From paper to pixels - digitized maps of vascular plant distributions in Denmark in the early 20th century

From paper to pixels - digitized maps of vascular plant distributions in Denmark in the early 20th century | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Data Note From paper to pixels - digitized maps of vascular plant distributions in Denmark in the early 20th century Ditte Marie Christiansen, Hans Henrik Bruun, Matilda Arnell, Conny Bruun Asmussen Lange, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8277973/v2 This work is licensed under a CC BY 4.0 License Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Abstract Historic data are essential for quantifying changes in biodiversity and their drivers. Much legacy data remains undigitized in archives such as natural history museums, representing untapped resources for assessing past biodiversity patterns. In 1904, the first systematic survey of species distributions of the entire Danish flora was initiated. Most field surveys were conducted in the early 20th century. Results were published as black and white printed maps (1931–1976). We used automated georeferencing and image classification to extract data from all published maps. We present 1340 historic distribution maps of vascular plant species, subspecies and varieties in Denmark at 10 × 10 km resolution. These maps represent the Danish flora of native and archaeophyte species known at the time, except some of the most common native species. By comparison with modern distribution data, long-term increases and declines can be accurately quantified, contributing to large-scale analysis of national, European or global plant diversity changes in the modern era. historic distribution vascular plants temporal biodiversity patterns image recognition Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Full Text Additional Declarations The authors declare no competing interests. Cite Share Download PDF Status: Posted Version 2 posted You are reading this latest preprint version Show more versions Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8277973","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Data Note","associatedPublications":[],"authors":[{"id":558923404,"identity":"fd64093b-360d-4032-bec7-ea59f482a1d9","order_by":0,"name":"Ditte Marie 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Copenhagen","correspondingAuthor":false,"prefix":"","firstName":"Hans","middleName":"Henrik","lastName":"Bruun","suffix":""},{"id":558923406,"identity":"17ca6d69-e71c-4b1c-a779-6658392884e6","order_by":2,"name":"Matilda Arnell","email":"","orcid":"https://orcid.org/0000-0002-2153-4672","institution":"Department of Ecology, Environment and Plant Sciences, Stockholm University","correspondingAuthor":false,"prefix":"","firstName":"Matilda","middleName":"","lastName":"Arnell","suffix":""},{"id":558923407,"identity":"c2c4145a-bc09-494a-8ae2-1297634c301f","order_by":3,"name":"Conny Bruun Asmussen Lange","email":"","orcid":"https://orcid.org/0000-0002-3072-8786","institution":"Department of Plant and Environmental Sciences, University of Copenhagen","correspondingAuthor":false,"prefix":"","firstName":"Conny","middleName":"Bruun Asmussen","lastName":"Lange","suffix":""},{"id":559265334,"identity":"83efd717-49c9-4da1-a07b-28363f5e5608","order_by":4,"name":"Tankred 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20:36:34","extension":"html","order_by":26,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":89398,"visible":true,"origin":"","legend":"","description":"","filename":"earlyproof.html","url":"https://assets-eu.researchsquare.com/files/rs-8277973/v2/59ae082674936a443f6b4dde.html"},{"id":98101255,"identity":"798c1633-8d78-4d05-987d-8de8c5fa3272","added_by":"auto","created_at":"2025-12-12 20:36:33","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":267049,"visible":true,"origin":"","legend":"\u003cp\u003eExamples of four historic maps from the Topographical-Botanical Survey (TBU) for 1) \u003cem\u003eLysimachia arvensis\u003c/em\u003e, 2) \u003cem\u003eEryngium maritimum, \u003c/em\u003e3) \u003cem\u003eLysimachia maritima\u003c/em\u003e, and 4) \u003cem\u003ePrimula farinosa\u003c/em\u003e. Black dots and ‘bird’s eye’ i.e. open circles with a dot (Figure 1A, C, D, F) represent records based on herbarium specimens and records based on TBU reports, letters or published literature, respectively. Full hatching (Figure 1A) indicates presence and expert-estimated abundance “common to very common”. Dashed hatching (Figure 1B) indicates presence and expert-estimated abundance “here and there”. No hatching in areas with scattered occurrence symbols may be taken to indicate presence as “rare or rather rare.” As shown in Figure 1C, 1D and 1E, presence of species restricted to coastal habitats can be depicted as hatching or small dots along the coastline. All three are categorised as present (category 1). Figure 1G refers to background without any information, categorised as absence of the focal species by our digitization procedure. In some published maps, in particular in the more recent TBU papers, open circles (Figure 1H) an older record of occurrence at a site, from which the species has later disappeared.\u003c/p\u003e","description":"","filename":"1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8277973/v2/8cff13f28bdd1b2123a63dce.jpg"},{"id":98101253,"identity":"b8670283-c2ae-4a7d-a562-fae6c17a72af","added_by":"auto","created_at":"2025-12-12 20:36:33","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":112062,"visible":true,"origin":"","legend":"\u003cp\u003eConceptual figure of the TBU maps digitization process. 1) Scanning of the map pages to high resolution (600 dpi) pdf format. We converted the pdf map pages to png format keeping the resolution to 600 dpi. 2) Maps are extracted from the page and are aligned in angle and size based on a reference map using written macros in Fiji. From Fiji, all map images are saved as jpeg files. 3) Georeferencing of the reference map with 33 points located all around the Danish coastline. The georeferenced map coordinates are used to automatise the georeferencing for all other maps. 4) Division of georeferenced maps into 10 × 10 km grid cells and annotation of each grid cell image of 50 random maps after distribution category (species absence, species presence 1 and species presence 2). 