Point Shapefile of Interpreted Base of Mud Isopach Based on Seismic-Reflection Profiles Collected in Apalachicola Bay in 2006 from U.S. Geological Survey Cruise 06001 (BASEMUD_GEOG.SHP, Geographic, WGS84)

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Frequently anticipated questions:

What does this data set describe?

Title:
Point Shapefile of Interpreted Base of Mud Isopach Based on Seismic-Reflection Profiles Collected in Apalachicola Bay in 2006 from U.S. Geological Survey Cruise 06001 (BASEMUD_GEOG.SHP, Geographic, WGS84)
Abstract:
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 http://woodshole.er.usgs.gov/operations/ia/public_ds_info.php?fa=2005-001-FA and http://woodshole.er.usgs.gov/operations/ia/public_ds_info.php?fa=2006-001-FA.
  1. How might this data set be cited?
    Twichell, David C., and Cross, VeeAnn A., 2012, Point Shapefile of Interpreted Base of Mud Isopach Based on Seismic-Reflection Profiles Collected in Apalachicola Bay in 2006 from U.S. Geological Survey Cruise 06001 (BASEMUD_GEOG.SHP, 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, Reston, VA.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -85.095589
    East_Bounding_Coordinate: -84.875268
    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 (238796)
    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.
      Vertical_Coordinate_System_Definition:
      Depth_System_Definition:
      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?
    basemud_geog
    ESRI point shapefile (Source: ESRI)
    FID
    Internal feature number. (Source: ESRI) Sequential unique whole numbers that are automatically generated.
    Shape
    Feature geometry. (Source: ESRI) Coordinates defining the features.
    easting
    Easting coordinate of the point in meters, UTM Zone 16, WGS84. (Source: U.S. Geological Survey)
    Range of values
    Minimum:684365.14
    Maximum:705608.91
    Units:meters
    northing
    Northing coordinate of the point in meters, UTM Zone 16, WGS84. (Source: U.S. Geological Survey)
    Range of values
    Minimum:3276237.22
    Maximum:3290109.99
    Units:meters
    ms
    The depth below the sea floor to the base of the mud in milliseconds two-way travel time. (Source: Software calculated.)
    Range of values
    Minimum:0
    Maximum:3.79
    Units:milliseconds
    line
    Line name used in Landmark SeisWorks as the unique identifier for each seismic line. (Source: Data processor.) Character set.
    filter_ms
    Where the base of mud points are within 75 meters of a man-made feature. In these cases this attribute is set to the NODATA value of -9999. Otherwise, the ms attribute is present here. This enables points to be excluded based on a selection criteria. (Source: Data processor.)
    Range of values
    Minimum:0
    Maximum:3.79
    Units:milliseconds
    mtrs_1800
    The depth below the sea floor to the base of the mud converted from milliseconds to meters based on a speed of sound of 1800 meters per second. Values of -9999 reflect those same values in the filter_ms attribute. (Source: Data processor.)
    Range of values
    Minimum:0
    Maximum:3.411
    Units:meters
    Entity_and_Attribute_Overview:
    Depth values are recorded as negatives with more negative values indicating deeper water.
    Entity_and_Attribute_Detail_Citation: U.S. Geological Survey

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • David C. Twichell
    • VeeAnn A. Cross
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    VeeAnn A. Cross
    U.S. Geological Survey
    Marine Geologist
    Woods Hole Coastal and Marine Science Center
    Woods Hole, MA

    (508) 548-8700 x2251 (voice)
    (508) 457-2310 (FAX)
    vatnipp@usgs.gov

Why was the data set created?

This point shapefile contains the interpretation of the isopach thickness of the base of mud unit based on seismic-reflection profiles collected in 2006 in Apalachicola Bay. The base of mud surface separates the late Holocene estuarine deposits into two units based on changes in the depositional history of the bay.

How was the data set created?

  1. From what previous works were the data drawn?
    none (source 1 of 1)
    U.S. Geological Survey, unpublished material, Data acquisition.

