SCDNRoyster2010Wash

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Tags
intertidal oyster, Crassostrea virginica, NOAA, DNR, washed shell

Summary
This dataset was produced as part of the South Carolina Oyster Beds Imaging effort per USGS Contract # This dataset was produced as part of the South Carolina Oyster Beds Imaging effort per USGS Contract # 01CRCN0012 for NOAA, to support the mapping of intertidal oyster reefs for management of the state's shellfish resources.


Description

This dataset contains digitized boundaries of washed oyster shell deposits found along the South Carolina coast. The deposits were digitized through a combination of automated and manual techniques using 4-band (blue, green, red, near-infrared) digital orthophotos with a theoretical ground resolution of 0.25 meters. The photos are dated from 2003 to 2006. The project area was selected specifically to cover those sections of the SC coastal critical zone where oysters had historically been mapped by the SC Department of Natural Resources (SCDNR). The area spans 122 USGS quarter quadrangles (DOQQs). Sixty of the DOQQs were ground-truthed by boat to assess accuracy. Some areas were verified through photographs taken from low-altitude helicopter flights conducted from 2006 to 2008 by SCDNR. The initial digitization process has met with the minimum accuracy requirements of the project (80% correct classification) and was completed through a joint effort between Photo Science Inc. and SCDNR. The entire dataset has been reviewed by SCDNR for quality using all known information through 2010. Edits and improvements were completed by SCDNR on April 28, 2011. Updated versions of this dataset will be produced as more information becomes available. Information on accuracy and completeness of the data are contained in the Data Quality Sections of this report.

Credits
None. The South Carolina Department of Natural Resources should be acknowledged in products derived from these data.

Access and use limitations
Neither the State of South Carolina, the Department of Natural Resources, nor any of its employees, is responsible for any improper or incorrect use of the information described and/or contained herein, and assume no responsibility for the use of the information. The South Carolina Department of Natural Resources should be acknowledged as the data source in products derived from these data.

ArcGIS Metadata 

Resource Identification 

Citation
Title SCDNRoyster2010Wash


*Presentation format  digital map


Tags for searching  intertidal oyster, Crassostrea virginica, NOAA, DNR, washed shell


Keywords 002
Thesaurus

Abstract (Description)
This dataset contains digitized boundaries of washed oyster shell deposits found along the South Carolina coast. The deposits were digitized through a combination of automated and manual techniques using 4-band (blue, green, red, near-infrared) digital orthophotos with a theoretical ground resolution of 0.25 meters. The photos are dated from 2003 to 2006. The project area was selected specifically to cover those sections of the SC coastal critical zone where oysters had historically been mapped by the SC Department of Natural Resources (SCDNR). The area spans 122 USGS quarter quadrangles (DOQQs). Sixty of the DOQQs were ground-truthed by boat to assess accuracy. Some areas were verified through photographs taken from low-altitude helicopter flights conducted from 2006 to 2008 by SCDNR. The initial digitization process has met with the minimum accuracy requirements of the project (80% correct classification) and was completed through a joint effort between Photo Science Inc. and SCDNR. The entire dataset has been reviewed by SCDNR for quality using all known information through 2010. Edits and improvements were completed by SCDNR on April 28, 2011. Updated versions of this dataset will be produced as more information becomes available. Information on accuracy and completeness of the data are contained in the Data Quality Sections of this report.
Purpose (Summary)
This dataset was produced as part of the South Carolina Oyster Beds Imaging effort per USGS Contract # This dataset was produced as part of the South Carolina Oyster Beds Imaging effort per USGS Contract # 01CRCN0012 for NOAA, to support the mapping of intertidal oyster reefs for management of the state's shellfish resources.
Dataset languages* English (UNITED STATES)


Resource constraints
Constraints
Limitations of use
Neither the State of South Carolina, the Department of Natural Resources, nor any of its employees, is responsible for any improper or incorrect use of the information described and/or contained herein, and  assume no responsibility for the use of the information.  The South Carolina Department of Natural Resources should be acknowledged as the data source in products derived from these data.
*Spatial representation type  vector


*Processing environment Microsoft Windows XP Version 5.1 (Build 2600) Service Pack 3; ESRI ArcGIS 10.0.2.3200


