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