Biological Sciences
The research category of Biological Sciences focuses on research pertaining to living organisms, environmental procedures and habitats. GRI scientists are creating specific datasets and tools which are helpful in understanding our ecosystem.

2017 Survey of Aquatic Plant Species in Mississippi Waterbodies
The state of Mississippi (MS) has significant water resources that, many times, are impaired by invasive aquatic and wetland plant species. These waterbodies can then act as source populations to introduce non-native vegetation to other waterbodies in the region. The likelihood of being a source population increases if the waterbody in question has a high frequency of boat traffic. Many times small waterbodies that have significant amounts of boat traffic are overlooked due to the size of the waterbody. To date, no statewide survey of small and medium sized (100

Adaptive Management of Flowering Rush Using the Contact Herbicide Diquat in Detroit Lakes, Minnesota 2016 - Final Report
Flowering rush (Butomus umbellatus L.) is an emergent invasive plant that has invaded the Detroit Lakes area, specifically, Detroit Lake (Big Detroit, Little Detroit, and Curfman Lakes), Lake Sallie, Lake Melissa and Mill Pond (Becker County) since the 1960s. It is native to Europe and Asia and first entered the United States in 1928. Flowering rush has continued to be a problem in the Detroit Lakes system for the past three decades. However, applications of the contact herbicide diquat over the last six years have helped to control the spread and density of the plant. Although flowering rush has been in North America for over forty years, very little information is known about its biology, ecology, and management. Bellaud (2009) reports that it was first observed in North America in St. Lawrence River (Quebec) in 1897. Flowering rush is currently found in all of the southern Canadian provinces, and all of the states bordering Canada and the Great Lakes (NRCS 2013)

Adaptive Management of Flowering Rush Using the Contact Herbicide Diquat in Detroit Lakes, Minnesota 2016 - Interim Report
Flowering rush (Butomus umbellatus L.) is an emergent invasive plant that has invaded the Detroit Lakes area, specifically, Detroit Lake (Big Detroit, Little Detroit, and Curfman Lakes), Lake Sallie, Lake Melissa and Mill Pond (Becker County) since the 1960s. It is native to Europe and Asia and first entered the United States in 1928. Flowering rush has continued to be a problem in the Detroit Lakes system for the past three decades. However, applications of the contact herbicide diquat over the last four years have helped to control the spread and density of the plant.
Document--Interim Report 2017

Advection of Karenia Brevis Blooms from the FL Panhandle towards the MS Bight and Sound
Harmful Algal Blooms (HABs) of Karenia brevis have been documented along coastal waters of every state bordering the Gulf of Mexico (GoM). Some Gulf Coast locations, such as Florida and Texas, suffer from recurrent intense and spatially large blooms, while others such as Mississippi seem to rarely observe them. The main objective of this work is to understand the dynamics that led to the K. brevis bloom in Mississippi coastal waters in fall 2015. Blooms of K. brevis from the Florida Panhandle region are often advected westward towards the Mississippi-Alabama coast; however there is interannual variability in their presence and intensity in Mississippi coastal waters. The 2015 K. brevis bloom was compared to the 2007 Florida Panhandle K. brevis bloom, which showed a westward advection pattern, but did not intensify along the Mississippi coast. Cell counts and flow cytometry were obtained from the Mississippi Department of Marine Resources, Alabama Department of Public Health, Florida Fish and Wildlife Conservation Commission and The University of Southern Mississippi. Ocean color satellite imagery from the Moderate Resolution Imaging Spectroradiometer onboard the Aqua satellite was used to detect and delineate the blooms in 2007 and 2015.
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Aquatic Invasive Species- Habitat Suitability Modeling
GRI researchers are using Habitat Suitability Modeling which uses computer algorithms to manipulate data that create models to predict, control and narrow the expansive search area required for detection of new non-native species of likely avenues for the spread of existing plant populations. Researchers have found four ways to control aquatic invasive species. They include chemical, biological, physical and mechanical methods. These methods can control or eradicate invasive plant species in an area.
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Coastal Ocean Color Trade Study
GRI scientists have created a system of unique data sets to enable a better understanding of environmental processes that occur in coastal environments. Coastal and inland waters and their environments were targeted for the initial mission due to their importance to various aspects of human activity and the inability of current systems to accurately sense these unique environments. This mission works in support of the planned GEO-CAPE satellite mission that monitors these environments and is critical for evaluating and understanding the spatial variations and dynamics associated with coastal environments.
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Coastal Resiliency from Hurricane Impacts
Coastal wetlands provide a line of defense for coastal communities against hurricane impacts. The wetlands can reduce wind, wave, and surge energy which will in-turn reduce the damaging effects of hurricanes on coastal infrastructure and communities. Research has been developed to improve our understanding of coastal resiliency from hurricane impacts in regards to wetland areas. This was achieved by using integrated numerical modeling and in-situ observations and remote sensing techniques.
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Comparing an Annual and a Daily Time-Step Model for Predicting Field-Scale Phosphorus Loss
A wide range of mathematical models are available for predicting phosphorus (P) losses from agricultural fields, ranging from simple, empirically based annual time-step models to more complex, process-based daily time-step models. In this study, we compare field-scale P-loss predictions between the Annual P Loss Estimator (APLE), an empirically based annual time-step model, and the Texas Best Management Practice Evaluation Tool (TBET), a process-based daily time-step model based on the Soil and Water Assessment Tool. We first compared predictions of field-scale P loss from both models using field and land management data collected from 11 research sites throughout the southern United States. We then compared predictions of P loss from both models with measured P-loss data from these sites. We observed a strong and statistically significant (p
Abstract Document

Control of Common Duckweed and Watermeal by a New Flumioxazin Formulation
Floating plants are increasingly becoming widespread problems in waterways in the southern United States. Nuisance problems are often exacerbated with increased nutrient inputs into waterbodies from point and non-point sources. Common duckweed (Lemna minor) and watermeal (Wolffia spp.) are two such floating aquatic plants that thrives in high nutrient environments. Infestations of these species can shade submersed aquatic plants and cause oxygen depletions in the water column (Parr et al. 2002) resulting in fish kills. Common duckweed and watermeal are also aesthetically displeasing to most land owners or pond managers. Herbicide applicators consider these species some of the most difficult aquatic plants to control. Currently, watermeal does not have management recommendations that produce consistent and predictable results. Additionally, floating plants are quite capable of re-colonizing a site rapidly after control efforts have been carried out as more plants may drift into the site due to water and wind currents. The purpose of this study was to verify the efficacy of liquid flumioxazin on common duckweed and watermeal as a foliar application.

