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- Publication: Unpublished
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- Authors: Clement Garcia & Paul McIlwaine (Cefas)
- Tool contributors: N/A
- Project general coordinator: Jan Marcin Węsławski
- Project Scientific manager: Julie Bremner
- Project manager: Gary Saggers (Cefas), Joanna Piwowarczyk (IOPAN)
- Abràmoff et al. (2004). Image processing with ImageJ. Biophotonics International, 11: 36-42.
- Cranford et al. (2011). Bivalve filter feeding: variability and limits of the aquaculture biofilter. In Shumway, S.E. ed. Shellfish aquaculture and the environment. John Wiley & Sons.
- Gorsky et al. Digital zooplankton image analysis using the ZooScan integrated system. Journal of Plankton Research 32: 285-303.
- Jones et al. (1992). Gill dimensions, water pumping rate and body size in the mussel Mytilus edulis. Journal of Experimental Marine Biology and Ecology 155: 213 – 237.
- Picheral et al. (2017). EcoTaxa, a tool for the taxonomic classification of images: http://ecotaxa.obs-vlfr.fr
- Name: Clement Garcia
- Organization: Cefas
- Email: clement.garcia@cefas.gov.uk
Deriving Faunal Function from Benthic Samples Using the ZooScan – an Automated Imaging System
The traditional approach for assessing biomass of benthic macrofauna in marine seabed monitoring is to identify taxa and record taxa-level biomass as blotted wet weight. However, this method fails to incorporate individual-based measurements, leading to a lack of insight into size structure variability within species. We adapted and tested a method to derive individual-based measurement for benthic invertebrate using a method developed for automated zooplankton assessment, the wet bed scanner (Hydroptic© ZooScan), associated with the processing software, and routines within the Ecotaxa online database for tidying and storing the images. The approach is best suited to small, robust taxa which can readily be scanned but traditional methods of measurement for larger individual or species are compatible with outputs of the tool. MARBEFES has defined a protocol that 1) demonstrated the utility of the combination of ZooScan and Ecotaxa in collecting individual based size measures from benthic macrofaunal samples to allow individual biomass measures to be determined and 2) collated information on size and biomass measures from intact specimens to aid the development of appropriate ‘size’ – biomass relationships for benthic taxa (e.g., by species, by major taxonomic group or by generalised body shape). Body-mass (by identified taxon) is apportioned to each scanned individual relative to its ‘size’ (as described by the 2D surface area in the scanned image). Individual biomass is determined by calculating a value for biomass per pixel (with the known total taxa-level biomass) and then apportioning the recorded biomass relative to body size – by multiplying the biomass per pixel value by the individual total pixel area. In addition, due to the physiological link between body-mass or length and various metabolic rates (e.g., respiration, feeding), the information collated will be more easily translatable into estimates of processes and functions using allometric relationships published in the literature.
The ZooScan tool generates data and so has no data pre-requisites. Benthic macroinvertebrates are routinely stored for several years, preserved in an ethanol mixture, following the completion of reports and outputs associated with the original purpose for their collection. These faunal residues are ideally suited for application of the ZooScan protocol allowing for collection of additional information (at the individual level for each taxon). This tool is best suited to small, robust taxa as those taxa generally remain intact during the extraction and identification process. However, the tool allows for definition of size-to-biomass relationships and “reconstruction” individuals offering promising avenue for accurately estimating fragile taxa.
- Availability / URL: Protocol developed as a report, not currently published. Can make it available on my Github if that’s helpful