5) Annotated data are divided into train (60%), test (20%) and validation (20 %) and a pre-trained image classification algorithm is fine-tuned for predicting the three image categories. 6) Prediction of all grid cell categories and estimation of precision of algorithm. Output is shapefile formatted maps with three distribution categories at a 10 × 10 km resolution. See the “Methods” section for specific details.\u003c/p\u003e","description":"","filename":"2.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8277973/v2/0721891e9b5c15e78d839ce3.jpg"},{"id":98101254,"identity":"3eadd851-5c00-4f8a-954c-452e00561c12","added_by":"auto","created_at":"2025-12-12 20:36:33","extension":"jpg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":98309,"visible":true,"origin":"","legend":"\u003cp\u003eSpecies richness across Denmark in a 10 × 10 km grid net based on plant species recorded and mapped in TBU publications. Colour scheme represents species richness distribution from the 1340 TBU maps of 1401 taxa.\u003c/p\u003e","description":"","filename":"3.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8277973/v2/677c39b4fb7c3fab5bcbb0bf.jpg"},{"id":98430112,"identity":"942a5daf-57b8-4841-be81-5fdcfe85cc76","added_by":"auto","created_at":"2025-12-17 16:44:50","extension":"jpg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":69052,"visible":true,"origin":"","legend":"\u003cp\u003eDensity plot of occupancy levels across the 57 TBU districts for TBU mapped species and the Danish flora excluding non-naturalized and hybrid species as in Hansen et. al\u003csup\u003e25\u003c/sup\u003e. Orange color shows the distribution of the number of districts for each 1424 species and subspecies included in Hansen et al.\u003ca href=\"https://www.zotero.org/google-docs/?7LsgEJ\"\u003e\u003csup\u003e25\u003c/sup\u003e\u003c/a\u003e (excluding hybrids and non-naturalized species). Purple colour shows the distribution of the number of districts for each 1207 species and subspecies represented with a map in the TBU publications and included with recorded occupancy in Hansen et al\u003csup\u003e25\u003c/sup\u003e.\u003c/p\u003e","description":"","filename":"4.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8277973/v2/ef6e7e9e7be023fe5de444af.jpg"},{"id":98429907,"identity":"0fe41f38-793a-43fb-98e0-732779bce81e","added_by":"auto","created_at":"2025-12-17 16:44:21","extension":"jpg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":63169,"visible":true,"origin":"","legend":"\u003cp\u003eProportional distribution in nativeness status between species mapped in TBU publications and the entire Danish flora as in Hansen et al.\u003csup\u003e20\u003c/sup\u003e. Most of the species that were not mapped in TBU publications were non-native; most alien species were not mapped in the TBU, the same for distantly native species, while a third of species with an uncertain nativeness status are mapped and half of the near native species were mapped in the TBU.\u003c/p\u003e","description":"","filename":"5.jpg","url":"https://assets-eu.researchsquare.com/files/rs-8277973/v2/98d105162dcd626a75d63ab4.jpg"},{"id":98622328,"identity":"4bc9a802-94a7-4f6f-bde4-bd4308b8f028","added_by":"auto","created_at":"2025-12-19 16:52:08","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":5088882,"visible":true,"origin":"","legend":"","description":"","filename":"Digitizedhistoricmapsdatadescriptorms.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8277973/v2_covered_2573dc19-5ae0-4ba8-81e4-142792fb6c1a.pdf"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"From paper to pixels - digitized maps of vascular plant distributions in Denmark in the early 20th century","fulltext":[],"fulltextSource":"","fullText":"","funders":[{"identity":"9a59a835-4ec6-4d5e-a292-92667c487f97","identifier":"10.13039/501100009708","name":"Novo Nordisk Fonden","awardNumber":"NNF22OC0078703","order_by":0}],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"University of Copenhagen","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"historic distribution, vascular plants, temporal biodiversity patterns, image recognition","lastPublishedDoi":"10.21203/rs.3.rs-8277973/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8277973/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eHistoric data are essential for quantifying changes in biodiversity and their drivers. Much legacy data remains undigitized in archives such as natural history museums, representing untapped resources for assessing past biodiversity patterns. In 1904, the first systematic survey of species distributions of the entire Danish flora was initiated. Most field surveys were conducted in the early 20th century. Results were published as black and white printed maps (1931\u0026ndash;1976). We used automated georeferencing and image classification to extract data from all published maps. We present 1340 historic distribution maps of vascular plant species, subspecies and varieties in Denmark at 10 \u0026times; 10 km resolution. These maps represent the Danish flora of native and archaeophyte species known at the time, except some of the most common native species. By comparison with modern distribution data, long-term increases and declines can be accurately quantified, contributing to large-scale analysis of national, European or global plant diversity changes in the modern era.\u003c/p\u003e","manuscriptTitle":"From paper to pixels - digitized maps of vascular plant distributions in Denmark in the early 20th century","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2025-12-12 20:36:28","doi":"10.21203/rs.3.rs-8277973/v2","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}},{"code":1,"date":"2025-12-08 15:37:45","doi":"10.21203/rs.3.rs-8277973/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"3f7d8595-ad76-438c-a97f-b205d590253c","owner":[],"postedDate":"December 12th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-12-08T15:37:46+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-12 20:36:28","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v2","identity":"rs-8277973","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8277973","identity":"rs-8277973","version":["v2"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}