{"id":1113,"date":"2021-04-22T10:38:00","date_gmt":"2021-04-22T10:38:00","guid":{"rendered":"https:\/\/www.plant-phenomics.ac.uk\/?p=1113"},"modified":"2022-04-06T10:39:41","modified_gmt":"2022-04-06T10:39:41","slug":"development-of-an-image-analysis-pipeline-to-estimate-sphagnum-colony-density-in-the-field","status":"publish","type":"post","link":"https:\/\/www.plant-phenomics.ac.uk\/index.php\/2021\/04\/22\/development-of-an-image-analysis-pipeline-to-estimate-sphagnum-colony-density-in-the-field\/","title":{"rendered":"Development of an Image Analysis Pipeline to Estimate Sphagnum Colony Density in the Field"},"content":{"rendered":"\n<p><i>Sphagnum<\/i> peatmosses play an important part in water table management of many peatland ecosystems. Keeping the ecosystem saturated, they slow the breakdown of organic matter and release of greenhouse gases, facilitating peatland&#8217;s function as a carbon sink rather than a carbon source. Although peatland monitoring and restoration programs have increased recently, there are few tools to quantify traits that <i>Sphagnum<\/i> species display in their ecosystems. Colony density is often described as an important determinant in the establishment and performance in <i>Sphagnum<\/i> but detailed evidence for this is limited. In this study, we describe an image analysis pipeline that accurately annotates <i>Sphagnum<\/i> capitula and estimates plant density using open access computer vision packages. The pipeline was validated using images of different <i>Sphagnum<\/i> species growing in different habitats, taken on different days and with different smartphones. The developed pipeline achieves high accuracy scores, and we demonstrate its utility by estimating colony densities in the field and detecting intra and inter-specific colony densities and their relationship with habitat. This tool will enable ecologists and conservationists to rapidly acquire accurate estimates of <i>Sphagnum<\/i> density in the field without the need of specialised equipment.<\/p>\n<p><span class=\"identifier doi\"><span class=\"id-label\">DOI: <\/span> <a class=\"id-link\" href=\"https:\/\/doi.org\/10.3390\/plants10050840\" target=\"_blank\" rel=\"noopener\" data-ga-category=\"full_text\" data-ga-action=\"DOI\"> 10.3390\/plants10050840 <\/a> <\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Sphagnum peatmosses play an important part in water table management of many peatland ecosystems. Keeping the ecosystem saturated, they slow the breakdown of organic matter and release of greenhouse gases, &#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"ngg_post_thumbnail":0,"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[3],"tags":[],"class_list":["post-1113","post","type-post","status-publish","format-standard","hentry","category-publication"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Development of an Image Analysis Pipeline to Estimate Sphagnum Colony Density in the Field &#8212; National Plant Phenomics Centre<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.plant-phenomics.ac.uk\/index.php\/2021\/04\/22\/development-of-an-image-analysis-pipeline-to-estimate-sphagnum-colony-density-in-the-field\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Development of an Image Analysis Pipeline to Estimate Sphagnum Colony Density in the Field &#8212; National Plant Phenomics Centre\" \/>\n<meta property=\"og:description\" content=\"Sphagnum peatmosses play an important part in water table management of many peatland ecosystems. 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