SEAFLOOR_GEOG.SHP: Point Shapefile of the Interpreted Seafloor Horizon Based on Seismic-Reflection Profiles Collected in Apalachicola Bay in 2006 from U.S. Geological Survey Cruise 06001 (Geographic, WGS84)

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Frequently-anticipated questions:

What does this data set describe?

SEAFLOOR_GEOG.SHP: Point Shapefile of the Interpreted Seafloor Horizon Based on Seismic-Reflection Profiles Collected in Apalachicola Bay in 2006 from U.S. Geological Survey Cruise 06001 (Geographic, WGS84)
Apalachicola Bay and St. George Sound contain the largest oyster fishery in Florida, and the growth and distribution of the numerous oyster reefs here are the combined product of modern estuarine conditions and the late Holocene evolution of the bay. A suite of geophysical data and cores were collected during a cooperative study by the U.S. Geological Survey, the National Oceanic and Atmospheric Administration Coastal Services Center, and the Apalachicola National Estuarine Research Reserve to refine the geology of the bay floor as well as the bay's Holocene stratigraphy. Sidescan-sonar imagery, bathymetry, high-resolution seismic profiles, and cores show that oyster reefs occupy the crests of sandy shoals that range from 1 to 7 kilometers in length, while most of the remainder of the bay floor is covered by mud. The sandy shoals are the surficial expression of broader sand deposits associated with deltas that advanced southward into the bay between 6,400 and 4,400 years before present. The seismic and core data indicate that the extent of oyster reefs was greatest between 2,400 and 1,200 years before present and has decreased since then due to the continued input of mud to the bay by the Apalachicola River. The association of oyster reefs with the middle to late Holocene sandy delta deposits indicates that the present distribution of oyster beds is controlled in part by the geologic evolution of the estuary. For more information on the surveys involved in this project, see <> and <>.
  1. How should this data set be cited?

    Twichell, David C. , and Cross, VeeAnn A. , 2012, SEAFLOOR_GEOG.SHP: Point Shapefile of the Interpreted Seafloor Horizon Based on Seismic-Reflection Profiles Collected in Apalachicola Bay in 2006 from U.S. Geological Survey Cruise 06001 (Geographic, WGS84): Open-File Report 2012-1003, U.S. Geological Survey, Coastal and Marine Geology Program, Woods Hole Coastal and Marine Science Center, Woods Hole, MA.

    Online Links:

    This is part of the following larger work.

    Cross, V.A., Twichell, D.C., Foster, D.S., and O'Brien, T.F., 2012, Apalachicola Bay Interpreted Seismic Horizons and Updated IRIS Chirp Seismic-Reflection Data: Open-File Report 2012-1003, U.S. Geological Survey, Coastal and Marine Geology Program, Woods Hole Coastal and Marine Science Center, Woods Hole, MA.

    Online Links:

  2. What geographic area does the data set cover?

    West_Bounding_Coordinate: -85.095589
    East_Bounding_Coordinate: -84.874916
    North_Bounding_Coordinate: 29.725093
    South_Bounding_Coordinate: 29.601369

  3. What does it look like?

  4. Does the data set describe conditions during a particular time period?

    Beginning_Date: 31-May-2006
    Ending_Date: 27-Jun-2006
    Currentness_Reference: ground condition

  5. What is the general form of this data set?

    Geospatial_Data_Presentation_Form: vector digital data

  6. How does the data set represent geographic features?

    1. How are geographic features stored in the data set?

      This is a Vector data set. It contains the following vector data types (SDTS terminology):

      • Entity point (315112)

    2. What coordinate system is used to represent geographic features?

      Horizontal positions are specified in geographic coordinates, that is, latitude and longitude. Latitudes are given to the nearest 0.000001. Longitudes are given to the nearest 0.000001. Latitude and longitude values are specified in Decimal degrees.

      The horizontal datum used is D_WGS_1984.
      The ellipsoid used is WGS_1984.
      The semi-major axis of the ellipsoid used is 6378137.000000.
      The flattening of the ellipsoid used is 1/298.257224.

      Depth_Datum_Name: Mean lower low water
      Depth_Resolution: 0.1
      Depth_Distance_Units: meters
      Depth_Encoding_Method: Explicit depth coordinate included with horizontal coordinates

  7. How does the data set describe geographic features?

    ESRI point shapefile (Source: ESRI)

    Internal feature number. (Source: ESRI)

    Sequential unique whole numbers that are automatically generated.

    Feature geometry. (Source: ESRI)

    Coordinates defining the features.

    Easting coordinate of the point in meters, UTM Zone 16, WGS84. (Source: U.S. Geological Survey)

    Range of values

    Northing coordinate of the point in meters, UTM Zone 16, WGS84. (Source: U.S. Geological Survey)

    Range of values

    Depth to the seafloor horizon in milliseconds two-way travel time. (Source: Software calculated.)

