
Planar_Coordinate_Information:
Planar_Coordinate_Encoding_Method: row and column
Coordinate_Representation:
Abscissa_Resolution: 0.025
Ordinate_Resolution: 0.025
Planar_Distance_Units: meters
Geodetic_Model:
Horizontal_Datum_Name: NAD83 (National Spatial Reference System 2011) (EPSG:1116)
Ellipsoid_Name: GRS 1980 (EPSG:7019)
Semi-major_Axis: 6378137.0
Denominator_of_Flattening_Ratio: 298.257222101
Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label: GeoTIFF
Entity_Type_Definition: GeoTIFF containing RGB color bands.
Entity_Type_Definition_Source: Producer defined
Attribute:
Attribute_Label: Band_1
Attribute_Definition: Red band
Attribute_Definition_Source: Producer defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0
Range_Domain_Maximum: 255
Attribute:
Attribute_Label: Band_2
Attribute_Definition: Green band
Attribute_Definition_Source: Producer defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0
Range_Domain_Maximum: 255
Attribute:
Attribute_Label: Band_3
Attribute_Definition: Blue band
Attribute_Definition_Source: Producer defined
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 0
Range_Domain_Maximum: 255
Distribution_Information:
Distributor:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey - ScienceBase
Contact_Address:
Address_Type: mailing address
Address: Denver Federal Center, Building 810, Mail Stop 302
City: Denver
State_or_Province: CO
Postal_Code: 80225
Country: United States
Contact_Voice_Telephone: 1-888-275-8747
Contact_Electronic_Mail_Address: sciencebase@usgs.gov
Resource_Description:
The Whale's Tail Marsh orthomosaic images are available as Cloud Optimized GeoTIFF files accompanied by CSDGM FGDC-compliant metadata.
Distribution_Liability:
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.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: GeoTIFF
Format_Version_Number: GDAL 3.5.1
Format_Information_Content:
Cloud Optimized GeoTIFF contains a three-band RGB orthomosaic with 8-bit unsigned integer values stored with high quality JPEG compression. Transfer size reflects the largest size image that may be downloaded. Other GeoTIFFS in this dataset are smaller.
File_Decompression_Technique: none
Transfer_Size: 3740
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name: Network_Resource_Name: Network_Resource_Name: Network_Resource_Name: Network_Resource_Name: Network_Resource_Name: Network_Resource_Name: Network_Resource_Name: Network_Resource_Name: Network_Resource_Name: Network_Resource_Name: Network_Resource_Name: https://doi.org/10.5066/P9L9R2VS
Access_Instructions:
Data can be downloaded using the Network_Resource_Name links. The first five links are direct links to download the DSMs in GeoTIFF format. The next five links are for accessing the DSMs on cloud-based storage and can be used for cloud-based queries or viewing. The eleventh link points to a landing page with the orthomosaics, metadata, and a browse image. The twelfth link points to the landing page for the entire data release, including links to pages of the various data files.
Fees: None.
Technical_Prerequisites:
These data can be viewed with GIS software or other software capable of displaying geospatial raster data.
Metadata_Reference_Information:
Metadata_Date: 20230508
Metadata_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Person: PCMSC Science Data Coordinator
Contact_Address:
Address_Type: mailing and physical
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060
Contact_Voice_Telephone: 831-427-4747
Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov
Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001-1998

This page is <https://cmgds.marine.usgs.gov/catalog/pcmsc/DataReleases/ScienceBase/DR_P9L9R2VS/WhaleTailMarsh_orthomosaic_images_metadata.html>
Generated by mp version 2.9.51 on Thu May 11 17:41:12 2023