Projects

A listing of all digitisation projects with current status and summary and a link to the project webpage if it exists
Individual pages for projects that are active and want to use this wiki

Synthesys3

General Information about the Project

• Title:
  
• Funded by: European Union, Framework 7
  
• Duration: 4 Years (from September 2014 to September 2017)
  
• Project Partners:

• Botanischer Garten und Botanisches Museum Berlin-Dahlem, Freie Universität Berlin (BGBM)
• Agencia Estatal Consejo Superior de Investigaciones Cientificas (CSIC)
• Hellenic Centre for Marine Research (HCMR)
• Magyar Termeszettudomanyi Muzeum (HNHM)
• Museum fur Naturkunde - Leibniz-Institut fur Evolutions und Biodiversitatsforschung an der Humbolt-Universitat zu Berlin (MfN)
• Museum National d'Histoire Naturelle (MNHN)
• Musee Royal de l'Afrique Centrale
• Stichting Naturalis Biodiversity Center (NBC)
• Natural History Museum (NHM)
• Naturhistorisches Museum (NHMW)
• Narodni Muzeum-National Museum NM (NMP)
• Naturhistoriska Riksmuseet (NRM)
• Royal Botanic Garden Edinburgh (RBGE)
• Royal Botanic Gardens Kew (RBGK)
• Institut Royal des Sciences Naturelles de Belgique (RBINS)
• Seckenberg Gesellschaft für Naturforschung (SGN)
• State Museum of Natural History Stuttgart (SMNS)
• Kobenhavns Unviversitet (UCPH)
• Vizzuality SL (VIZZ)
• Stichting VU-VUMC (VU)

• Aim: SYNTHESYS3 is designed to produce an accessible, integrated European resource for researchers primarily in the natural sciences, with a major aim of broadening the User Group by making the data held within collections more easily available and thus increasing their research potential.
• Abstract

The Consortium will create a common, high quality approach to the management, preservation, and long-term access to Europe’s major Natural History (NH) collections including virtual collections and new physical collections. This will be achieved by providing improved access to the physical collections within SYNTHESYS3 Consortium and also to the electronically stored data associated with these collections. A significant digitisation element within the Joint Research Activity which has an associated wiki and the Network Activity 3 which also has an associated wiki.

WorkPackage 2: Improving collections management and enhancing accessibility

Objective 2.1: Managing new (virtual and physical) collections

• Task 2.1.1: Develop policies for virtual CM (CM) and integrate JRA outputs
• Task 2.1.2: Produce handbook of best practice and standards for 3D imaging of NH specimens
• Task 2.1.3: Develop policies for new physical CM

WorkPackage 3: Innovation, Impact and sustainability

Objective 3.1: Innovation

• Task 3.1.3: Pilot study into optimal digitisation technologies and equipment
• Task 3.1.4: Pilot study into optimal crowdsourcing processes for NH institutions

WorkPackage 4: Moving from physical to digital collections

Objective 4.1: Automated data collection from digital images

• Task 4.1.1: Automatic processing (segmentation) of digital images
• Task 4.1.2: Automatic metadata capture
• Task 4.1.3: High Resolution 3D colour image acquisition

Objective 4.2: New methods for 3D digitisation of NH collections

• Task 4.2.1: Research on different 3D techniques
• Task 4.2.2: Micro-Computed Tomography (Micro-CT) for NH collections

Objective 4.3: Crowdsourcing metadata enrichment of digital images

• Task 4.3.1: Research into crowdsourcing methodologies for NH collections
• Task 4.3.2: Development of website to allow crowdsourcing data capture

Objective 4.4: Access and management of an integrated European digital collection

• Task 4.4.1: Feasibility research on a “digitise on demand” (DoD) service for European NH Institutions
• Task 4.4.2: Open Access to captured data

== StanDAP-Herb (Standard Data Acquisition Process) ==
General Information about the Project

• Title: A standardised and optimised process for data acquisition from digital images of herbarium specimens
  
• Funded by: DFG German Research Foundation, Literaturversorgung und Information / Erschließung und Digitalisierung, Call: Standardbildung zur Erschließung und / oder Digitalisierung von Objektgattungen in wissenschaftlichen Sammlungen
  
