Developing Rapid Remote Assessments of Oyster Reef Health and Biodiversity (2019-2020)

This Bass Connections project team aimed to develop, assess and improve tools for coastal conservation practices. This team had three overall focuses.

Using two-dimensional, georeferenced UAV imagery, the team created 3-D renderings of oyster reefs through a process called Structure from Motion, in which they used the software package Pix4D to identify unique pixel clusters across multiple images, examine the relative positions of these unique pixel clusters, and output an orthomosaic of each reef.

In addition, the team deployed a hydrophone on three different oyster reefs – one recently constructed reef, one reef that was constructed over a decade ago, and a natural reef. They quantified different qualities of the recorded soundscape, such as the intensity and frequency distribution of the sound. By comparing the soundscapes to the biological communities measured by using quadrats and ARMS, and to the habitat structure measured using UAVs, they developed passive acoustic monitoring proxies to assess reef health and biodiversity.

The team also conducted a social survey in order to assess managers’ impressions of these innovative monitoring methodologies. Broadly, though these managers were excited about the prospect of incorporating innovative, remote technologies into their restoration and conservation efforts, many of them also flagged two central limitations: time and money.


Fall 2019 – Summer 2020

Team Outputs

Alexandra E. DiGiacomo, Walker E. Harrison, David W. Johnston, Justin T. Ridge. "Elasmobranch Use of Nearshore Estuarine Habitats Responds to Fine-Scale, Intra-Seasonal Environmental Variation: Observing Coastal Shark Density in a Temperate Estuary Utilizing Unoccupied Aircraft Systems (UAS)." 2020. Drones 4(4):74.

Alexandra E. DiGiacomo, Clara N. Bird, Virginia G. Pan, Kelly Dobroski, Claire Atkins-Davis, David W. Johnston. "Modeling Salt Marsh Vegetation Height Using Unoccupied Aircraft Systems and Structure from Motion." 2020. Remote Sens 12(14):2333. 

Tools for Conserving Coastal Ecosystems (Fortin Foundation Bass Connections Virtual Showcase 2020)

Project team site

What Are ARMS?

This Team in the News

Meet the Members of the 2019-2020 Bass Connections Student Advisory Council

See earlier related team, Developing Rapid, Cost-effective Methods for Evaluating Coastal Biodiversity and Resilience (2018-2019).


Image: Oyster Reef, by Lia McLaughlin/U.S. Fish and Wildlife Service Northeast Region, public domain

Oyster reef.

Team Leaders

  • Jason Dinh, Trinity-Biology-Ph.D. Student
  • Douglas Nowacek, Nicholas School of the Environment-Marine Science and Conservation
  • Julianna Renzi, Nicholas School of Environment-Marine Science & Conservation-Ph.D. Student
  • Justin Ridge, Nicholas School of the Environment-Marine Science and Conservation

/graduate Team Members

  • Molly Bruce, Juris Doctor, Master of Environmental Management, Coastal Environmental Management

/undergraduate Team Members

  • Eve Adelson
  • Catherine Bailey, Biology (BS), Theater Studies (AB2)
  • Melissa Baldino, Biology (BS), Environmental Sci/Policy (AB2)
  • Avery Indermaur, Environmental Sciences (BS)
  • Haynes Lynch

/yfaculty/staff Team Members

  • David Johnston, Nicholas School of the Environment-Marine Science and Conservation
  • Brian Silliman, Nicholas School of the Environment-Marine Science and Conservation