Bounding rectangle
*Extent type  Full extent in decimal degrees
*West longitude -80.927007
*East longitude -78.537618
*North latitude 33.907739
*South latitude 32.060161
*Extent contains the resource Yes

Other extent information
Geographic extent
Bounding rectangle
*Extent type  Extent used for searching
*West longitude -80.927007
*East longitude -78.537618
*North latitude 33.907739
*South latitude 32.060161
*Extent contains the resource Yes

Bounding rectangle
*Extent type  Extent used for searching
*West longitude -80.927007
*East longitude -78.537618
*North latitude 33.907739
*South latitude 32.060161
*Extent contains the resource Yes

Credits
None. The South Carolina Department of Natural Resources should be acknowledged in products derived from these data.

Spatial Representation 

Reference System 

Distribution Information 

Metadata Details 

ESRI Metadata and Item Properties 

ESRI Spatial Information 

ESRI Feature Class 

ESRI Fields and Subtypes 

ESRI Geoprocessing History 

FGDC Metadata 

Identification 

Citation
Citation Information
Originator South Carolina Department of Natural Resources (SCDNR)
Publication Date July 2011
Title
SCDNRoyster2010Wash
Edition 1
Geospatial Data Presentation Form vector digital data
Online Linkage\\Mrdnas\ShellMap\Databases\CurrentOysterDatabase2010\SCDNR_Oyster2010.mdb

Description
Abstract
This dataset contains digitized boundaries of washed oyster shell deposits found along the South Carolina coast. The deposits were digitized through a combination of automated and manual techniques using 4-band (blue, green, red, near-infrared) digital orthophotos with a theoretical ground resolution of 0.25 meters. The photos are dated from 2003 to 2006. The project area was selected specifically to cover those sections of the SC coastal critical zone where oysters had historically been mapped by the SC Department of Natural Resources (SCDNR). The area spans 122 USGS quarter quadrangles (DOQQs). Sixty of the DOQQs were ground-truthed by boat to assess accuracy. Some areas were verified through photographs taken from low-altitude helicopter flights conducted from 2006 to 2008 by SCDNR. The initial digitization process has met with the minimum accuracy requirements of the project (80% correct classification) and was completed through a joint effort between Photo Science Inc. and SCDNR. The entire dataset has been reviewed by SCDNR for quality using all known information through 2010. Edits and improvements were completed by SCDNR on April 28, 2011. Updated versions of this dataset will be produced as more information becomes available. Information on accuracy and completeness of the data are contained in the Data Quality Sections of this report.
Purpose
This dataset was produced as part of the South Carolina Oyster Beds Imaging effort per USGS Contract # This dataset was produced as part of the South Carolina Oyster Beds Imaging effort per USGS Contract # 01CRCN0012 for NOAA, to support the mapping of intertidal oyster reefs for management of the state's shellfish resources.
Time Period of Content
Time Period Information
Range of Dates/Times
Beginning Date 2003
Ending Date 2010
Currentness Reference
ground condition
Status
Progress Complete
Maintenance and Update Frequency None planned

Spatial Domain
Bounding Coordinates
West Bounding Coordinate -80.927007
East Bounding Coordinate -78.537618
North Bounding Coordinate 33.907739
South Bounding Coordinate 32.060161

Keywords
Theme
Theme Keyword Thesaurus REQUIRED: Reference to a formally registered thesaurus or a similar authoritative source of theme keywords.
Theme Keyword intertidal oyster
Theme Keyword Crassostrea virginica
Theme Keyword NOAA
Theme Keyword DNR
Theme Keyword washed shell

Place
Place Keyword South Carolina
Place Keyword coastline
Place Keyword ACE Basin
Place Keyword North Island
Place Keyword Little River
Place Keyword Bulls Bay

