Facilities, Equipments and Other Resources at USF
The University of South Florida College of Marine Science (USF/CMS) is situated on
Bayboro Harbor amidst a burgeoning oceanographic research environment in St. Petersburg,
Florida. There are nearly 600 oceanographic researchers employed in St. Petersburg. The new
USF/CMS Knight Oceanographic Research Center (KORC) is a 140,000 sq. ft., $21M joint-use
facility shared with the Florida Department of Environmental Protection. USF/CMS also
manages the Physical Oceanography Real-Time System (PORTS), which operates real-time
meteorological and physical oceanography stations situated throughout the Tampa Bay area. A
similar system that extends into shelf waters is being implemented. Nearby institutions include
the USGS Center for Coastal Geology and Regional Marine Studies, the Florida Marine
Research Institute, the National Marine Fisheries Service, Eckerd College Marine Mammal
Laboratory, the Mote Marine Laboratories, and the Clearwater Marine Science Center.
The Remote Sensing Facility available for this project includes a High Resolution Picture
Transmission (HRPT) ground station and a new X-band earth station with real-time, highresolution data capture capability for the SeaWiFS, NOAA Polar Orbiters, and NASA’s Terra
and Aqua satellites (for MODIS). MODIS direct broadcast (DB) data are captured and processed
in near real-time, and archived at USF/CMS (http://modis.marine.usf.edu). The facility also
includes computer equipment (12 SGI Octane and O2 workstations and numerous high-end PCs)
and software that allows direct implementation of the GSFC/Univ. Miami SeaWiFS/CZCS
database software, SEADAS, DSP, and U. Miami MODIS processing software. For data
archiving, we have two 600-CD jukeboxes, one 600-DVD jukebox, and a few data (hard disk)
servers (each has > 1000 GB space). We maintain current licenses for IDL and ENVI (RSI),
Erdas Imagine, and Arc-Info. More information can be obtained at http://www.marine.usf.edu
and http://imars.marine.usf.edu.
Work Statement
Coastal waters are not isolated, but rather connected to river discharges and terrestrial
runoffs. Consequently, water quality (salinity, temperature, phytoplankton and dissolved matter
abundance, nutrient, turbidity) can be a great variable, depending on the intensity and durance of
these discharges and runoffs, which may carry considerable amount of nutrients and other
pollutants from agriculture upstream (Rudnick et al., 1999). Recent “black” water event near the
Florida Keys (SWFDOG, 2002) presents an example of how ocean color anomaly events, a
result due in part to local river runoff, can cause severe damage to the delicate coral reef
communities (Hu et al., 2003; Fig. 1). River plumes may also cause fish mortality, as speculated
from the connection between the 1999 fish mortality in the southern Caribbean and the
Amazon’s plume (Sookbir et al., in preparation).
Because ocean color and temperature and important water quality indexes to monitor the
health of the coastal ecosystem, and because they can be routinely obtained from satellite
observations (daily, real-time observation), we will use several ocean color and temperature
satellite sensors in this project, namely
 Moderate Resolution Imaging Spectrometer (MODIS, Terra/morning pass and
Aqua/afternoon pass):
o Sea Surface Temperature (1x1 km2 pixels; Infrared (IR))
o Ocean Color (1x1 km2 pixels; 12 bits, bands 8-16; Visible)
o “Sharpening” bands:
 250 x 250 m2 pix. (bands 1-2, Visible and Near-IR)
 500 x 500 m2 pix. (bands 3-7, Visible and Near-IR)
AVHRR (Advanced Very High Reolution Radiometer) estimates:
o Sea Surface Temperature
SeaWiFS (Sea-viewing Wide Field-of-view Sensor; OrbImage/NASA):
o Ocean Color (1x1 km2 pixels; 10 bits, bands 1-8)


Jan Feb Mar
Apr May Jun
Jul Aug Sep
Oct Nov Dec
Water-leaving radiance (555 nm)
6
SeaWiFS
Florida Bight
March 21, 2002
Smith Shoal
1997
1998
1999
5
2000
2001
2002
4
3
2
1
0
Lat = 24.8221
Lon = -81.4889
Jan Feb Mar
Content Keys
Key West
Apr May Jun
Jul Aug Sep
Oct Nov Dec
Time of the year
Jan Feb Mar
Apr May Jun
Jul Aug Sep
Oct Nov Dec
EPTOMS ozone (dobson units)
330
10.0%
1.0%
0.1%
Species Number
Percent Cover
100.0%
30
20
10
0
1996
1998
2000
2002
1997
1998
1999
310
2000
2001
2002
290
270
250
230
Jan Feb Mar
Apr May Jun
Jul Aug Sep
Oct Nov Dec
Time of the year
Figure 1. From top left clockwise: SeaWiFS RGB composite image shows “black” water
near the Floriday Keys (SWFDOG, 2002); Lw data (555 nm, in units of mW cm-2 m-1 sr-1)
shows abnormally low values in March and April 2002 for one patchy reef site, Content Keys;
EPTOMS ozone data shows abnormally low ozone from late 2001 to spring 2002; Coral percent
cover and species number at the two sites declined significantly after the “black” water event.