Control of Cuban Bulrush (Oxycaryum Cubense) through Submersed Herbicide Applications - Interim Report
Cuban bulrush (Oxycaryum cubense) is a perennial invasive aquatic plant species native to South America (Bryson et al. 1996) that is spreading across Florida and the Southeastern US (Anderson2007, Bryson et al. 1996, Lelong 1988, Thomas and Allen 1993, Turner et al. 2003, and Cox et al. 2010). In FL, and elsewhere, Cuban bulrush is known to form large floating islands (tussocks)that can block boat launches, impede navigation along river channels, negatively affect drainage canals, and degrade fishery habitat by lowering dissolved oxygen under the tussock (Mallison et al. 2001). Cuban bulrush is capable of outcompeting and displacing native and other invasive species for resources thereby disrupting ecosystem processes (Robles et al. 2007). Cuban bulrush is capable of sexual and asexual reproduction (Haines and Lye 1983). During initial colonization, it exists as an epiphytic species that utilize other aquatic plants or structures for habitat (Tur1971). However, once a plant mat has captured enough sediment from the water column in the root/rhizome network the species is capable of surviving independently of other structures as a floating tussock (Haines and Lye 1983). Portions of these tussocks can break off, float away, and start new infestations of Cuban bulrush elsewhere. Limited data exist concerning selective chemical control (herbicides) methods that are effective at controlling Cuban bulrush. To date, only one study examining the chemical control of Cuban bulrush has been published in a peer review journal (Watson and Madsen 2014). Watson and Madsen (2014) evaluated the efficacy of 10 foliar-applied herbicides to control Cuban bulrush but did not investigate selective or submersed control options. This work was conducted to investigate short and long-term selective submersed chemical control options for Cuban bulrush. Results reported here are only for the short-term portion of this study.
Document--Interim Report 2017

Control of Cuban bulrush (Oxycaryum cubense) through submersed herbicide applications --A final report to the Florida Fish and Wildlife Conservation Commission
Cuban bulrush (Oxycaryum cubense) is a perennial invasive aquatic plant species native to South America (Bryson et al. 1996) that is spreading across Florida and the Southeastern US (Anderson 2007, Bryson et al. 1996, Lelong 1988, Thomas and Allen 1993, Turner et al. 2003, and Cox et al. 2010). In FL, and elsewhere, Cuban bulrush is known to form large floating islands (tussocks) that can block boat launches, impede navigation along river channels, negatively affect drainage canals, and degrade fishery habitat by lowering dissolved oxygen under the tussock (Mallison et al. 2001). This work was conducted to investigate short and long-term selective submersed chemical control options for Cuban bulrush.

Control of Torpedograss (Panicum Repens) through Submersed Applications of Systemic and Contact Herbicides
Torpedo grass (Panicum repens) is an invasive plant species that is capable of surviving in terrestrial and aquatic settings (Sutton 1996; Smith et al. 2004; Toth 2007). In aquatic systems, the species causes problems by impeding boat access and drainage flow in waterbodies (Smith et al. 1993; Smith et al. 2004). If left uncontrolled, torpedo grass can shade out native submersed, floating, and emergent plant species that are beneficial habitat for native fauna (Hanlon and Brady 2005; Toth 2007) thereby causing ecological problems. Currently, the plant is distributed across the Southeastern US, California, and Hawaii. It is capable of aggressive range expansion in shallow water bodies where no management activities are occurring. Foliar applications of the herbicides imazapyr and glyphosate are typically used to control the species, however, these are non-selective systemic herbicides capable of drifting onto non-target species and damaging them (Hanlon and Langeland 2000; Shilling et al. 1990; Smith et al. 1993; Smith et al. 1999).

Cost Effective BMPs for Resilient Communities
This project developed a tool that will enable the development industry to design and build more resilient and sustainable communities through the inclusion of BMPs (Best Management Practices) in new commercial and residential construction.
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Detecting Aflatoxin using Hyperspectral Imaging
Hyperspectral imaging is a way of seeing what is invisible to the human eye. GRI researchers are using this to detect biological and chemical toxins that contaminate crops. This is done by splitting the electromagnetic spectrum into many spectral bands, which expose hidden information invisible to the natural eye. The specific contaminant being studied is a fungal metabolite called aflatoxin. This lethal toxin is produced by a fungus called Aspergillus. It is a known carcinogen associated with liver and lung cancers in humans. Many external stresses cause the fungi to react but hot and humid weather conditions increase its production of aflatoxin that invades corn and other commodities. The goal is to help improve detection and accuracy.
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Developing New Strategies for Management of Invasive Aquatic Plants
GRI is developing new strategies for the management of invasive aquatic plants through research at our mesocosm tank facility on the campus of Mississippi State University. We are evaluating new aquatic herbicides, combinations of existing aquatic herbicides, and applying management techniques based on a new understanding of plant species life history. These projects may be proprietary; and funded by private industry, federal, state, and local government agencies, and nonprofit foundations.
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Development and Validation of Geospatial Tools to Optimize Implementation of Precision Conservation
Conservation programs under the Farm Bill provide economic incentives for agricultural producers to divert marginally profitable land from production to targeted conservation practices. The adoption of conservation practices may depend on the profitability of program participation, relative to full production. Spatially explicit yield data, combined with production budgets, commodity prices, and program eligibility criteria can inform producers regarding the economical optimality of production vs. conservation. The objectives of this research are to develop decision support tools within ArcGIS that identify opportunities for implementation of conservation programs on agricultural landscapes, measure profitability of alternative programmatic enrollments vs. whole field production, and predict wildlife population benefits of these alternatives. This research will help producers to make informed economic decisions regarding land usage for conservation programs and crop production, benefiting both the farmer and native wildlife.
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Development of a Water Budget for Tail-water Recovery Systems
Unsustainable groundwater use for agricultural irrigation has led to declining aquifer levels across the United States, necessitating implementation of water conservation practices. One conservation practice being implemented throughout the lower Mississippi River alluvial valley (LMAV) that collects and stores surface water for irrigation is a tailwater recovery (TWR) system. Accordingly, the overall objective of this study was to develop a water budget for TWR systems. Eight TWR systems were continuously monitored for water depth, allowing rates of water gain and loss to be quantified. Volumes of water movement were calculated based on change in water depth and system dimensions. Using water budgets derived from TWR systems the water volume was calculated and found to be gaining, except during months of irrigation. Extrapolating the water budget to all TWR systems shows a total offset of 15% of the annual groundwater deficit. Tailwater recovery system efficiencies show designs may be altered to improve the water savings and use of these systems.
Journal of Irrigation and Drainage OnlineSite ASCE Online SIte