Access Constraints
None
Use Constraints
Neither the State of South Carolina, the Department of Natural Resources, nor any of its employees, is responsible for any improper or incorrect use of the information described and/or contained herein, and  assume no responsibility for the use of the information.  The South Carolina Department of Natural Resources should be acknowledged as the data source in products derived from these data.
Point of Contact
Contact Information
Contact Person Primary
Contact Person Kristin Schulte
Contact Organization South Carolina Department of Natural Resources (SCDNR)
Contact Position Biologist - Shellfish Research Section
Contact Address
Address Type mailing address
Address Marine Resources Division, SCDNR
Address 217 Ft. Johnson Rd. P.O. Box 12559
City Charleston
State or Province SC
Postal Code 29422
Country UNITED STATES

Contact Address
Address Type physical address
Address Marine Resources Research Institute
Address 217 Ft. Johnson Rd.
City Charleston
State or Province SC
Postal Code 29412
Country UNITED STATES

Contact Voice Telephone 843-953-5977
Contact Electronic Mail Addressschultek@dnr.sc.gov
Hours of Service 8:30 AM - 5:00 PM

Data Set Credit
None. The South Carolina Department of Natural Resources should be acknowledged in products derived from these data.
Native Data Set Environment
Microsoft Windows XP Version 5.1 (Build 2600) Service Pack 3; ESRI ArcCatalog 9.3.1.3000

Data Quality 

Attribute Accuracy
Attribute Accuracy Report
The Accuracy of the mapped oyster reefs was assessed for 60 of the 122 DOQQs using mapping grade GPS and video transects captured by boat along the length of the reef.  Approximately 100 reefs including some washed shell deposits were mapped per DOQQ, and 30 textured mud areas were mapped to check for errors of omission.  The horizontal accuracy of the GPS measurements was 0.3-0.5 meters.  The spatial accuracy of the images from which the reefs were digitized was 4 meters.   Two metrics were used to assess accuracy.  The first metric assessed was Presence/Absence, or the correct identification of oyster or textured mud.  Four possible scoring categories were available for this metric:  1) Correct positive (correctly classified shell), 2) Correct negative (correctly classified as  mud), 3) False positive (mud incorrectly classified as shell), False Negative (shell incorrectly classified as mud).  If 25% of the measured transect contained the correct classification, it was scored as correct (Present).  The second metric assessed was Extent.  It was defined as the correct delineation of the entire length of an oyster reef or mud patch. The extent of the reef was considered incorrect if the length of the reef was different from the length of the transect by more than 10 meters in the case of a fringing reef. In the case of a hummock or "patch reef" if there was a gap within the reef greater than 10 m2, it was considered incorrect.  It is important to note that although correct classifications tend to be 80% or above, these measurements are primarily for oysters along shorelines.  Reefs in mud flats were difficult to assess by boat, so DOQQs containing large areas of flats could have poorer accuracy than reflected by the score.  The flats were difficult to digitize due to the patchiness of the shell in the mud, and it was often hard to see.  Manual editing is often required in these areas.  Helicopter photos were used to correct some of the accepted product, especially in areas inaccessible to boats.  Accuracy numbers for the helicopter process are not available, but the reefs are easily visible on the low altitude photos.  For DOQQs not assessed for accuracy, SCDNR used their knowledge of the resource and photo interpretation skills to improve them as much as possible, but no accuracy numbers will be available.  SCDNR is also correcting DOQQs that have been assessed for accuracy, so the accuracy scores reported should be considered as the minimum accuracy.

Before SCDNR edits, the cumulative metric scores of this data set were 87% correct for Presence/Absence and 84% correct for Extent.  Individual DOQQ scores ranged from 71% to 100% correct  for Presence/Absence classification. Scores ranged from 50% to  97% correct for Extent.

