Download SeaFlow data v1

Zenodo available at Simons CMAP

The data set consists of SeaFlow-based cell abundance, cell size (equivalent spherical diameter), cellular carbon content and total carbon biomass for picophytoplankton populations, namely the cyanobacteria Prochlorococcus, Synechococcus and small-sized Crocosphaera (2-5 um), and picoeukayotes phytoplankton and nanophytoplankton (2-5 μm ESD), collected during oceanographic cruises since 2010 in the North Pacific Ocean. See data description at Scientifc Data: Nature Publishing Group for more information.

Computational Flow Cytometry Analysis of Marine Phytoplankton

Since 2010, the shipboard underway cytometer SeaFlow has been operated for 14,000 hours across 140,000 km of ocean, collecting over 300,000 samples in surface waters.

Meet the Team

Principal Investigators


François Ribalet

Principal Research Scientist

Oceanography, Plankton Ecology, Flow Cytometry


E Virginia Armbrust


Phytoplankton, Oceanography



Annette Hynes

Research Scientist

Phytoplankton, Ecology, Diversity, Mathematical Modeling


Chris Berthiaume

Software Developer

Compute Infrastructure, Software Analysis Tools, Reproducible Research


Kelsy Cain

Research Assistant

Flow cytometry, Bacteria, Phytoplankton



Jordan Winter

Undergraduate student


Kristof Glauninger

PhD Candidate in Statistics

Error Estimation, Causal Inference


SeaFlow v1

Continuous shipboard flow cytometer

Meet the instrument

The SeaFlow instrument is a shipboard underway flow cytometer that provides continuous multi-parameter single particle measurements without the need for clean water. The instrument eliminates the traditional need for a sheath fluid by employing a unique optical system that relies on three photodetectors to create a virtual core in the sample stream within which the properties of particles are accurately measured. In this way, the instrument is able to collect the equivalent of 1 sample every 3 minutes or every 1 km (for a ship moving at 10 knots) from the ship’s flow-through seawater system. See article for more information.”

The SeaFlow instrument was developed by Jarred Swalwell at the University of Washington, feel free to contact him with any questions related to the SeaFlow instrument and technologies.

Recent Publications

A kernel-based change detection method to map shifts in phytoplankton communities measured by flow cytometry

Automated, ship-board flow cytometers provide high-resolution maps of phytoplankton composition over large swaths of the world’s …

Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities

The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular …

Diel oscillations in the feeding activity of heterotrophic and mixotrophic nanoplankton in the North Pacific Subtropical Gyre

Daily oscillations in photosynthetically active radiation strongly influence the timing of metabolic processes in picocyanobacteria, …


Matrix Population Model

A size-structured matrix population model to estimate rates of cell division, carbon fixation and carbon loss in phytoplankton measured by flow cytyometry.


A Kernel-based change detection method to map shifts in phytoplankton communities measured by flow cytometry. In this project in collaboration with Dr.


Popcycle is an R package that offers a reproducible approach to process, calibrate and curate flow cytometry data measured by SeaFlow.


A Python package for SeaFlow flow cytometer data, available on Gihub. Seaflowpy A Python package for SeaFlow flow cytometer data.


  • Benjamin Hall Interdisciplinary Research Building, Seattle, WA 98105
  • Center for Environmental Genomics - 3rd floor