Ecological Genetics of the Invasive South American Cactus Moth, Cactoblastis cactorum
Datasets have been developed of locations of C. cactorum and its host plants (pricklypear cacti, Opuntia species) in the United States and in Argentina, across the majority of the moth's native and North American range. Researchers have identified a steep environmental gradient correlated with separation of the genetic group used for biological control from other genetic groups in Argentina. We have so far found those genetic data to be a significant contributor to patterns in expected and realized habitat associations of the moth within Argentina and in the moth's non-native range. Currently, researchers are working to streamline the modeling process in order to more rapidly conduct analyses as additional genetic and/or environmental data become available. The aim of these studies is to evaluate potential environmental and biological mechanisms contributing to the invasion success of C. cactorum at a global scale, in order to better estimate the expected distribution of the moth in North America.
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Effects of Rainfall, Geometrical and Geomorphological Variables on Vulnerability of the Lower Mississippi River Levee System to Slump Slides
This study investigated the importance of rainfall and various geomorphological and geometrical factors to the vulnerability of earthen levees to slump slides. The study was performed using a database including 34 slump slides that occurred in the lower Mississippi River levee system from 2008 to 2009. The impact of rainfall within the six months prior to slide occurrence was studied for 23 slides for which an accurate occurrence date was available. Several variables were used to develop a logistic regression model to predict the probability of slump slide occurrence. The proposed model was verified for both slide and non-slide cases. The regression analysis depicts the impact of channel width, river sinuosity index, riverbank erosion, channel shape condition and distance to river. Excluding the sinuosity index, the impact of the other independent variables examined was found to be significant. Occurrence of riverbank erosion around the slide locations was the most significant predictor factor. A channel width of less than 1000 m was ranked as the second most significant variable. The proposed model can aid in locating high-risk areas on levees in order to take prompt protective measures, increase monitoring efforts and enable early response under emergency conditions.

Enhanced Soils Mapping For Productive Capacity Assessments
This research uses geospatial technologies to create methodology used in defining soil management zones that address soil variability in distinct areas and identify the soil properties that limit crop production while increasing soil conservation. Determining appropriate soil management zones can lead to an increased profit by either increasing yield in areas of fields that are being underutilized or decreasing fertilization in areas of fields where maximum economic yield has already been attained. Moreover, robust and repeatable methodology for construction of management zones will provide an empirical basis for developing variable rate fertilizer prescriptions that optimize profitability and minimize off-site nutrient transport, thereby benefiting the producer, the public, and the environment.
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Estuarine Influence on Biogeochemical Properties of the Alabama Shelf during the Fall Season
Estuarine-shelf exchange can drive strong gradients in physical and biogeochemical properties in the coastal zone and exert a significant influence on biological processes and patterns. Physical, biogeochemical, and plankton data from an across-shelf transect extending south of Mobile Bay, Alabama, in conjunction with regional time series data, were used to determine the relative importance of estuarine-shelf interactions on the physical-biological structuring of the shelf environment during fall conditions (i.e., well-mixed, low discharge).This period was also characterized by a relatively unique weather event associated with the remnants of Hurricane Patricia, which drove a meteorological flushing of estuarine water onto the shelf. Survey data indicated generally low N:P ratios across the shelf, with slightly elevated dissolved inorganic nitrogen in the Region of Freshwater Influence (ROFI) that extended approximately 30 km offshore. The ROFI had higher values of chlorophyll-a, diatom-specific production, marine snow, and primary productivity, with notable contributions from the larger size cells (
Abstract Document

Evaluation of Geospatial Tools to Map Dispersal of Invasive Aquatic Plants in Agroecosystems
This study validates new techniques of mapping and tracking the distribution and transport of invasive aquatic plants by using remote sensing technology to map known locations of these plants, sampling dispersal rates under normal and stormy weather conditions and modeling the output using ArcPro, and comparing these rates to those already recorded through GPS tracking. Gaining an understanding of how invasive aquatic weeds disperse through agricultural areas and creating a tool to reduce the negative effects these weeds have on agronomic crops is vital for the improvement in crop yields and the management of unwanted weed species invading otherwise healthy ecosystems.
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Evaluation of the APEX Model to Simulate Runoff Quality from Agricultural Fields in the Southern Region of the U.S.
The Agricultural Policy Environmental eXtender (APEX) model has been widely applied to assess phosphorus (P) loss in runoff water and has been proposed as a model to support practical decisions regarding agricultural P management, as well as a model to evaluate tools such as the P Index. The aim of this study is to evaluate the performance of APEX to simulate P losses from agricultural systems to determine its potential use for refinement or replacement of the P Index in the southern region of the United States. Uncalibrated and calibrated APEX model predictions were compared against measured water quality data from row crop fields in North Carolina and Mississippi and pasture fields in Arkansas and Georgia. Calibrated models satisfactorily predicted event-based surface runoff volumes at all sites (Nash-Sutcliffe efficiency [NSE]