Accuracy values are available at the DOQQ level in the associated table:  SCDNRoyster2010MetadataTable.pdf
Logical Consistency Report
Photo Science Inc. was responsible for oyster reef digitization of 75 DOQQs or 61% of the data.  The remaining 47 DOQQs were mapped at SCDNR.   The techniques used by Photo Science and SCDNR for initial digitization using Feature Analyst are similar with a few exceptions.  Photo Science trained two types of oyster reefs, fringing and patch reefs (flats), and took the best training set from each to create one file with minimal manual editing.  The resulting files were manually edited by SCDNR.  When SCDNR digitized reefs, more training sets were created to better capture variations in the appearance of the shell.  Instead of picking the best single output, SCDNR then used parts from all training sets to piece together the final product.  This second method is more time consuming, but manual editing could be completed at the same time.
Completeness Report
The initial digitization process has been completed for all contracted 122 DOQQs or 443 mosaiked images.   All of the DOQQs have been manually edited by SCDNR to correct known and/or clearly visible errors. The edits were generally done at the DOQQ level, but low-altitude helicopter flights were conducted to photograph additional areas at the image level (one quarter of a DOQQ).   The majority of the photographs from flights conducted between 2004-2008 have been used to assist with error correction.  The editing status of each DOQQ is contained in the associated table:  SCDNRoyster2010MetadataTable.pdf.  Any additional information gathered from low-altitude photographs will be incorporated in a new data file.
Positional Accuracy
Horizontal Positional Accuracy
Horizontal Positional Accuracy Report
The data was digitized from 0.25 m resolution multispectral digital imagery with reported horizontal accuacy of 4 meters or less.
Lineage
Process Step
Process Description
Initial Digitization: Each photo (one fourth of a DOQQ), was interpreted and had its own training samples due to the variable appearance of the oyster and the imagery itself. Training polygons were created for each photo and input into Feature Analyst for automated feature extraction/creation. Feature Analyst is an extension developed by Virtual Learning Systems for ESRI's ArcGIS desktop. Feature Analyst Versions 4.0-4.2 were used and the ArcGIS versions ranged from 9.0-9.2. Training sets were developed separately for fringing reefs, patch reefs and washed shell due to the difference in appearance of the three types of shell. Starting in June 2007, additional training sets were also used when the color or texture of shell differed widely within an image due to: light angles, dryness of the shell, or degree of contrast with surrounding mud. Masks were created to eliminate dry land and large areas of water from analysis. Within Feature Analyst's Set-Up Learning step, the Image Resolution was set at 1 foot. The Manhattan 5x5 Input Representation was determined to be the most versatile and used for most extractions. Within Learning Options, "Aggregate areas" was set at a minimum area of 64 pixels and "Find rotated features" was checked. All primary extractions were run with the learning algorithm "Approach 1". When layers were filtered for incorrect features (clutter), "Approach 2" was used. Manual editing or clean-up of shapes was not generally done by Photo Science. The manual clean-up step was completed by SCDNR and is listed as a separate step.
Source Used Citation Abbreviation
\\DNR32691\C$\Documents and Settings\SchulteK\My Documents\DataFiles\OysterDatabase\RemoteFinalDOQQEdits\FinalDBsections\SCDNR_Oyster2008DOQQKrisLatest.mdb
Process Date 2008


Process Step
Process Description
Ground-truthing by Boat:   Sixty of the 122 DOQQs were ground-truthed by boat for accuracy assessments.  Using a Trimble XR GPS unit, approximately 100 reefs in each DOQQ were measured.  The areas had to be assessed before the imagery was available, so efforts were made to randomly select reefs spread out over the DOQQ using historical maps of oyster as a guide.    Some DOQQs did not have 100 accessible reefs to measure, so in these cases as many as were accessible were measured.  Reefs also had to be 10 m2 or more in size per the contract agreement with Photo Science.  Using the GPS unit, transects were measured lengthwise for each reef.  A video of the entire length of the reef was also filmed as the reef's approximate width and condition were recorded.  In addition to the oyster reefs, approximately 30 areas of textured mud or sand were marked to check for errors of commission.   Ground-truthing efforts were conducted no more than two hours before or after low tide.  Data collected from these efforts were used to score the accuracy of the digitization process.
Process Date 2006


Process Step
Process Description
QA/QC for Accuracy:   The accuracy of the product was scored using two metrics:  1) the presence/absence of oyster adjoining each transect measured, an 2) the extent of the reef that was captured.  For presence/absence, a matrix of four possible scoring categories were available:  1) Correct positive (correct shell), 2) Correct negative (correct mud), 3) False positive (mud incorrectly classified as shell), False Negative (shell incorrectly classified as mud).  If 25% of the measured transect contained the correct classification, it was scored as correct. The score reported for presence/absence was calculated as the number of correct classifications divided by the total number of observations.  To score extent, if there was an error in extent of more than 10m, it was scored as incorrect.  If the extent of the mapped reef exceeded that of the field transect, we reviewed the video records.  If the tide in the video appeared to be covering shell that was captured on the photo, the length was not graded.  Oyster reefs that extended past the transect could be graded as correct if notes were made in the field record about the inaccessibility of the remaining shell from the boat.  Reefs that extend past a transect can only be graded as incorrect if there is no doubt on the error. Extent was scored as number of correct lengths divided by total number of observations.  These scores are listed in an associated table (SCDNRoyster2010MetadataTable.pdf) for the corresponding DOQQs.

