{"id":955,"date":"2026-02-09T13:11:52","date_gmt":"2026-02-09T12:11:52","guid":{"rendered":"https:\/\/marbefes.lifewatch.eu\/?post_type=project&#038;p=955"},"modified":"2026-03-03T15:54:16","modified_gmt":"2026-03-03T14:54:16","slug":"51_ecological-traits-animal-imager-zooscan","status":"publish","type":"project","link":"https:\/\/marbefes.lifewatch.eu\/index.php\/project\/51_ecological-traits-animal-imager-zooscan\/","title":{"rendered":"51_Deriving faunal function from Zooscan imagery"},"content":{"rendered":"<p>[et_pb_section fb_built=&#8221;1&#8243; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; custom_margin=&#8221;-51px|||||&#8221; custom_padding=&#8221;0px|||||&#8221; global_colors_info=&#8221;{}&#8221;][et_pb_row column_structure=&#8221;1_2,1_2&#8243; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221;][et_pb_column type=&#8221;1_2&#8243; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221;][et_pb_gallery gallery_ids=&#8221;850&#8243; fullwidth=&#8221;on&#8221; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; border_width_all=&#8221;4px&#8221; global_colors_info=&#8221;{}&#8221;][\/et_pb_gallery][et_pb_tabs _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221;][et_pb_tab title=&#8221;Tools details&#8221; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221;]<\/p>\n<ul>\n<li><strong><span>Category:<\/span><\/strong><\/li>\n<li><strong><span>Subcategory:<\/span><\/strong><\/li>\n<li><strong><span>Tool Type\u00a0:<\/span><\/strong><\/li>\n<li><strong><span>Input data:<\/span><\/strong><\/li>\n<li><strong><span>Output:<\/span><\/strong><\/li>\n<li><strong><span>Target users:<\/span><\/strong><\/li>\n<li><strong><span>Location tested:\u00a0<\/span><\/strong><\/li>\n<\/ul>\n<p>[\/et_pb_tab][et_pb_tab title=&#8221;Technical details&#8221; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221;]<\/p>\n<ul>\n<li>Version:\u00a0<\/li>\n<li>Publication: Unpublished<\/li>\n<li>Rights:\u00a0<\/li>\n<\/ul>\n<ul><\/ul>\n<p>[\/et_pb_tab][et_pb_tab title=&#8221;Developer information&#8221; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221;]<\/p>\n<ul>\n<li>Authors: Clement Garcia &amp; Paul McIlwaine (Cefas)<\/li>\n<li>Tool contributors: N\/A<\/li>\n<li>Project general coordinator: Jan Marcin W\u0119s\u0142awski<\/li>\n<li>Project Scientific manager:\u00a0Julie Bremner<\/li>\n<li>Project manager:\u00a0Gary Saggers (Cefas), Joanna Piwowarczyk (IOPAN)<\/li>\n<\/ul>\n<p>[\/et_pb_tab][et_pb_tab title=&#8221;Citation&#8221; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221;]<\/p>\n<ul>\n<li><u>Abr\u00e0moff <em>et al.<\/em> (2004).<\/u> Image processing with ImageJ. <em>Biophotonics International<\/em>, 11: 36-42.<\/li>\n<li><u>Cranford<em> et al.<\/em> <\/u><u>(2011).<\/u> Bivalve filter feeding: variability and limits of the aquaculture biofilter. In Shumway, S.E. ed. <em>Shellfish aquaculture and the environment<\/em>. John Wiley &amp; Sons.<\/li>\n<li><u>Gorsky <em>et al.<\/em><\/u> Digital zooplankton image analysis using the ZooScan integrated system. <em>Journal of Plankton Research<\/em> 32: 285-303.<\/li>\n<li><u>Jones <em>et al.<\/em> (1992).<\/u> Gill dimensions, water pumping rate and body size in the mussel <em>Mytilus edulis<\/em>. <em>Journal of Experimental Marine Biology and Ecology<\/em> 155: 213 \u2013 237.<\/li>\n<li><u>Picheral <em>et al.<\/em> (2017).