FloodViz: Visual Analytics for Assessment and Interpretation of Simulated River Flooding
The FloodViz project involves the development and testing of visual analytics software to enable scientists and forecasters to better interpret and distribute hydrologic information. This software will be useful in the research community as an interpretation tool for river level and flood data. The tools developed serve as a useful platform for hydrologic forecasters within the National Weather Service to more quickly and accurately determine areas at risk for flooding and allow NOAA river forecasters to better visualize the extent of flooding. Additionally, these tools allow forecasters to relay more information to the emergency management community while issuing forecasts to help protect lives, property and the nation.
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GIS for Aquatic Plant Management
Geographic Information Systems (GIS) have become the new tool for information management, planning and presentation for invasive aquatic plant management programs and is critical in every component of the program.
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Gulf Coastal Plains and Ozarks Landscape Conservation Cooperative (GCPO LCC)
GRI has partnered with the GCPO LCC to provide critical LCC research and computing capacity for LCC activities. As a research hub for the GCPO LCC, GRI has established over $4 million in cooperative agreements with the U.S. Fish and Wildlife Service to fund more than 20 different LCC research projects. This diverse research program includes exploration of ecosystem health, resilience to climate change and urbanization and interrelationships among species and their habitats.
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Health and Productivity of Louisiana Salt Marshes
This study will allow the identification of hotspots of marsh degradation in Louisiana by evaluating marsh biophysical characteristics including distribution of chlorophyll content, green leaf area and green marsh canopy cover. This assessment of marsh health and productivity is due to the Deepwater Horizon oil spill. NASA's Moderate Resolution Imaging Spectroradiometer (MODIS) satellite images will be used to retrieve and map these characteristics across the coastal Louisiana salt marshes before and after the spill. The maps and tools produced from the study will be helpful to coastal managers across Louisiana as they evaluate and prioritize the marsh restoration effort which will take place due to the oil spill. Tangible map products will be generated for the first time that can quantitatively assess the effect of the restoration activities and speed of marsh ecosystem recovery.
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Inflow of Shelf Waters into the Mississippi Sound and Mobile Bay Estuaries in October 2015
The exchange of coastal waters between the Mississippi Sound (MSS), Mobile Bay and Mississippi Bight is an important pathway for oil and pollutants into coastal ecosystems. This study investigated an event of strong and persistent inflow of shelf waters into MSS and Mobile Bay during October 2015 by combining in-situ measurements, satellite ocean color data and ocean model predictions. Navy Coastal Ocean Model (NCOM) predicted high salinity shelf waters continuously flowing into the estuarine system, and forecasted low salinity waters trapped inside the estuaries which did not flush out until the passage of tropical cyclone Patricia
Abstract and Document

Integrated Ecosystem Assessment (IEA) Tool
This research was implemented as part of an overall Ecosystem Approach to Management (EAM). It looks at all indicators, such as tourism and recreation, climate change, fish populations and conservation and energy demands to evaluate ocean health. In the past, scientists, because of the limits of scientific knowledge and technology could only concentrate on individual segments and species of the ocean. The EAM approach using IEA management assessment tool allows them to combine data and look at the ocean as a whole. Research is being carried out at four sites in the Northern Gulf of Mexico: Perdido Bay, Florida; Mississippi Sound, Mississippi; Barataria Basin, Louisiana; and Galveston Bay, Texas.
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Integrated Pest Management Systems and Resistance Management Using Geospatial Technologies
This research has evaluated the use of remote sensing technologies to detect and predict spatial distribution of weed populations for the purpose of designing site-specific herbicide prescriptions and monitoring the spread of herbicide resistant weed species. Associated spatial technologies have been used to generate guidelines for creation of site-specific harvest-aid, plant growth regulator, and insecticide prescriptions. A unique contribution of this research has been the development of novel statistical models that more fully characterize geographic, topographic, hydrological, edaphic, and producer-induced sources of variation in yield than previously understood. The research also highlights the immense complexity of spatial data collection, management, geoprocessing, and integration for decision support in site-specific agriculture. Outcomes of this study may increase efficiency and profitability, reduce the threat of off-target movement of residual herbicides in runoff to surface and groundwater, and reduce herbicide usage through precision applications.
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Invasive Aquatic Plant Control for Noxon Rapids and Cabinet Gorge Reservoirs, Montana: An Adaptive Management Plan
Noxon Rapids and Cabinet Gorge reservoirs are run-of-the river impoundments along the Lower Clark Fork River System in northwestern Montana. The dams that create these water bodies are owned and operated by Avista Utilities. The primary function of these reservoirs is for hydroelectric power generation, with flood control being a secondary purpose. To achieve the prescribed level of electrical output, daily dam operations and water discharge schedules are fairly consistent but are dependent upon daily and/or seasonal demands on the regional power grid. In addition to power generation and flood control, these reservoirs provide an important regional source of outdoor recreational activities, including boating and angling. The shallow water littoral zones have traditionally supported diverse stands of native aquatic plants, which provide considerable fish and wildlife habitat, and other beneficial ecological services. A brief overview of key physical properties of the reservoirs and status of the aquatic plant communities is provided below.