        The images were processed based on batches of 15 DOQQs.  Half of the DOQQs in each batch were ground-truthed.  For each DOQQ scored, the two metrics were averaged for an overall score.  If the cumulative score of the batch was greater than 80%, it was accepted.   If not, the failing DOQQs were returned for reprocessing, as well as any images that were not ground-truthed and had obvious problems.  Individual DOQQs that failed in an "accepted batch" were edited by SCDNR.
Process Date 2008


Process Step
Process Description
Edge Matching: Edge matching of the shellfish polygons was performed on both live and washed shell layers produced from the Feature Analyst software for each DOQQ (Digital Ortho Quarter Quad).  There were three steps to editing these layers.   Step A:  Merging the QQQ shapefiles to QQ feature classes within a geodatabase, Step B: Editing within DOQQs, and Step C: Working between DOQQs.  For each of these steps, the washed shell layer was processed before the live shell layer.
        Step A:  Feature Analyst produced a series of shapefiles for each DOQQ.  These were merged into two feature classes (one washed, one live) per DOQQ (e.g. NW, NE, SW, SE), and they were merged into a geodatabase.
        Step B:  Starting with the washed shell, the polygons were checked for obvious errors (e.g. polygons on houses, streets).  Then the interior lines of each DOQQ were checked for overlapping or duplicate polygons.  These polygons were either merged or one was deleted.  When choosing between polygons, we chose the one the more attribute information (e.g. helicopter data) or the one associated with the photo within the same DOQQ. Then the washed shell layer was used to clip the live shell layer using the Erase tool.  The wash and live shell layers were both checked for polygon size.  Any polygons smaller than 1 meter were deleted.  Also any polygons with a gridcode of 0 AND no neighboring 'ADD' comment field were deleted.  Finally, after the wash and live layers had been edited, a new ID column was created that identified the quad, the quarter quad, the year, and whether it was live or wash shell (e.g. adamrNE2008oysterW).
        Step C:  Starting with the wash shell, several adjacent DOQQs were opened and compared.  There were three possible issues to fix.  First, any polygons that crossed DOQQ boundaries were cut and then were appended into one or the other DOQQ wash/live feature class.  Second, due to the fact that polygons were digitized from several photos, some polygons were associated with the wrong quad.  Any polygons that appeared in the wrong quarter quad were selected, appended to the proper file, and then deleted out of the original file.  Finally, some polygons were duplicated or overlapping in multiple quarter quads.  The polygons were either merged or one of the duplicate polygons was deleted.  If necessary, the polygons were then appended into the proper quarter quad feature class.  When choosing between polygons that represent the same shellfish bed, we always choose the polygon that was associated with the photo in that quad, not the adjacent quad and photo, unless the combination of the polygons better represented the shellfish bed, in which case, we merged the two polygons.
Process Date 2008


Process Step
Process Description
Low Altitude Helicopter -Based Validation: Photographs have been taken of areas not accessible by boat or not previously ground-truthed. The photos were taken from a helicopter at an altitude of 200-400 feet. A Trimble Pro XRS GPS antenna was attached to the helicopter to collect continuous points along the path of the helicopter. The photos were collected using a Canon EOS 30 D digital camera with 10 megapixel resolution. All photos were collected during a negative low tide within +/- 1 hour of noon to reduce shadow effects. Using the GPS points as a guide and going through the chronological file of photos, all reefs along the flight patch were checked and edited in ArcGIS 9.2 for accuracy.  Photographs were taken from 2004-2010 and were used to validate oyster presence/absence.  Photographs used to validate this dataset were dated between 2004-2008, however, not all available photographs from these years have been viewed to date. Information pertaining to areas flown and validated using these methods are available in the associated file: SCDNRoyster2010MetadataTable.pdf.
Process Date Not complete