    Range of values

    Line name used in Landmark SeisWorks as the unique identifier for each seismic line. (Source: Data processor.)

    Character set.

    Depth to the seafloor horizon converted from milliseconds to meters based on an assumed speed of sound. The speed of sound used in the calculation is in the "spd_of_snd" attribute. (Source: Data processor.)

    Range of values

    Speed of sound in water used to convert the depth horizon from milliseconds to meters. Only two speed of sound values are used. One is 1700 m/s for the Rafael seismics, and the other is 1476 m/s from the IRIS seismics. (Source: Data processor.)

    Range of values
    Units:meters per second

    Depth extracted from the published swath bathymetry 2-meter grid in the area of interest. Values of -9999 indicate NODATA values where 2-meter swath bathymetry values were unavailable. (Source: Software calculated.)

    Range of values

    Depth in meters used in the gridding process to generate a seafloor surface. In places where valid swath_dep values exist (not -9999), those values are used. When swath_dep values are nodata (-9999) then the ms_meters values are used. (Source: Data processor.)

    Range of values

    This attribute flags points that fall within 75 meters of man-made features or are on cross lines. (Source: Data processor.)

    -9999This point falls within 75 meters of man-made features or is on a cross line.
    0This feature is more than 75 meters from a man-made feature and is not on a cross line.

    Depth values are recorded as negatives with more negative values indicating deeper water.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)

  2. Who also contributed to the data set?

  3. To whom should users address questions about the data?

Why was the data set created?

This point shapefile contains the interpretation of the sea floor surface based on seismic-reflection profiles collected in 2006 in Apalachicola Bay. Added to the shapefile are the swath bathymetry values (when available) at each seismic shot point location. This point shapefile will be used to verify the gridding method and cellsize for a known surface (sea floor) to be used with the subsurface interpretations based solely on the seismic-reflection data.

How was the data set created?

  1. From what previous works were the data drawn?

    (source 1 of 1)
    The seismic data used for the interpretation comes from two different seismic systems. The bulk of the data are from the EdgeTech FSSB 424 system pole mounted on the R/V Rafael. These data were logged in SEG-Y format using SBLogger. This system had a 1/4 second fire rate. The remainder of the data, in the shallower areas, were acquired with the USGS IRIS system. IRIS is a remotely operated vehicle that has an EdgeTech FSSB 424 chirp sub-bottom profiling system mounted to it. The seismic data were recorded by JSTAR, a software package developed by EdgeTech. This system had a much faster fire rate, almost 15 times per second. The EdgeTech FSSB 424 is a chirp sub-bottom profiler that operates within a 4-24kHz frequency range. The IRIS vehicle is navigated using Real-Time Kinematic (RTK) GPS. The antenna is mounted directly on the platform to minimize navigational error. The R/V Rafael was also navigated with an RTK GPS system with the navigation antenna approximately 1.5 meters forward of the seismic transducer. This offset was not accounted for. The swath bathymetry data were collected aboard the R/V Rafael with an SEA Submetrix 2000 interferometric sonar operating at a frequency of 234 kHz. The motion (heave, pitch roll and yaw) was measured with a TSS DMS 2-05 attitude sensor mounted directly above the Submetrix transducers. More information on the swath bathymetry system can be found in USGS Open-File Report 2006-1381.

  2. How were the data generated, processed, and modified?

    Date: 2006 (process 1 of 9)
    Two different seismic systems acquired data in Apalachicola Bay in 2006. One system was the EdgeTech FSSB 424 (4-24kHz) aboard the R/V Rafael. These data were acquired as SEG-Y files using SBLogger. The second seismic system was also an EdgeTech FSSB 424 chirp system mounted on the USGS autonomous vehicle IRIS. These data were acquired with JSTAR in JSF format and converted to SEG-Y format using a C-program written by Tom O'Brien (USGS, Woods Hole). These SEG-Y files were then converted from IEEE format to IBM floating point using SIOSEIS, and the shots were renumbered starting at one. With initial preparation work on the seismic data complete, these data and navigation needed to be loaded into Landmark SeisWorks software for interpretation. In order to load the seismic data and navigation into Landmark SeisWorks software the navigation needed to be extracted from the header of the seismic data. An AWK script was used to extract the navigation from the seismic data headers and export in UTM, Zone 16 eastings and northings, rounded to the nearest meter.