Invasive Species Program
GRI researchers actively study invasive plants that take over agricultural and natural areas, with expertise for studies ranging from regional impacts through use of remote sensing and GIS, to cellular and molecular studies of plant uptake, and genetic composition. GRI brings together multidisciplinary research teams comprised of university and government researchers to address diverse questions on the management of invasive species.
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Investigating the Correlation between Radar Backscatter and In Situ Soil Property Measurements
Utilizing remote sensing techniques to extract soil properties can facilitate several engineering applications for large-scale monitoring and modeling purposes such as earthen levees monitoring, landslide mapping, and off-road mobility modeling. This study presents results of statistical analyses to investigate potential correlations between multiple polarization radar backscatter and various physical soil properties. The study was conducted on an approximately 3 km long section of earthen levees along the lower Mississippi river as part of the development of remote levee monitoring methods. Polarimetric synthetic aperture radar imagery from UAVSAR was used along with an extensive set of in situ soil properties. The following properties were analyzed from the top 30
Abstract and Document

IPAMS - Invasive Plant Atlas of the MidSouth
The Invasive Plant Atlas of the Mid-South (IPAMS) is an integrated research and extension project to develop an invasive plant program for the Mid-South states of Alabama, Arkansas, Louisiana, Mississippi, and Tennessee. Research activities include conducting systematic regional vegetation surveys to assess the distribution of key invasive plants, developing models for predicting the occurrence of target species based on land use and cover, and evaluating the relative effectiveness of professional versus volunteer surveys.
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Levee Evaluation through Remote Sensing
GRI researchers are developing a means to use remote sensing to determine the strength of river levees through the utilization of airborne synthetic aperture radar for levee condition assessment and develop classification software. The team has set out to develop new methods and software to improve knowledge of levee conditions and help levee managers prioritize their efforts to inspect, test and repair levees.
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Linking Cultural, Biological and Economic Values into Wetland Programs: Mississippi Band of Choctaw Indians' Pearl River Wetland Demonstration Project
This project aims to develop procedures for more reliably regenerating rivercane and for planting potential restoration sites in the Coastal Plain, and for maintenance of stands for cultural use by native peoples. We are assessing ecological factors associated with the establishment and maintenance of rivercane stands, developing methods for vegetative propagation of rivercane from rhizome segments, and attempting to transfer our findings directly to the Choctaw and other American Indian groups through local and regional symposia, workshops, and field days.
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Mapping of Invasive Phragmites (Common Reed) in Gulf of Mexico Coastal Wetlands Using Multispectral Imagery and Unmanned Aerial Systems
In coastal wetlands of the Gulf of Mexico, the invasive plant species Phragmites australis (common reed) rapidly alters the ecology of a site by shifting plant communities from heterogeneous mixtures of plant species to homogenous stands of Phragmites. Phragmites grows in very dense stands at an average height of 4.6 m and outcompetes native plants for resources. To restore affected wetlands, resource managers require an accurate map of Phragmites locations. Previous studies have used satellite and manned aircraft-based remote-sensing images to map Phragmites in relatively large areas at a coarse scale; however, low-altitude high-spatial-resolution pixel-based classification approaches would improve the mapping accuracy. This study explores the supervised classification methods to accurately map Phragmites in the coastal wetlands at the delta of the Pearl River in Louisiana and Mississippi, USA, using high-resolution (8 cm ground sample distance; GSD) multispectral imagery collected from a small unmanned aerial system platform at an altitude of 120 m. We create a map through pixel-based Support Vector Machines (SVM) classification using blue, green, red, red edge, and near-infrared spectral bands along with a digital surface model (DSM), vegetation indices, and morphological attribute profiles (MAPs) as features. This study also demonstrates the effects of different features and their usefulness in generating an accurate map of Phragmites locations. Accuracy assessment based on a) a subset of training/testing samples (to show classifier performance) and b) the entire ground reference (GR) map (to show the quality of mapping) is demonstrated. Kappa, overall accuracy (OA), class accuracies, and their confidence intervals (CIs) are reported. An OA of 91% and kappa of 63 is achieved. The results of this study indicate that features such as MAPs are very useful in accurately mapping invasive Phragmites compared with existing region-based approaches.
Abstract and Document

Micromechanics of Undrained Response of Dilative Granular Media Using a Coupled DEM-LBM Model: A Case of Biaxial Test
In this paper, the Discrete Element Method (DEM) is coupled with the Lattice-Boltzmann Method (LBM) to model the undrained condition of dense granular media that display significant dilations under highly confined loading. DEM-only models are commonly used to simulate the micromechanics of an undrained specimen by applying displacements at the domain boundaries so that the specimen volume remains constant. While this approach works well for uniform strain conditions found in laboratory tests, it does not realistically represent non-uniform strain conditions that exist in the majority of real geotechnical problems. The LBM offers a more realistic approach to simulate the undrained condition since the fluid can locally conserve the system volume. To investigate the ability of the DEM-LBM model to effectively represent the undrained constraint while conserving volume and accurately calculating the stress path of the system, a two-dimensional biaxial test is simulated using the coupled DEM-LBM model, and the results are compared with those attained from a DEM-only constant volume simulation
Abstract Document

Nitrogen and Organic Carbon Contents of Agricultural Drainage Ditches of the Lower Mississippi Alluvial Valley
Use of agricultural fertilizers as a means of increasing production has resulted in excessive nutrient loading to agricultural drainage ditches, contributing to the Gulf of Mexico hypoxic zone. Drainage ditches can have wetland characteristics and functionality, including the capacity to remediate nutrient loading, which can be promoted using management practices. The purpose of this study was to assess relationships between organic carbon (C) and nitrogen (N) contents of drainage ditch sediment and waters and to evaluate the spatial scope in which organic C is potentially limiting N removal in drainage ditches throughout the Lower Mississippi Alluvial Valley (LMAV).

Nutrient and Sediment Runoff from Agricultural Landscapes with Varying Suites of Conservation Practices in the Mississippi Alluvial Valley
Increasing concern regarding environmental degradation in coastal areas that experience annual hypoxic zones has led to the need for mitigation of nutrient laden runoff from inland landscapes. An annual occurrence of a hypoxic zone in the Gulf of Mexico has led to the development and implementation of nutrient reduction strategies throughout the Mississippi River Basin (MRB). With federal, state, and private financial and technical assistance, landowners have implemented best management practices (BMPs) to combat nutrient and sediment nonpoint source pollution; however, the effectiveness of these BMPs alone or utilized together has not been quantified. This study uses a field-scale, paired watershed approach in two watersheds in the Mississippi Alluvial Valley to test for differences in sediment and nutrient runoff concentrations between four management systems.
Abstract and publication site

