Zooplankton abundance data derived from the Plankton Imager system from the Western English Channel and Eastern Irish Sea from 2016 to 2019

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The Plankton Imager is a high-speed colour line scan-based imaging instrument connected to the ships water supply and can take images of all zooplankton of size above 20 microns passing through a cell at a 27 litre per minute flow rate. The flow cell is 25mm brass tube that has two quartz optical windows halfway along its length. The flow cell at the windows is square, with the same cross-sectional area as the 25mm tube. A Basler 2048-70kc camera, sampling at 70K lines per second, images the water running through the flow cell. The flow rate is monitored by a Bell electro-magnetic flow meter. Colour images are captured using an EPIX E4 frame store. RGB composite images are constructed by joining consecutive lines together, thresholding and extracting a region of interest ROI, or vignette, that is saved to hard drive as a TIF file. Raw images are stored to maximize dynamic range of the captured particles. These are converted to 8-bit resolution through a process of scaling and conversion from 12 to 8-bit resolution, for viewing and for subsequent processing. Due to operational requirements (continuous image processing while maintaining manageable file-size), only those particles within the mesozooplankton range 200 microns – 2cm were processed and saved. In order to reproduce the sub-sampling procedure used for physical samples (as collected with a ring net), random images were extracted until each sample contained approximately 200 mesozooplankton individuals and then identified using the with the Plankton Imager software to derive taxon groupings which were then validated by an expert taxonomist manually. The following paper describes the Plankton Imager system in further detail. Pitois *et al.* (2018). Comparison of a Cost-Effective Integrated Plankton Sampling and Imaging Instrument with Traditional Systems for Mesozooplankton Sampling in the Celtic Sea. Frontiers in Marine Science. 5. 10.3389/fmars.2018.00005.