Long term, high-resolution measurements of phytoplankton abundance and cell properties: Imaging FlowCytobot
A fundamental understanding of the interaction between physical and biological factors that regulate plankton species composition requires, first of all, detailed and sustained observations. Only now is it becoming possible to acquire these types of observations, as we develop and deploy instruments that can continuously monitor individual organisms in the ocean. With the goal of better understanding how coastal plankton communities are regulated, we designed and built an in-situ autonomous submersible imaging flow cytometer at WHOI, Imaging FlowCytobot (IFCB), which is now commercially available. IFCB effectively samples larger phytoplankton cells (such as diatom and dinoflagellate cells 10 to 150 microns in size) which often dominate the phytoplankton in coastal waters. These larger cells often have recognizable shapes, which enabled us to develop automated image analysis and classification based on Random Forest classification software which allows enumeration of more than 53 categories of plankton. IFCB uses a combination of video and flow cytometric technology to both capture images of organisms for identification and measure chlorophyll fluorescence and light scattering associated with each image. The measurements of chlorophyll fluorescence allow us to more efficiently analyze phytoplankton cells by triggering on chlorophyll-containing particles.
Since 2006, IFCB has been successfully deployed at 4m depth at the Martha’s Vineyard Coastal Observatory (MVCO) forming a nearly continuous time series. The instrument is able to operate unattended for months at a time, using power and communications from a shore lab for real-time operation, monitoring and data download. It has been successfully deployed for more than 10 years at the MVCO Offshore Tower alongside FlowCytobot, which was also developed at WHOI, to allow for continuous long-term observations of plankton community structure over a wide range of cell sizes and types. The continuous high-resolution (hourly) measurements provide information on a variety of temporal scales, including inter-annual and seasonal patterns in abundance of different types of phytoplankton, and (for some cell types) daily estimates of cell growth rate (from diel patterns in cell size resulting from photosynthesis and cell division). Imaging FlowCytobot IFCB provides a powerful new approach for investigating plankton dynamics in coastal waters.
The success of the original IFCB, designed and built at WHOI, showed that it would be very beneficial to have the technology available to researchers and resource managers around the US and the world. The IFCB design is now licensed with McLane Research Laboratories, where we worked closely with the engineers to make sure an optimized, high-quality version is now commercially available.
The IFCB Data Dashboard is a project developed to make Imaging FlowCytobot images available over the web. Near real time image data and the complete archive are accessible for browse and download at the dashboard. The homepage displays the latest real time data from Martha's Vineyard Coastal Observatory (MVCO) in UTC time. It is possible to navigate to past data using the timeline at the top of the screen. Click on an image to see a close-up on the right of the screen. For more information about the dashboard, including user's guide, click here.
The WHOI-Plankton wiki documents example images from categories used to classify data from the Martha's Vineyard Coastal Observatory (MVCO) that correspond to the published annotation set in WHOI-Plankton. This subset of images is part of a much larger data set of over 700 million images collected by IFCB at the MVCO starting in 2006 and continuing to the present. The WHOI-Plankton wiki is not meant as a definitive taxonomic guide. Additional categories can be found in the "expanded version", which is not yet part of the published WHOI-Plankton annotation set.
For more information about the published annotated data set used for developing and evaluating classification methods, go to: https://github.com/hsosik/WHOI-Plankton