Opuntia (Pricklypear Cactus) and Cactoblastis Cactorum (Cactus Moth) Habitat Models and Population Genetics
A research group has worked to characterize habitat of southeastern U.S. Opuntia species throughout Mississippi, Florida, and southwestern Alabama. One goal of this research is to develop predictive models for locations of Opuntia species populations in the region. A related goal is to better understand what large-scale environmental factors may be influencing the spread of C. cactorum in North America. Recently, researchers have begun to incorporate genetic analyses into our environmental modeling research. Integration of ecological habitat models with C. cactorum genetic data is expected to help better understand mechanisms of host preference and environmental tolerance, and may eventually lead to the ability to track sources of new moth infestations in the United States or Mexico.
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Post-Logging Estimation of Loblolly Pine (Pinus Taeda) Stump Size, Area and Population Using Imagery from a Small Unmanned Aerial System
This study describes an unmanned aerial system (UAS) method for accurately estimating the number and diameters of harvested Loblolly Pine (Pinus taeda) stumps in a final harvest (often referred to as clear-cut) situation. The study methods are potentially useful in initial detection, quantification of area and volume estimation of legal or illegal logging events to help estimate the volumes and value of removed pine timber. The study sites used included three adjacent pine stands in East-Central Mississippi. Using image pattern recognition algorithms, results show a counting accuracy of 77.3% and RMSE of 4.3 cm for stump diameter estimation. The study also shows that the area can be accurately estimated from the UAS collected data. Our experimental study shows that the proposed UAS survey method has the potential for wide use as a monitoring or investigation tool in the forestry and land management industries.
Post-Logging Estimation of Loblolly Using UAS Document

Potential for recycling of suspended solids and nutrients by irrigation of tailwater from tailwater recovery systems
Within the Lower Mississippi Alluvial Valley, conservation practices are being utilized to mitigate nutrient loading to streams from agricultural landscapes. This study was conducted to determine the potential to use solids, phosphorus (P) and nitrogen (N) captured by tailwater recovery (TWR) systems for reuse onto production fields through irrigation applications.
Abstract and Document

Providing Accurate Data for Field Monitoring of Peanut Production
Reliable yield monitors have been developed for a variety of crops including corn, soybeans, wheat, and cotton. Due to the nature of harvesting and threshing peanuts, however, the ability to provide accurate yield data has been rudimentary, at best. The objective of this research is to use a system for yield measurement previously developed at Mississippi State University and commercialized through MSTX Agricultural Sensor Technologies (MAST), LLC to compare management zones, buy-point and field weights from adjusted and raw yield data in peanuts. The results of this study will potentially allow peanut producers to evaluate inputs, manage pests, make better land-use decisions and perform economic analysis in peanut production.
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Quantifying Capture and Use of Tailwater Recovery Systems
The government has provided financial assistance on approximately 200 tailwater recovery systems in the state of Mississippi, and more in other states. The objective of this study was to quantify surface water capture and use within 31 tailwater recovery ditches (TWR) and on-farm storage reservoirs (OFS), so that conservation benefits could be evaluated. Water-level data were combined with system dimensions, rainfall data, and evaporation estimates to assess total gains and losses over the course of a year. Systems had a net positive balance of approximately 2,200,000 m3m3 (2,200 ML) of captured surface water. Losses from evaporation and infiltration were between 8.68 and 10.97
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Recent development of optical methods in rapid and non-destructive detection of aflatoxin and fungal contamination in agricultural products
The demand for developing rapid and non-destructive techniques that is suitable to real-time and on-line detection of aflatoxin and fungal contamination has received significant attentions. Measurement techniques based on fluorescence spectroscopy (FS), near-infrared spectroscopy (NIRS) and hyperspectral imaging (HSI) have provided interesting and promising results for detecting aflatoxin and/or fungal contamination in a variety of foods. As such, the main goal of this article is to give an overview of the current research progress of FS, NIRS and HSI techniques in rapid detection of aflatoxin and fungal contamination in different varieties of agricultural products.
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Recent Developments and Applications of Hyperspectral Imaging for Rapid Detection of Mycotoxins and Mycotoxigenic Fungi in Food Products
Mycotoxins are the foremost naturally occurring contaminants of food products such as corn, peanuts, tree nuts, and wheat. As the secondary metabolites, mycotoxins are mainly synthesized by many species of the genera Aspergillus, Fusarium and Penicillium, and are considered highly toxic and carcinogenic to humans and animals. Most mycotoxins are detected and quantified by analytical chemistry-based methods. While mycotoxigenic fungi are usually identified and quantified by biological methods. However, these methods are time-consuming, laborious, costly, and inconsistent because of the variability of the grain-sampling process. It is desirable to develop rapid, non-destructive and efficient methods that objectively measure and evaluate mycotoxins and mycotoxigenic fungi in food. In recent years, some spectroscopy-based technologies such as hyperspectral imaging (HSI), Raman spectroscopy, and Fourier transform infrared spectroscopy have been extensively investigated for their potential use as tools for the detection, classification, and sorting of mycotoxins and toxigenic fungal contaminants in food. HSI integrates both spatial and spectral information for every pixel in an image, making it suitable for rapid detection of large quantities of samples and more heterogeneous samples and for in-line sorting in the food industry. In order to track the latest research developments in HSI, this paper gives a brief overview of the theories and fundamentals behind the technology and discusses its applications in the field of rapid detection and sorting of mycotoxins and toxigenic fungi in food products. Additionally, advantages and disadvantages of HSI are compared, and its potential use in commercial applications is reported.

Reduction of solids and nutrient loss from agricultural land by tailwater recovery systems
Best management practices are being implemented throughout the Lower Mississippi River Alluvial Valley with the aim of alleviating pressures placed on downstream aquatic systems by sediment and nutrient losses from agricultural land; however, research evaluating the performance of tail-water recovery (TWR) systems, an increasingly important practice, is limited. This study evaluated the ability of TWR systems to retain sediment and nutrients draining from agricultural landscapes.