    Person who carried out this activity:

    U.S. Geological Survey
    Woods Hole Coastal and Marine Science Center
    Woods Hole, MA 02543

    508-548-8700 (voice)
    508-457-2310 (FAX)

    Date: 2007 (process 2 of 9)
    Once the navigation is extracted from the seismic data, this navigation has to be loaded into the interpretation software - Landmark SeisWorks version R2003. The navigation is loaded using Data - Management - Seismic Data Manager. A new survey is created for each acquisition system (06001 for the Rafael data, asv06 for the IRIS data). Then, Data - Import - Seismic Data Loader and point to the navigation text file. When loading the navigation, use a decimation of 0, use first shot point if duplicates are found, and overwrite data in target project if necessary. A decimation of zero was used because the IRIS navigation had already been decimated to take every 5th record from the complete navigation extracted from the headers of the IRIS seismics. The Rafael data did not need decimation. The Rafael data had a 1/4 second fire rate while the IRIS data fired at approximately 15 shots per second. Once the navigation is loaded and verified, then the actual seismic data can be loaded. To do this, use PostStack Data Loader. There was a small issue in working with seismic data in SeisWorks where it's better to have all the seismic profiles at the same sample rate. It's a display issue in the interpretation phase where opening a profile in a window with a different sample rate than the previously loaded profile doesn't always refresh the window properly. The result is an incorrect interpretation - the interpreted line falls in the wrong spot vertically. The seismic data were resampled to the same sample rate to eliminate this problem. The Rafael acquired data at two different sample rates: 40 microseconds and 80 microseconds. The Rafael seismics were all resampled to 40 microseconds in the PostStack data loader. Additionally, the lines had an automatic 8-bit scaling applied to each profile when loaded. The IRIS seismic lines were acquired with two sample rates - 23 microseconds and 46 microseconds. All of the lines were resampled to a 40 microsecond sampling interval in PostStack data loader and had an automatic 8-bit scaling applied to each profile when loaded. With the seismic data now loaded, the project has to be modified so these changes are reflected in the surveys and the data can be interpreted. This process step and all subsequent process steps were overseen by the same person - VeeAnn A. Cross.

    Person who carried out this activity:

    VeeAnn A. Cross
    U.S. Geological Survey
    Marine Geologist
    Woods Hole Coastal and Marine Science Center
    Woods Hole, MA 02543-1598

    (508) 548-8700 x2251 (voice)
    (508) 457-2310 (FAX)

    Date: 2007 (process 3 of 9)
    The seafloor horizon was created in SeisWorks, and the seafloor was digitized from each seismic-reflection profile.

    Date: 2008 (process 4 of 9)
    Once the interpretation was complete, the horizon was exported as a text file with the following information in separate columns for each point: line name, easting, northing, and depth to the horizon in milliseconds.

    Date: 2008 (process 5 of 9)
    A header line is added to the exported text file, and converted from a tab-delimited file to a comma-delimited file.

    Date: 2008 (process 6 of 9)
    ArcMap 9.2 was used to load this text file as an event theme using Tools - Add XY data. The projection is defined on input as UTM, Zone 16, WGS84.

    Date: 2008 (process 7 of 9)
    This event theme is converted to a shapefile by right mouse click - Data - Export Data and generating the output shapefile seafloor.shp.

    Date: 2008 (process 8 of 9)
    Any points falling outside Apalachicola Bay were deleted. Five new attributes were added to the shapefile: ms_meters, spd_of_snd, swth_dep, dep2grd, and include. Based on the swath data collected simultaneously with the seismic data, the speed of sound in water value for the very shallow IRIS work was 1476 meters per second. The speed of sound in the deeper water associated with the R/V Rafael collected data was measured at approximately 1510 meters per second. However, for the purposes of these data, a value of 1700 meters per second is used. The increased speed is necessary to have the seismic data agree with the swath bathymetry data in areas of overlap and close proximity. This higher value accounts for seismic transducer depth that was not accounted for at acquisition and processing time. All lines with the line designation starting with "asv", indicating the IRIS system, used field calculator to populate the spd_of_snd attribute with 1476. The remaining records populated the spd_of_snd with 1700. Field calculator was then used on the ms_meters attribute to calculate the depth in meters based on the ms attribute (two-way travel time) and the spd_of_snd attribute. Using VACExtras v2.02, swath bathymetry values from published (USGS Open-File Report 2006-1381) 2-m data were extracted at each seismic navigation point and placed in the attribute swath_dep. Where no 2-m bathymetry exists, the swath_dep attribute was assigned a value of -9999. All records from the swath_dep attribute that did not equal -9999 were copied to the attribute dep2grd using the field calculator. The remaining dep2grd records were assigned the value in the ms_meters attribute. And finally, the test attribute will be used to omit any points that coincide with a manmade feature. To do this, any points falling within 75 meters of a man-made feature had the value -9999 assigned to the include attribute (-9999 is a common NODATA value). This was accomplished by using the Selection tool - Select by Location. Features were selected in the seafloor point shapefile that intersected the ApalachicolaBaseMap polygon shapefile with a buffer applied to the polygon of 75 meters. The ApalachicolaBaseMap polygon is available from USGS Open-File Report 2006-1381. A value of -9999 was also assigned to the include attribute for all cross-lines. All remaining values were left at zero.