    Type_of_Source_Media: digital files
    Source_Contribution:
    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.
  2. How were the data generated, processed, and modified?
    Date: 2006 (process 1 of 14)
    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

    508-548-8700 (voice)
    508-457-2310 (FAX)
    Date: 2007 (process 2 of 14)
    Once the navigation is extracted from the seismic data, this navigation has to be loaded into the interpretation software. In this case, that's Landmark SeisWorks version R2003. The navigation is loaded using Data - Management - Seismic Data Manager. A new survey is created (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 used to 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. 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. 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. 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

    (508) 548-8700 x2251 (voice)
    (508) 457-2310 (FAX)
    vatnipp@usgs.gov
    Date: 2007 (process 3 of 14)
    The base of mud surface separates the late Holocene estuarine deposits into two units based on changes in the depositional history of the bay. The older unit is characterized by closely-spaced weak-amplitude reflectors that locally are capped by a single high-amplitude flat-lying reflector. The younger unit is acoustically transparent, buries the weak-amplitude unit and onlaps and in places completely buries the high-amplitude reflectors. The unit is best represented as an isopach due to the nature of the surface (sometimes very thin but present and in other places uninterpretable from the seismics). The base of mud horizon in some areas of the seismics pinches out and other areas it couldn't be interpreted. These areas that were uninterpretable have to be accounted for, otherwise when this horizon is merged with the sea floor to generate the isopach map - the non-interpretable areas would appear as pinch outs. The interpreter (Dave Twichell) actually generated several base of mud horizons in Landmark - and all of these horizons had to be merged together. Landmark only allows two horizons to be merged at a time, so these individual horizons were merged in a series of process steps. The obvious data were in the horizon "base_of mud". These interpreted lines were merged with base_of_mud-poor_data to form basemud_mrg1. Then basemud_mrg1 was merged with base_of_oyster-top _of_delta_sand to form basemud_mrg2. In order to distinguish where mud pinched out and where the mud just couldn't be seen to interpret, a new horizon "mud_cant_interpret" was created. This horizon will be in the water column - exactly where it's located doesn't matter as long as it's above the sea floor. The idea is that this horizon can be merged with the mud prior to merging the mud horizon with the sea floor. Then when the sea floor horizon is subtracted from the mud horizon to generate the isopach unit the negative values will be obvious and can be deleted. So the next merge is to merge basemud_mrg2 with mud_cant _interpret to form basemud_mrg4. Then to generate a complete unit over the study area, merge basemud_mrg4 with sea floor to create basemud_mrg5. And finally, the mud isopach data is placed in basemud_mrg5_minus_sf by basemud_mrg5 minus seafloor. The interpretation of the various surfaces was done by Dave Twichell while the merging of the interpreted layers was done by VeeAnn Cross. Person who carried out this activity:
    David C. Twichell
    U.S. Geological Survey
    Oceanographer
    Woods Hole Coastal and Marine Science Center
    Woods Hole, MA

    (508) 548-8700 x2266 (voice)
    (508) 457-2310 (FAX)
    dtwichell@usgs.gov
    Date: 2008 (process 4 of 14)
    Once the interpretation is complete, the unit is exported as a text file with the line name, easting, northing, and the depth to the unit - in this case that depth represents an isopach thickness - in milliseconds (two-way travel time). 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

