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Travis J. Harrison

Publications and source records attributed to Travis J. Harrison.

13 recordsLinked to original sources

Challenges and solutions for automated avian recognition in aerial imagery

Remote aerial sensing provides a non-invasive, large geographical-scale technology for avian monitoring, but the manual processing of images limits its development and applications. Artificial Intelligence (AI) methods can be used to mitigate this manual image processing requirement. The implementation of AI methods, however, has several challenges: (1) imbalanced (i.e., long-tailed) data distribution, (2) annotation uncertainty in categorization, and (3) dataset discrepancies across different study sites. Here we use aerial imagery data of waterbirds around Cape Cod and Lake Michigan in the United States to examine how these challenges limit avian recognition performance. We review existing solutions and demonstrate as use cases how methods like Label Distribution Aware Marginal Loss with Deferred Re-Weighting, hierarchical classification, and FixMatch address the three challenges. We also present a new approach to tackle the annotation uncertainty challenge using a Soft-fine Pseudo-Label methodology. Finally, we aim with this paper to increase awareness in the ecological remote sensing community of these challenges and bridge the gap between ecological applications and state-of-the-art computer science, thereby opening new doors to future research.

Remote Sensing in Ecology and Conservation

Assessment of three methods to evaluate the distribution of submersed aquatic vegetation in western Lake Erie

Submersed aquatic vegetation (SAV) plays an important role in ecosystems. Inventories of SAV spatial distribution and composition are important for monitoring changes in SAV. In this study, we compared three common SAV sampling methods to quantify SAV in western Lake Erie. Aerial imagery of near-shore areas in western Lake Erie was classified using object-based image analysis (OBIA) and evaluated against field-based surveys using single-beam sonar or rake samples. To assess variation among methods, data were assigned either vegetation ‘presence’ or ‘absence’ and compared for simple correspondence and agreement (Cohen’s Kappa, κ ). The two field-based methods had the highest correspondence at 78% ( n = 782) and the highest κ = 0.545. Correspondence between OBIA and rake surveys was 69% ( n = 245) and κ = 0.36. Correspondence between OBIA and hydroacoustics was the lowest of 54% ( n = 30,768) with an agreement of κ = 0.17. Environmental factors such as water turbidity may have played a role in reduced agreement between OBIA and field methods. Determining the optimal method or combination of methods will depend upon research goals, effort, and cost, but each method can provide reliable SAV information for resource management.

Michigan, Ohio

USGS invasive carp database management and integration support

Bigheaded carps (Bighead Carp and Silver Carp) tracking, monitoring, and contracted removal will continue throughout the Illinois River and Upper Mississippi River as part of an adaptive management effort to mitigate, control, and contain bigheaded carps. Other fish will also be tracked to maintain a holistic view of the transmitter distribution in the Upper Illinois River Waterway. To facilitate these actions, a need to compile and analyze invasive carp-related data from all agencies exists. Invasive carp-related data include all data sources that could inform the MRWG objectives or projects. These data, often in disparate formats, must be integrated into a common format that allows all agencies the opportunity to assess invasive carp monitoring, control, and removal efforts. Ensuring the interoperability of these datasets allows for their use in various analyzes and modeling efforts. Implementing an interoperable data management framework provides the mechanisms for end users to find and use integrated data. Integrating data for use in modeling and analysis furthers the partnership’s collective understanding of bigheaded carp life history, distribution, and movement and can be used to facilitate adaptive management actions (e.g., directing monitoring, sampling, and removal efforts, assessing invasive carp abundance to support modeling efforts, informing deployment of control actions, etc.). An effective data management strategy will streamline the data update process, providing all agencies with timely data and analyses in support of informed decision-making processes.

Illinois, Iowa, Minnesota, Missouri, Wisconsin

Visualizing proximity of non-native species to protected areas of the United States—A proximity visualization tool for BISON

The Proximity Visualization Tool is a simple lightweight tool that can be placed on web pages that allows users to identify non-native species near Department of Interior lands. The tool works by accessing the more than 400 million species occurrence records in the Biodiversity Information Serving Our Nation (BISON) database using the BISON Application Programming Interface (API).

Fact Sheet

USGS Illinois River monitoring and evaluation

Asian carp monitoring and contract removal will continue throughout the Upper Illinois Waterway system as needed for adaptive management to mitigate, control, and contain Asian carp. Compiling data from monitoring and removal efforts into a centralized database (Illinois River Catch Database application) facilitates data standardization, quality, accessibility, sharing, and analysis to aid in Asian carp removal efforts, evaluations of management actions, and modeling efforts (e.g., SEACarP model). Data summarization, visualization, and modeling supports a better understanding of bigheaded carp life history, behavior, and habitat use. Integrating Asian carp-related data and analyses into decision support tools and products aids in applying control and containment methods in an informed and transparent manner (e.g., improved efficiencies in implementations of the Unified Method, inform targeted removal efforts or deterrent deployments in key locations based on preferential benthic characteristics and environmental conditions).

