Pilot PlanktoScope for Climate Change Research (2022-2023)


Microbes are core components of the ecology and functioning of all ecosystems, including plants, animals and engineered systems. While there is a burgeoning understanding of the abundance and diversity of microbial communities, comparatively little work has focused on the impact of “grazers” (small plankton that eat microbes) on their mortality.

The importance of grazers is broadly recognized, but there remain significant technological challenges to characterizing and quantifying these organisms. Developing a better understanding of these plankton has important implications for the sustainable production of food, feed and fuel.

Project Description

This project team will fabricate and test a beta version of a “planktoscope” that has the ability to automatically take pictures of and identify larger plankton (including zooplankton/predators) from marine samples. 

In the first phase of the project, the team will work in the Co-Lab on campus in Durham to build the device using open source instructions. This initial part of the project will include reviewing the long-term goals of the project (characterizing grazers in natural and engineered communities), assessing current hardware and software design suggestions in the context of goals and hardware availability, and making recommendations for any initial modifications. After developing an engineering plan, the team will build the first version of the planktoscope. 

In the second phase of the project, the beta design will be evaluated at the Duke Marine Lab in Beaufort for two applications relevant to energy and environment: a coastal marine time series with weekly microbiome sampling; and marine microalgae ponds for sustainable production of food, feed and fuel. 

For the first system, sampling will occur as part of the Pivers Island Coastal Observatory and will leverage ongoing weekly time-series monitoring of coastal waters. The second sampling will occur as part of the Marine Algae Industrialization Consortium, where marine microalgae are being grown at commercially relevant scales. Both systems have unique characteristics — the first is a relatively dilute environment where diversity of plankton is expected to be high; the second a highly concentrated environment where diversity is expected to be low. The primary goal of this broad testing is to determine the effectiveness of identifying and quantifying diverse types of plankton, and to determine the robustness of the instrument. 

After initial testing, the team will brainstorm and suggest design changes. If feasible, these alternations will be made onsite, and the engineering cycle iterated. Larger changes will be compiled for the final evaluation and future design recommendation report.

Anticipated Outputs

Physical device (prototype) of planktoscope; data/results from testing in a natural marine ecosystem and an engineered system; reports on initial findings from applications and recommendations for improvements for long-term monitoring/remote observations; data for future research and grant applications

Student Opportunities

Ideally, this project team will be comprised of 2-3 graduate students and 4-6 undergraduate students from a variety of backgrounds (e.g., prospective microbiologists, engineers, computational biologists, marine scientists) with a common interest in using technology to solve environmental (including sustainable energy) problems. An ideal makeup for the team would include one or more members with experience in the following categories: computational (R, Python, MATLAB, image analysis); environmental (field sampling); ecology (computational/data analysis, microbial ecology); and engineering (electronics, fabrication).

Each major component of the project will be assigned a lead student and contributor/team lead. The team will meet weekly to address a theme or discussion point. All meetings will be Zoom-enabled so that both Durham and Beaufort members can contribute. Additional interactions will occur using Microsoft Teams. Tasks will be divided among members on a consensus and mutually agreeable basis. 

All students will be exposed to a variety of environmental sciences and engineering. Students will work with faculty from across the university including in the Nicholas School of the Environment, Pratt School of Engineering and Trinity College of Arts & Sciences. Students will gain tangible skills in engineering, design, environmental analysis and problem-solving. 

A final report with design recommendations may be refined into a patent, if warranted. Graduate students will be able to develop leadership skills, while also getting exposure and training in a cutting-edge field. Students and leaders will be exposed to a unique learning opportunity and experience disciplinary exchange. All will enhance their teamwork skills.

Junyao Gu will serve as project manager.


Fall 2022 – Spring 2023

  • Fall 2022: Finalize project goals/products and agree upon timeline; fabricate planktoscope; take part in weekly meetings documenting progress/setbacks
  • Spring 2023: Test planktoscope using two sites (natural ocean and engineered microalgae system); develop recommendations for future design iterations


Academic credit available for fall and spring semesters


Image: Zooplankton Sampling, by NOAA Great Lakes Environmental Research Laboratory, licensed under CC BY-SA 2.0

Zooplankton sampling.

Team Leaders

  • Junyao Gu, Nicholas School of the Environment–Marine Science and Conservation–Ph.D. Student
  • Zackary Johnson, Nicholas School of the Environment-Marine Science and Conservation
  • Douglas Nowacek, Nicholas School of the Environment-Marine Science and Conservation

/graduate Team Members

  • Patrick Gray, Marine Sci & Conservation-PHD

/yfaculty/staff Team Members

  • Sara Blinebry, Nicholas School of the Environment-Marine Science and Conservation
  • Nicolas Cassar, Nicholas School of the Environment-Earth and Climate Sciences
  • Julian Dale, Nicholas School of the Environment-Marine Science and Conservation
  • Claudia Gunsch, Pratt School of Engineering-Civil & Environmental Engineering
  • Dana Hunt, Nicholas School of the Environment-Marine Science and Conservation
  • David Johnston, Nicholas School of the Environment-Marine Science and Conservation