<\/u> EcoTaxa, a tool for the taxonomic classification of images: <span><a href=\"http:\/\/ecotaxa.obs-vlfr.fr\">http:\/\/ecotaxa.obs-vlfr.fr<\/a><\/span><\/li>\n<\/ul>\n<p>[\/et_pb_tab][et_pb_tab title=&#8221;Contact&#8221; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221;]<\/p>\n<ul>\n<li><strong>Name<\/strong>:\u00a0Clement Garcia<\/li>\n<li><strong>Organization<\/strong>: Cefas<\/li>\n<li><strong>Email<\/strong>: clement.garcia@cefas.gov.uk<\/li>\n<\/ul>\n<p>[\/et_pb_tab][\/et_pb_tabs][\/et_pb_column][et_pb_column type=&#8221;1_2&#8243; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221;][et_pb_text _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221;]<\/p>\n<h3><strong>Deriving Faunal Function from Benthic Samples Using the ZooScan &#8211; an Automated Imaging System<\/strong><\/h3>\n<p>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\u00a9 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 \u2018size\u2019 &#8211; 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 \u2018size\u2019 (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 &#8211; 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.<\/p>\n<p>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 \u201creconstruction\u201d individuals offering promising avenue for accurately estimating fragile taxa.<\/p>\n<p>&nbsp;<\/p>\n<ul>\n<li><strong>Availability \/ URL:<\/strong> Protocol developed as a report, not currently published. Can make it available on my Github if that\u2019s helpful<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<p>[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221; theme_builder_area=&#8221;post_content&#8221;][et_pb_column type=&#8221;4_4&#8243; _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; global_colors_info=&#8221;{}&#8221; theme_builder_area=&#8221;post_content&#8221;][et_pb_text _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; text_font=&#8221;|700|||||||&#8221; header_2_font=&#8221;|700|||||||&#8221; header_3_font=&#8221;|700|||||||&#8221; global_colors_info=&#8221;{}&#8221; theme_builder_area=&#8221;post_content&#8221;]<\/p>\n<h3>Related Tools:<\/h3>\n<p>[\/et_pb_text][et_pb_code _builder_version=&#8221;4.27.4&#8243; _module_preset=&#8221;default&#8221; custom_padding=&#8221;||5px|||&#8221; global_colors_info=&#8221;{}&#8221; theme_builder_area=&#8221;post_content&#8221;][\/et_pb_code][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"<p>ZooScan is used to derive individual size and biomass of benthic macrofauna from scanned images, overcoming limitations of traditional bulk biomass methods.<br \/>\nIt captures size-structure variability and allows individual biomass estimation from image surface area. These data support functional and metabolic ecosystem analyses through allometric relationships.<\/p>\n","protected":false},"author":1,"featured_media":51,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"categories":[38,87,68,67,59,54,51,42,43,37,108,41,50,53,95,58,66,137,86,106,129],"project_tag":[],"class_list":["post-955","project","type-project","status-publish","has-post-thumbnail","hentry","category-ecological","category-biological","category-equipment-protocol","category-instruments-activities","category-sampling-measurements","category-researchers","category-generating-understanding-data","category-biological-understanding-taxonomy","category-ecosystem-functioning-biodiversity","category-main-category","category-quantitative-analytical","category-subtopic","category-purpose","category-target-user","category-biological-samples","category-data-type","category-tool-type","category-irish-sea","category-input","category-output","category-location-tested"],"_links":{"self":[{"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/project\/955","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/comments?post=955"}],"version-history":[{"count":5,"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/project\/955\/revisions"}],"predecessor-version":[{"id":1546,"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/project\/955\/revisions\/1546"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/media\/51"}],"wp:attachment":[{"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/media?parent=955"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/categories?post=955"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/marbefes.lifewatch.eu\/index.php\/wp-json\/wp\/v2\/project_tag?post=955"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}