Gradients2-MGL1704-IFCB-ESD_2020-04-01_v1.0

Cruise: Gradients 2, MGL1704

Project Name: Simons Foundation, Gradient NPSG

Dataset Description:

The Imaging FlowCytoBot (IFCB) is an in situ automated imaging flow cytometer that generates images of particles suspended in seawater, in this case from the underway uncontaminated seawater system.  The IFCB uses a recycled sheath fluid (0.2 µm filtered seawater) to align and drive particles individually towards a light source (red laser, 4.5 mW) in order to detect and identify single or colonial cells using a combination of optical properties (red fluorescence and light scattering intensities) and high resolution images (3.2 pixels per microns) by a mounted camera. Both optical properties are used to trigger targeted image acquisition of suspended particles in the size range <4 to 100 μm. The instrument continuously samples from ~5 ml aliquots from the intake, and processes all particles contained in that volume for the next 20 minutes.  Images corresponding to the "Sample" variable are available on the cruise's dashboard (http://ifcb-data.soest.hawaii.edu/IFCB_NPTZ).  This dataset is the size, or equivalent spherical diameter, of imaged cells by genus. Equivalent spherical Diameter (ESD) is converted from the cell's biovolume (BV) assuming a spherical cell, according to the formula: ESD=[(6XBV)/(PI)]^(1/3). We use a series of matlab scripts provided by the H. Sosik (https://github.com/hsosik/ifcb-analysis/wiki) to outline cells and extract  their corresponding biovolume using a pixels-distance map algorithm (Moberg and Sosik: 2012, doi:10.4319/lom.2012.10.278) and a fixed conversion factor (3.2 px/µm).