Representation of Solid and Nutrient Concentrations in Irrigation Water from Tailwater-Recovery Systems by Surface Water Grab Samples
Tailwater recovery (TWR) systems are being implemented on agricultural landscapes to create an additional source of irrigation water. Existing studies have sampled TWR systems using grab samples; however, the representation of solids and nutrient concentrations in these samples to water being irrigated from TWR systems has yet to be investigated. In order to test whether grab samples are representative of water pumped from TWR systems for irrigation use, this study compared concentrations of total suspended solids (TSS), total phosphorus (TP), total nitrogen (TN), total Kjeldahl nitrogen (TKN), nitrate-nitrite (NO−3NO−2NO3−NO2−), and ammonium (NH 4NH4 ). Grab samples were collected simultaneously from the surface water and from the respective outflow of irrigation infrastructure in six TWR systems. Comparison of 14 irrigation events showed TSS, TP, TN, TKN, NO−3NO−2NO3−NO2−, and NH 4NH4 did not differ (Pillai’s trace5,1=0.307trace5,1=0.307, p>0.5p>0.5) between surface water grab samples and irrigation water samples. No differences (p>0.05p>0.05) were found for TN, TP, NH 4NH4 , and TKN across sites. This research suggests surface water grab samples from TWR systems represent the solid and nutrient concentrations being irrigated at that moment of time.
Tailwater-Recovery Systems ...Grab Samples

Satellite Rainfall Applications for Surface Hydrology
GRI has evaluated results which examine how soil moisture states simulated by land surface models are impacted when forced with various precipitation datasets. These datasets are from a collection of Global Precipitation Mission satellite constellation configurations gathered over the continental United States.
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Screening Mississippi River Levees Using Texture-based and Polarimetric-based Features from Synthetic Aperture Radar Data
This article reviews the use of synthetic aperture radar remote sensing data for earthen levee mapping with emphasis on finding the slump slides on the levees. Earthen levees built on the natural levees parallel to the river channel are designed to protect large areas of populated and cultivated land in the Unites States from flooding. One of the signs of potential impending levee failure is the appearance of slump slides. On-site inspection of levees is expensive and time-consuming, therefore, a need to develop efficient techniques based on remote sensing technologies is mandatory to prevent failures under flood loading. Analysis of multi-polarized radar data is one of the viable tools for detecting the problem areas on the levees. In this study, we develop methods to detect anomalies on the levee, such as slump slides and give levee managers new tools to prioritize their tasks. This paper presents results of applying the NASA JPL’s Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) quad-polarized L-band data to detect slump slides on earthen levees. The study area encompasses a portion of levees of the lower Mississippi river in the United States. In this paper, we investigate the performance of polarimetric and texture features for efficient levee classification. Texture features derived from the gray level co-occurrence matrix and discrete wavelet transform were computed and analyzed for efficient levee classification. The pixel-based polarimetric decomposition features, such as entropy, anisotropy, and scattering angle were also computed and applied to the support vector machine classifier to characterize the radar imagery and compared the results with texture-based classification. Our experimental results showed that inclusion of textural features derived from the SAR data using the discrete wavelet transform (DWT) features and gray level co-occurrence matrix (GLCM) features provided higher overall classification accuracies compared to the pixel-based polarimetric features.
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Sediment and Mercury Path and Fate Modeling
Sediments are the main repository of mercury in the coastal Gulf of Mexico as well as the site of transformation of inorganic mercury to methylmercury, the more toxic form which is bioaccumulated in fish and enters into the food webs. This project develops methods which predict the path and fate of sediment and mercury in the Gulf coastal region from entry point to fish stocks.
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Southern P Indices, Water Quality Data, and Modeling (APEX, APLE, and TBET) Results: A Comparison
Phosphorus (P) Indices in the southern United States frequently produce different recommendations for similar conditions. We compared risk ratings from 12 southern states (Alabama, Arkansas, Florida, Georgia, Kentucky, Louisiana, Mississippi, North Carolina, Oklahoma, South Carolina, Tennessee, and Texas) using data collected from benchmark sites in the South (Arkansas, Georgia, Mississippi, North Carolina, Oklahoma, and Texas). Phosphorus Index ratings were developed using both measured erosion losses from each benchmark site and Revised Universal Soil Loss Equation 2 predictions; mostly, there was no difference in P Index outcome. The derived loss ratings were then compared with measured P loads at the benchmark sites by using equivalent USDA–NRCS P Index ratings and three water quality models (Annual P Loss Estimator [APLE], Agricultural Policy Environmental eXtender [APEX], and Texas Best Management Practice Evaluation Tool [TBET]). Phosphorus indices were finally compared against each other using USDA–NRCS loss ratings model estimate correspondence with USDA–NRCS loss ratings. Correspondence was 61% for APEX, 48% for APLE, and 52% for TBET, with overall P index correspondence at 55%. Additive P Indices (Alabama and Texas) had the lowest USDA–NRCS loss rating correspondence (31%), while the multiplicative (Arkansas, Florida, Louisiana, Mississippi, South Carolina, and Tennessee) and component (Georgia, Kentucky, and North Carolina) indices had similar USDA–NRCS loss rating correspondence—60 and 64%, respectively. Analysis using Kendall’s modified Tau suggested that correlations between measured and calculated P-loss ratings were similar or better for most P Indices than the models.
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Spatial and spectral Hyperspectral Classification Using Local Binary Patterns and Markov Random Fields
Local binary patterns (LBPs) have been extensively used to yield spatial features for the classification of general imagery, and a few recent works have applied these patterns to the classification of hyperspectral imagery. Although the conventional LBP formulation employs only the signs of differences between a central pixel and its surrounding neighbors, it has been recently demonstrated that the difference magnitudes also possess discriminative information. Consequently, a sign-and-magnitude LBP is proposed to provide a spatial
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Spatial Detection of Agri-terrorism
This GRI project develops and deploys an automated target recognition system that utilizes hyperspectral imagery to detect biological or chemical contamination of vegetation. The Automated Target Recognition - ATR - system is applied to the problem of BioSecurity, i.e. the detection of crop contamination via biological or chemical agents.
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Spatial Variation and Temporal Trend of Water Quality
NGI conducted ground truth observations and standardize algorithms to produce and evaluate the spatial and temporal variations of water quality parameters in the Northern Gulf of Mexico (NGOM). The effort is aimed at improving the monitoring of the NGOM ecosystem based on remote sensing and understanding the dynamics of harmful algae blooms in the region.
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Structure from Motion with UAVs: A Best Practice Guide for Users
Tips and tricks to help you get started using low-cost unmanned aerial vehicles to generate accurate three-dimensional models for stream channels and drainage ditches.
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Temporal Effects on Internal Fluorescence Emissions Associated with Aflatoxin Contamination from Corn Kernel Cross-sections Inoculated with Toxigenic and Atoxigenic Aspergillus Flavus
Non-invasive, easy to use and cost-effective technology offers a valuable alternative for rapid detection of carcinogenic fungal metabolites, namely aflatoxins, in commodities. One relatively recent development in this area is the use of spectral technology. Fluorescence hyperspectral imaging, in particular, offers a potential rapid and non-invasive method for detecting the presence of aflatoxins in maize infected with the toxigenic fungus Aspergillus flavus. Earlier studies have shown that whole maize kernels contaminated with aflatoxins exhibit different spectral signatures from uncontaminated kernels based on the external fluorescence emission of the whole kernels. Here, the effect of time on the internal fluorescence spectral emissions from cross-sections of kernels infected with toxigenic and atoxigenic A. flavus, were examined in order to elucidate the interaction between the fluorescence signals emitted by some aflatoxin contaminated maize kernels and the fungal invasion resulting in the production of aflatoxins.