    (508) 548-8700 x2251 (voice)
    (508) 457-2310 (FAX)
    vatnipp@usgs.gov
    Date: 2008 (process 5 of 14)
    A header line is added to the exported text file, and converted from a tab-delimited file to a comma-delimited file. The negative millisecond values are deleted at this time.
    Date: 2008 (process 6 of 14)
    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 14)
    This event theme is converted to a shapefile by right mouse click - Data - Export Data and generating the output shapefile bmmrg5.shp.
    Date: 2008 (process 8 of 14)
    Any points falling outside Apalachicola Bay were deleted. The attribute filter_ms was added to the shapefile. Any points known to fall within 75 meters of man-made features such as spoil areas and dredged navigation channels had the filter_ms attribute set to a value of -9999 (standard NODATA value). These points were flagged using the Selection tool - Select by Location. Points were selected in the shapefile that intersected with 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. Field calculator was used to fill the attribute filter_ms with -9999 values in the selected records.
    Date: 2008 (process 9 of 14)
    The attribute "mtrs_1800" was added to the shapefile. Field calculator was used to convert the seismic two-way millisecond travel time to meters using a speed of sound of 1800 meters per second. Records with the value -9999 in the filter_ms attribute were selected and the -9999 value was copied to the mtrs_1800 attribute.
    Date: 2010 (process 10 of 14)
    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.
    Date: 29-Jun-2016 (process 11 of 14)
    Edits to the metadata were made to fix any errors that MP v 2.9.32 flagged. This is necessary to enable the metadata to be successfully harvested for various data catalogs. In some cases, this meant adding text "Information unavailable" or "Information unavailable from original metadata" for those required fields that were left blank. Other minor edits were probably performed (title, publisher, publication place, etc.). The source information was incomplete and had to be modified to meet the standard. The distribution format name was modified in an attempt to be more consistent with other metadata files of the same data format. The metadata date (but not the metadata creator) was edited to reflect the date of these changes. The metadata available from a harvester may supersede metadata bundled within a download file. Compare the metadata dates to determine which metadata file is most recent. Person who carried out this activity:
    U.S. Geological Survey
    Attn: VeeAnn A. Cross
    Marine Geologist
    384 Woods Hole Rd.
    Woods Hole, MA

    508-548-8700 x2251 (voice)
    508-457-2310 (FAX)
    vatnipp@usgs.gov
    Date: 20-Jul-2018 (process 12 of 14)
    USGS Thesaurus keywords added to the keyword section. Person who carried out this activity:
    U.S. Geological Survey
    Attn: VeeAnn A. Cross
    Marine Geologist
    384 Woods Hole Road
    Woods Hole, MA

    508-548-8700 x2251 (voice)
    508-457-2310 (FAX)
    vatnipp@usgs.gov
    Date: 18-Nov-2019 (process 13 of 14)
    Crossref DOI link was added as the first link in the metadata. Person who carried out this activity:
    U.S. Geological Survey
    Attn: VeeAnn A. Cross
    Marine Geologist
    384 Woods Hole Road
    Woods Hole, MA

    508-548-8700 x2251 (voice)
    508-457-2310 (FAX)
    vatnipp@usgs.gov
    Date: 08-Sep-2020 (process 14 of 14)
    Added keywords section with USGS persistent identifier as theme keyword. Person who carried out this activity:
    U.S. Geological Survey
    Attn: VeeAnn A. Cross
    Marine Geologist
    384 Woods Hole Road
    Woods Hole, MA

    508-548-8700 x2251 (voice)
    508-457-2310 (FAX)
    vatnipp@usgs.gov
  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, Reston, VA.

    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, Reston, VA.

    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 the 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.
Use_Constraints 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

    (508) 548-8700 x2251 (voice)
    (508) 457-2310 (FAX)
    vatnipp@usgs.gov
  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?

Dates:
Last modified: 18-Mar-2024
Metadata author:
VeeAnn A. Cross
U.S. Geological Survey
Marine Geologist
Woods Hole Coastal and Marine Science Center
Woods Hole, MA

(508) 548-8700 x2251 (voice)
(508) 457-2310 (FAX)
whsc_data_contact@usgs.gov
Contact_Instructions:
The metadata contact email address is a generic address in the event the person is no longer with USGS. (updated on 20240318)
Metadata standard:
FGDC Content Standards for Digital Geospatial Metadata (FGDC-STD-001-1998)
This page is <https://cmgds.marine.usgs.gov/catalog/whcmsc/open_file_report/ofr2012-1003/basemud_geogmeta.faq.html>
Generated by mp version 2.9.51 on Mon Mar 25 16:05:40 2024