    Date: 2010 (process 9 of 9)
    The original shapefile in UTM, Zone 16, WGS84 was projected to Geographic, WGS84 using ArcMap 9.2 - ArcToolbox - Data Management Tools - Projections and Transformations - Feature - Project. No datum transformation was necessary.

  3. What similar or related data should the user be aware of?

    Twichell, D.C., Andrews, B.D., Edmiston, H.L., and Stevenson, W.R., 2007, Geophysical mapping of oyster habitats in a shallow estuary; Apalachicola Bay, Florida: Open-File Report 2006-1381, U.S. Geological Survey, Coastal and Marine Geology Program, Woods Hole Science Center, Woods Hole, MA.

    Online Links:

    Twichell, D.C., Pendleton, E.A., Poore, R.Z., Osterman, L.E., and Kelso, K.W., 2009, Vibracore, radiocarbon, microfossil, and grain-size data from Apalachicola Bay, Florida: Open-File Report 2009-1031, U.S. Geological Survey, Coastal and Marine Geology Program, Woods Hole Coastal and Marine Science Center, Woods Hole, MA.

    Online Links:

    Bergeron, E., Worley, C.R., and O'Brien, T.F., 2007, Progress in the development of shallow-water mapping systems: using an autonomous surface vehicle for shallow-water geophysical studies: Sea Technology v. 48, no. 6, p. 10-15, Compass Publications, Inc., Arlington, VA.

How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?

  2. How accurate are the geographic locations?

    The R/V Rafael acquired data recording navigation using a Real Time Kinematic (RTK) GPS at a one second interval. The GPS antenna was mounted over the bathymetric sonar. The seismic pole mount system was on the starboard side and approximately 1.5 meters aft of the bathymetry system. No offset was added to the navigation for the seismic data. For seismic data collected with the IRIS system, an RTK GPS system was also used. The GPS antenna for IRIS was mounted directly over the seismic transducer. This system can provide positions to within 0.1 meters. However, due to some errors with the acquisition software, this accuracy is reduced. The accuracy is approximately 2 m given the constraints of the acquisition system.

  3. How accurate are the heights or depths?

    For the Rafael seismic system, the transducers were located approximately 1 meter below the water surface. This offset was not adjusted for. For the IRIS system, the transducers are barely below the water surface, less than half a meter. This depth is not adjusted for.

  4. Where are the gaps in the data? What is missing?

    All useable seismic-reflection profiles collected in 2006 within Apalachicola Bay were used in the interpretation.

  5. How consistent are the relationships among the observations, including topology?

    All data were handled in the same manner.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?

Access_Constraints: None.
These data are not to be used for navigation purposes. Mariners should refer to the appropriate nautical chart. The public domain data from the U.S. Government are freely redistributable with proper metadata and source attribution. Please recognize the U.S. Geological Survey as the originator of the dataset.

  1. Who distributes the data set? (Distributor 1 of 1)

    VeeAnn A. Cross
    U.S. Geological Survey
    Marine Geologist
    Woods Hole Coastal and Marine Science Center
    Woods Hole, MA 02543-1598

    (508) 548-8700 x2251 (voice)
    (508) 457-2310 (FAX)

  2. What's the catalog number I need to order this data set?

    Downloadable Data

  3. What legal disclaimers am I supposed to read?

    Neither the U.S. government, the Department of the Interior, nor the USGS, nor any of their employees, contractors, or subcontractors, make any warranty, express or implied, nor assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, nor represent that its use would not infringe on privately owned rights. The act of distribution shall not constitute any such warranty, and no responsibility is assumed by the USGS in the use of these data or related materials. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

  4. How can I download or order the data?

  5. What hardware or software do I need in order to use the data set?

    This WinZip file contains data available in ESRI point shapefile format. The user must have software capable of uncompressing the WinZip file and reading/displaying the shapefile.

Who wrote the metadata?

Last modified: 12-Apr-2012
Metadata author:
VeeAnn A. Cross
U.S. Geological Survey
Marine Geologist
Woods Hole Coastal and Marine Science Center
Woods Hole, MA 02543-1598

(508) 548-8700 x2251 (voice)
(508) 457-2310 (FAX)

Metadata standard:
FGDC Content Standards for Digital Geospatial Metadata (FGDC-STD-001-1998)
Metadata extensions used:

Generated by mp version 2.9.6 on Wed Apr 18 17:10:58 2012