The Science of William M. Gray: His Contributions to the Knowledge of Tropical Meteorology and Tropical Cyclones
Advances in knowledge in tropical meteorological research are discussed in the context of contributions made by Professor William M. Gray. Gray pioneered the compositing approach to observational tropical meteorology through assembling of global radiosonde data sets and tropical cyclone research flight data. In the 1970s he made fundamental contributions to knowledge of convective-larger scale interactions. Throughout his career he wrote seminal papers on tropical cyclone structure, cyclogenesis, motion and seasonal forecasts. His conceptual development of a seasonal genesis parameter also laid an important framework for both seasonal forecasting as well climate change studies on tropical cyclones. His work was a blend of both observationally-based studies as well as the development of theoretical concepts. This paper reviews the progress in knowledge in the areas where Dr. Gray provided his largest contributions and describes the scientific legacy of Gray
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UAS with MicroSense RedEdge Payload Help Monitor and Manage Forest Resortation
Unmanned Aerial Systems (UAS) carry a multispectral senor that produce images that provides biologist and geographic information system specialists with changes in the woodlands and vegetation in almost real time. These systems also show the density and regrowth of woodland, marsh, and coastal areas. Mississippi State University’s Geosystems Research Institute is assisting the Grand Bay National Estuarine Research Reserve (GBNERR) and the U.S. Forestry Service with surveying the 4,200 acres that were burned during a large wildfire that reaches from southeast Jackson County into Alabama. These experts utilized the Altavian Nova Block III to inspect the area from 1,000 feet, and they deployed the MicaSense RedEdge. The MicaSense RedEdge has the ability to sense energy at five different wavelengths. Two of the five wavelengths exceed our vision in the Near Infrared Region (NIR) of the electromagnetic spectrum. The senor provides researchers with accurate data that projects the status of vegetation and stress of areas within the ecosystem. With this knowledge, researchers and specialists can aid in the revegetation of the burned woodlands and marsh of the GBNERR, the Grand Bay National Wildlife Refuge and neighboring lands.

UAV Research with NOAA
GRI scientists are using UAVs to assess the speed and rate of how rivers flow and rise and where the water goes, especially in flood type conditions. Partnering with NOAA, both are helping the U.S. to become a “Weather Ready Nation.” This effort can help prevent the loss of life and property before, during and after natural disasters, such as flooding, created by tropical storms and hurricanes. They are conducting research and gaining invaluable environmental and situational data along the lower Pearl River watershed, south of Bogalusa, Louisiana, all the way down to what is called the tidal plain.
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Using Unmanned Aerial Vehicles for High-Resolution Remote Sensing to Map Invasive Phragmites Australis in Coastal Wetlands
The wetland plant species, Phragmites australis, is present on every continent except Antarctica. Both native and non-native subspecies thrive in the USA with the non-natives quickly displacing native wetland plants. Along the Gulf Coast, Phragmites grows in very dense stands, and at heights of greater than 4.6 m, is usually the tallest grass species in a wetland, estuary, and marsh ecosystems. Phragmites is known to alter the ecology of these wetland systems making them less suitable as habitat for many species of flora and fauna. Furthermore, Phragmites presents a navigation hazard to smaller boats by impairing visibility along shorelines and around bends of canals and rivers. Management efforts targeting non-native Phragmites rely heavily on accurately mapping invaded areas. Historically, mapping has been done through walking the perimeter of a stand with a Global Positioning System (GPS) unit, using satellite imagery, or through the use of aerial photography from manned aircraft. These methods are time consuming, are expensive, can have an inadequate resolution, and in some cases are prone to human error. In this work, an Unmanned Aerial System (UAS) was used to capture visible imagery to create a basin-wide distribution map of a large wetland along the US Pearl River delta in southeastern Louisiana. The imagery was collected in the summer and individual images were mosaicked to create a larger map. We then evaluated the use of texture analysis on the mosaics to automatically map the invasive. Specifically, Gabor filters, grey level co-occurrence matrices, segmentation-based fractal texture analysis, and wavelet-based texture analysis were compared for mapping the Phragmites. Our experimental results, conducted using the imagery we collected over four study areas (approximately 2250 ha) along the US Pearl River delta, indicate the proposed texture-based approach yields an average accuracy of 85%, an average kappa accuracy of 70%. These maps have shown to be very useful for resource managers to hasten the eradication efforts of Phragmites.
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