Illinois

USGS Telemetry Project

Telemetry of acoustically tagged bigheaded carp (i.e., bighead carp Hypophthalmichthys nobilis and silver carp H. molitrix ) and surrogate fish species has become an invaluable tool in management for these species in the upper Illinois Waterway Systems (i.e., upper Illinois River, lower Des Plaines River, and Chicago Area Waterway System). For example, movement probabilities between adjacent navigation pools need to be estimated to parameterize the Spatially Explicit Asian Carp Population Model (SEAcarP). SEAcarP is a population model used in scenario planning by the Monitoring and Response Workgroup (MRWG) to evaluate alternative management actions. These movement probabilities are estimated from the telemetry data obtained from a longitudinal network of strategically placed receivers that detect bigheaded carp that have been implanted with acoustic transmitters. In addition, fish removal by contracted fishers has become the primary method of controlling bigheaded carp in the upper Illinois and lower Des Plaines Rivers. Variable patterns in bigheaded carp distribution, habitat, and movement, influenced by seasonal and environmental conditions, make targeting bigheaded carp for removal and containment challenging and costly. Understanding these movement patterns for bigheaded carp through modeling and real-time telemetry applications informs removal efforts and facilitates monitoring and contingency actions based on fish movements. To develop a better understanding of fish movement dynamics to meet management objectives, an existing network of real-time and data-logging acoustic receivers in the upper Illinois Waterway Systems is collaboratively managed by a multi-agency team (see Participating Agencies section above). A Telemetry Workgroup has been established by the MRWG to ensure that the multi-agency telemetry efforts are coordinated to efficiently and effectively meet the MRWG goals. This workgroup plans and executes the placement of receivers, tagging of bigheaded carp with acoustic tags, and management of the telemetry data. Three primary objectives to meet MRWG goals identified by the Telemetry Workgroup included (1) development of a common standardized telemetry database with visualization and analysis tools, (2) transitioning from Program MARK (http://www.phidot.org/software/mark/) to a custom Bayesian multi-state model for estimating movement probabilities needed for SEAcarP and (3) deploying, maintaining, and serving data from real-time acoustic receivers to inform contingency planning and fish removal. A telemetry database and visualization tools (FishTracks) will facilitate standardization, archiving, sharing, quality assurance, visualization and analysis of the telemetry data needed for management. Modifications and additions to FishTracks will facilitate more problem-free use of the database and associated applications, as well as useful extraction of information to meet management goals. The transition to a custom Bayesian multi-state model to estimate movement probabilities will support more efficient, effective, and robust population modeling with SEAcarP by overcoming short comings of Program MARK for this purpose. These shortcomings include lack of customizability and extensibility, problems of singularities and poor-convergence, software crashes, parameter exclusion from models, an inability to consistently generate estimates of movement probability, and a lack of uncertainty estimates for movement probabilities. A real-time receiver network that is maintained and tested annually will ensure reliability and accuracy of the real-time alerts to bigheaded carp movements that can be used by management to plan contingency actions.

Illinois

Patterns of mercury and selenium exposure in Minnesota common loons

Common loons ( Gavia immer ) are at risk of elevated dietary mercury (Hg) exposure in portions of their breeding range. To assess the level of risk among loons in Minnesota (USA), we investigated loon blood Hg concentrations in breeding lakes across Minnesota. Loon blood Hg concentrations were regressed on predicted Hg concentrations in standardized 12‐cm whole‐organism yellow perch ( Perca flavescens ), based on fish Hg records from Minnesota lakes, using the US Geological Survey National Descriptive Model for Mercury in Fish. A linear model, incorporating common loon sex, age, body mass, and log‐transformed standardized perch Hg concentration representative of each study lake, was associated with 83% of the variability in observed common loon blood Hg concentrations. Loon blood Hg concentration was positively related to standardized perch Hg concentrations; juvenile loons had lower blood Hg concentrations than adult females, and blood Hg concentrations of juveniles increased with body mass. Blood Hg concentrations of all adult common loons and associated standardized prey Hg for all loon capture lakes included in the study were well below proposed thresholds for adverse effects on loon behavior, physiology, survival, and reproductive success. The fish Hg modeling approach provided insights into spatial patterns of dietary Hg exposure risk to common loons across Minnesota. We also determined that loon blood selenium (Se) concentrations were positively correlated with Hg concentration. Average common loon blood Se concentrations exceeded the published provisional threshold.

Environmental Toxicology and Chemistry