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In this paper, we test a pose estimation approach based on Deep Learning capable of accurately placing point labels to identify key locations on specimen images. We then apply the approach to two distinct challenges that each requires identification of key features in a 2D image: (i) identifying body region-specific plumage colouration on avian specimens and (ii) measuring morphometric shape variation in <jats:italic>Littorina<\/jats:italic> snail shells. For the avian dataset, 95% of images are correctly labelled and colour measurements derived from these predicted points are highly correlated with human-based measurements. For the <jats:italic>Littorina<\/jats:italic> dataset, more than 95% of landmarks were accurately placed relative to expert-labelled landmarks and predicted landmarks reliably captured shape variation between two distinct shell ecotypes (\u2018crab\u2019 vs \u2018wave\u2019). Overall, our study shows that pose estimation based on Deep Learning can generate high-quality and high-throughput point-based measurements for digitised image-based biodiversity datasets and could mark a step change in the mobilisation of such data. We also provide general guidelines for using pose estimation methods on large-scale biological datasets.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010933","type":"journal-article","created":{"date-parts":[[2023,2,22]],"date-time":"2023-02-22T18:37:42Z","timestamp":1677091062000},"page":"e1010933","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["Using pose estimation to identify regions and points on natural history specimens"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3464-7526","authenticated-orcid":true,"given":"Yichen","family":"He","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher R.","family":"Cooney","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3179-0263","authenticated-orcid":true,"given":"Steve","family":"Maddock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1982-6051","authenticated-orcid":true,"given":"Gavin H.","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,2,22]]},"reference":[{"issue":"6215","key":"pcbi.1010933.ref001","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.1126\/science.1253451","article-title":"Whole-genome analyses resolve early branches in the tree of life of modern birds","volume":"346","author":"ED Jarvis","year":"2014","journal-title":"Science"},{"issue":"6215","key":"pcbi.1010933.ref002","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1126\/science.1251385","article-title":"Comparative genomics reveals insights into avian genome evolution and adaptation","volume":"346","author":"G Zhang","year":"2014","journal-title":"Science"},{"issue":"1","key":"pcbi.1010933.ref003","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1513\/pats.200607-142JG","article-title":"Computational Approaches to Phenotyping: High-Throughput Phenomics.","volume":"4","author":"YA Lussier","year":"2007","journal-title":"Proceedings of the American Thoracic Society"},{"key":"pcbi.1010933.ref004","doi-asserted-by":"crossref","DOI":"10.3389\/fevo.2021.642774","article-title":"Computer Vision, Machine Learning, and the Promise of Phenomics in Ecology and Evolutionary Biology.","volume":"9","author":"MD L\u00fcrig","year":"2021","journal-title":"Frontiers in Ecology and Evolution"},{"issue":"2","key":"pcbi.1010933.ref005","doi-asserted-by":"crossref","first-page":"81","DOI":"10.17161\/bi.v7i2.3991","article-title":"Approaches to estimating the universe of natural history collections data","volume":"7","author":"A. 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