Process Step
Process Description
Manual Edits and Updates of Initial Digitization: SCDNR manually checked and edited all products completed by Photo Science using known information about oyster resources and through visual interpretation of the image. ArcGIS 9.2-9.3 was used. Only clear errors were corrected, so as not to decrease any accuracy scores an image received during the QA/QC assessment. Visual interpretation was aided through comparisons with low altitude oblique aerial imagery available through Bing Maps from 2008-2010, and with SCDNR photographs taken by helicopter (see the Low Altitude Helicopter-Based Validation step).  Edits were finalized for this version in April 2011.  Any additional edits to the data will be contained in a new file.
Process Date April 28, 2011


Process Step
Process Description
Metadata imported.
Source Used Citation Abbreviation
\\Mrdnas\shellmap\Work\Wind\Metadata\SCDNRoyster2010Live.xml
Process Date 2011-07-13
Process Time 12090400


Spatial Data Organization 

Direct Spatial Reference Method Vector


Spatial Reference 

Horizontal Coordinate System Definition
Planar
Planar Coordinate Information
Planar Coordinate Encoding Method coordinate pair
Coordinate Representation
Abscissa Resolution 0.000100
Ordinate Resolution 0.000100
Planar Distance Units meters

Geodetic Model
Horizontal Datum Name North American Datum of 1983
Ellipsoid Name Geodetic Reference System 80
Semi-major Axis 6378137.000000
Denominator of Flattening Ratio 298.257222

Vertical Coordinate System Definition
Altitude System Definition
Altitude Resolution 0.000100
Altitude Encoding Method Explicit elevation coordinate included with horizontal coordinates

Entities and Attributes 

Distribution Information 

Distributor
Contact Information
Contact Organization Primary
Contact Organization South Carolina Department of Natural Resources
Contact Position Spatial Data Manager
Contact Address
Address Type mailing address
Address Rembert C. Dennis Building, P.O. Box 167
City Columbia
State or Province SC
Postal Code 29201
Country UNITED STATES

Contact Address
Address Type physical address
Address 1000 Assembly Street
City Columbia
State or Province SC
Postal Code 29201
Country UNITED STATES

Contact Voice Telephone 803-734-9100
Contact Facsimile Telephone 803-734-7001
Contact Electronic Mail Addressgisman@dnr.sc.gov
Hours of Service 8:30 AM - 5:00 PM
Contact Instructions
For additional information, refer to DNR web site: http://www.dnr.sc.gov/gis.html

Resource Description Downloadable Data
Distribution Liability
In no event shall the creators, custodians, or distributors of this information be liable for any damages arising out of its use (or inability to use it).

Metadata Reference 

Metadata Date 2011-07-22
Metadata Contact
Contact Information
Contact Person Primary
Contact Person Jessica Boynton, Kristin Schulte, or Jordan Felber
Contact Organization SCDNR, Marine Resources Division, MRRI
Contact Position GIS Manager (Boynton), Biologist II (Schulte and Felber)
Contact Address
Address Type mailing address
Address P.O. Box 12559
City Charleston
State or Province SC
Postal Code 29422-2599
Country UNITED STATES

Contact Address
Address Type physical address
Address 217 Ft. Johnson Rd.
City Charleston
State or Province SC
Postal Code 29412
Country UNITED STATES

Contact Voice Telephone 843-953-9163 (Boynton)
Contact Voice Telephone 843-953-5977 (Schulte)
Contact Voice Telephone 843-953-9681 (Felber)
Contact Facsimile Telephone 843-9539-820
Contact Electronic Mail Addressboyntonj@dnr.sc.gov
Contact Electronic Mail Addressschultek@dnr.sc.gov
Contact Electronic Mail Addressfelberj@dnr.sc.gov

Metadata Standard Name FGDC Content Standards for Digital Geospatial Metadata
Metadata Standard Version FGDC-STD-001-1998
Metadata Time Convention local time


Metadata Extensions
Online Linkagehttp://www.esri.com/metadata/esriprof80.html
Profile Name ESRI Metadata Profile