“Ocean color” means the spectral water-leaving radiance (Lw) and the associated data
products, including chlorophyll concentration, dissolved matter absorption, particle
backscattering (for suspended sediment concentration), and diffuse attenuation (for water
clarity/turbidity). Despite the enormous effort NASA and the science community have carried
out for calibration and algorithm development to ensure accurate and consistent data products, in
the complex coastal environment (Case II waters), such as the coastal water in the adjacency of
the Suwannee River, the accuracy of data products is still questionable. This is due to
uncertainties in both atmospheric correction and bio-optical inversion algorithms.
For turbid coastal waters where Lw in the near infrared is not negligible, the Gordon and
Wang (1994) atmospheric correction is no longer valid and large errors are encountered in the
retrieved Lw data products. Several alternative ways have been proposed to overcome this
problem, among which are iterative approaches (Arnone et al., 1998; Siegel et al., 2000), and
nearby aerosol approaches (Ruddick et al., 2000; Hu et al., 2000). Each method has its pros and
cons. Likewise, the band-ratio bio-optical algorithm (O’Reilly, et al., 1998, used for SeaWiFS
processing) and the semi-analytical bio-optical algorithm (Carder et al., 1999, used for MODIS
processing) also suffer in the shallow, turbid waters. There is currently no reliable way to obtain
accurate ocean color data products.
The limited spatial extent of the proposed study area may also pose a problem due to the
standard 1-km resolution, especially for near-shore stations. However, MODIS is equipped with
several 250-m and 500-m bands that provide unprecedented capability for coastal monitoring
(Hu et al., submitted). However, how to make quantitative use of these bands still remains
unsolved.
In a separate proposal to NASA (OES-02) the co-Investigator, C. Hu, has proposed
several alternative ways to overcome these difficulties to study large river plumes (the Amazon,
Mississippi, and Yangtze) and proposed to use the medium-resolution bands to study fine-scale
features in coastal waters. In particular, a spectra-matching optimization algorithm (Chmoko and
Gordon, 2001; Lee et al., 1999; Hu et al., 2002), starting from the top of atmosphere at-sensor
radiance but tuned to focus on Case II waters, was proposed to solve the atmospheric correction
and bio-optical inversion simultaneously. Once the atmospheric parameters are derived, they will
be applied to the medium-resolution bands, under the assumption that the calibration of these
bands is consistent with that for the standard 1-km ocean color bands. We hope that proposal will
be approved by NASA.
For SST data products, we will check the consistency between AVHRR and MODIS and
combine them for the long-term time-series study (AVHRR data started from 20 years ago, while
MODIS data started from late 1999).
Indeed, even without fine-tuning or existing algorithms or development of alternative
algorithms, the currently derived Lw data, as an ocean color index, can still be used to monitor
anomaly events. Fig. 1 shows that the coral reef decline (>70) from 2001 to 2002 is
unambiguously related to the “black” water event near the Florida Keys, which lasted for > two
months. Further examination of the meteorological ozone data from the Earth Probe Total Ozone
Mapping Spectrometer Sensor (EPTOMS) shows that ozone thickness (in Dobson units) is
abnormally lower than usual from late 2001 to spring 2002. However, it is unclear if the ozone
anomaly has triggered the “black” water event. Nevertheless, such an example demonstrates how
ocean color can be used to monitor water quality and study coastal ecosystem changes. With the
improved data products (absorption and backscattering, chlorophyll, and so on) we will be able
to study the water quality in more details.
The University of South Florida (C. Hu and F. Muller-Karger) will participate in this project
as follows:
1). Collect, analyze, and interpret AVHRR, SeaWiFS, and MODIS imagery for the West Florida
Shelf with the focus on the coastal waters near the Suwannee River mouth.
2) The data products will be provided in near real-time to help field campaign through web
broadcasting (http://imars.usf.edu) as well as for retrospective analysis. The data are in both
image and binary formats.
3). Coordinate with University of Florida (UF) to collect field data (chlorophyll concentration,
dissolved matter absorption, total suspended particle concentration, and other chemical variables
including oxygen and nutrient) to help better calibrate and validate the satellite data products.
This is an extremely complex environment with bottom depth as small as 1-2 meters. We will
evaluate the performance of the proposed optimization approach in this complex environment.
4). Work with UF to interpret the oceanographic features, especially river plumes, terrestrial
runoffs, and coastal upwelling, and their relationship with clam growth rate and health
5). Help prepare reports and manuscripts.