June 2025

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June 2025 | Oceanography

73

OCEAN EDUCATION

HANDS-ON POST-CALIBRATION

OF IN VIVO FLUORESCENCE USING

OPEN ACCESS DATA

A GUIDED JOURNEY FROM FLUORESCENCE TO PHYTOPLANKTON BIOMASS

By Pierre Marrec, Amanda Herbst, Stace E. Beaulieu, and Susanne Menden-Deuer

PURPOSE OF ACTIVITY

The goal of this activity is to help students become acquainted

with key procedures in oceanographic data acquisition, pro­

cessing, validation, and management. These skills are learned

through using sensor-based underway fluorescence and dis­

crete chlorophyll a (Chl-a) measurements. By encompassing a

wide range of skills necessary for oceanographic research—from

at-sea operations, to precise lab work, to data management—

this activity showcases the diverse learning opportunities that

oceanography offers for educating science and engineering stu­

dents. This activity highlights the critical, yet often overlooked,

steps required to process and validate high-resolution data from

autonomous sensors, such as those mounted on ocean observ­

ing platforms (e.g., research vessels, moorings, gliders), before

utilizing them to investigate relevant oceanographic processes. It

offers students the opportunity to develop proficiency in the var­

ious steps of managing open-access data from diverse sources,

while also introducing them to the principles of findable, acces­

sible, interoperable, and reusable (FAIR) data practices in sci­

entific research (Wilkinson et al., 2016). Additionally, it famil­

iarizes them with the requirements of the Open-Source Science

Initiative (OSSI) for open, transparent, accessible, inclusive,

and reproducible science. Emerging mandates that make fund­

ing availability contingent on open data managing and sharing

procedures make the skills delivered in this activity essential for

researchers and technicians (Kaiser and Brainard, 2023).

AUDIENCE

This manuscript is designed for instructors, serving as a guide

to the various steps involved in sharing this activity with stu­

dents. The intended audience for this project is undergraduates

enrolled in advanced environmental science courses. However,

the activity could be adapted for a less advanced student audi­

ence by focusing only on a subset of the activities (e.g., plot­

ting and interpreting the data). Moreover, the activity is thor­

oughly documented, and all necessary data are provided in

the format required for sequential steps so that instructors can

choose the appropriate starting points for their students. This lab

could also be modified to suit students in a statistics or data sci­

ence course. The project was developed with coauthor Amanda

Herbst as part of her SURFO (Summer Undergraduate Research

Fellowship in Oceanography) REU (Research Experience for

Undergraduates) at the University of Rhode Island Graduate

School of Oceanography (URI-GSO). All the fundamental steps

of this project can be completed using basic computer resources

(e.g.,  Open Office Calc, Microsoft Excel) and do not require

students to have programming skills. However, it also offers

the opportunity for students to enhance their proficiencies in

coding (e.g., using R, MATLAB, or Python) by automating and

streamlining data management steps. Additionally, this project

could serve as a self-study guide for advanced students who may

not yet be familiar with the procedures and importance of data

quality control and management.

APPROACH

The approach taken in this laboratory is to familiarize students

with the essential steps for accessing, validating, sharing, and

interpreting phytoplankton biomass inferred from the fluores­

cence signal acquired by sensors mounted on different types

of ocean observing platforms. The laboratory session includes

two main activities: (1) accessing both underway fluorescence

and discrete Chl-a measurements extracted from samples col­

lected during oceanographic cruises, and (2) post-calibrating

the fluorescence data with discrete Chl-a concentrations, inter­

preting the results, and publishing post-calibrated data. These

activities were conducted as part of the OCG561 – Biological

Oceanography Laboratory course at the University of Rhode

Island’s Graduate School of Oceanography, taught by coauthor

Menden-Deuer. The graduate students enrolled in this course

came from diverse backgrounds in oceanography, including

physical, chemical, geological, and biological disciplines. The

time allocations provided are approximate, and we encourage

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