• Duration: 3 Years (from July 2014)
  
• Project Partners:

• Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin
• Hochschule Hannover, University of Applied Sciences and Arts, Fakultät I Elektro – und Informationstechnik
• Fraunhofer Institute of Optronics, System Technologies and Image Exploitation, IOSB, Karlsruhe

• Aim: The project will develop and document a software-driven standard process for extracting metadata from images of herbarium specimens
• Abstract

On herbarium sheets, data like plant name, collection site, collector, barcode, accession number, etc. are found mostly on labels glued on the sheet. The data is thus visible on images taken of the specimen. Currently, they are mostly entered manually into collection databases. The StanDAP-Herb Project funded by the DFG (German Research Foundation) develops a standard process for (semi-) automatic detection of meta-data on Herbarium specimens to replace the time consuming manual data input as much as possible. Image processing software detects objects such as labels or barcodes on the digitized record and classifies them. Text objects are transformed into structured information using text mining algorithms. For handwriting, author identification is attempted. The project evaluates and enhances existing software to comply with standard interfaces and integrate them into an open software architecture based on established IT standards. The software modules thus become available for work flow processing, in order to verify data quality, facilitate data discovery and enhance the application of collection data in research.

The project addresses a large proportion of scientific collections: approximately 22 million herbarium specimens exist as botanical reference objects in Germany, about 500 million worldwide.

The Research Data Alliance

The Research Data Alliance (RDA) builds the social and technical bridges that enable open sharing of data. The RDA vision is researchers and innovators openly sharing data across technologies, disciplines, and countries to address the grand challenges of society. Some of the relevant Working Groups and Interest Groups are listed here:

• Publishing Data Workflows Working Group
• Biodiversity Data Integration Interest Group
• Education and Training on Handling of Research Data
• Metadata Interest Group
• Research Data Provenance

Global Plants Initiative

General Information about the Project

• Title: Global Plants Initiative, Latin American Plants Initiative, African Plants Initiative
  
• Funded by: Andrew W Mellon Foundation
  
• Duration: 2004 to 2015
  
• Project Partners: Over 300 partners in over 70 countries, the European partners were:

• National Academy of Sciences of Republic of Armenia, Institute of Botany (ERE)
• Karl-Franzens-Universität Graz (GZU)
• Naturhistorisches Museum Wien Botanische Abteilung (W)
• Universität Wien (WU)
• Institute of Botany of Azerbaijan National Academy of Sciences (BAK)
• Herbarium, Biology Department, Laboratory of Botany, Gent University (GENT)
• Herbarium, Département de Botanique, Université de Liège (LG)
• Laboratoire de Botanique Systématique et de Phytosociologie, Université Libre de Bruxelles (BRLU)
• Laboratorium voor Algemene Plantkunde en Natuurbeheer, Vrije Universiteit Brussel (BRVU)
• National Botanic Garden of Belgium (BR)
• Charles University in Prague Herbarium (PRC)
• Museum Botanicum Hauniense, University of Copenhagen (C)
• Botanical Museum, Finnish Museum of Natural History - University of Helsinki (H)
• University of Turku Herbarium (TUR)
• Campus International de Baillarguet, Montpellier, France (ALF)
• Herbier de l’Universite Montpellier II (MPU)
• Muséum d'Histoire Naturelle d'Aix-en-Provence (AIX)
• Muséum National d'Histoire Naturelle (P)
• Tela Botanica (Tela Botanica)
• Tbilisi Botanical Garden and Institute of Botany, Legal Entity of Public Law Institute of Botany, Ilia State University (TBI)
• Alfred Wegener Institute for Polar and Marine Research, Bremerhave (BRM)
• Biozentrum Klein Flottbek und Botanischer Garten der Universität Hamburg (HBG)
• Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin (B)
• Botanische Staatssammlung München (M)
• Friedrich-Schiller-Universität Jena (JE)
• Herbarium der Regensburgischen Botanischen Gesellschaft von 1790 e. V. (REG)
• Herbarium Fakultät für Biologie, Systematische Botanik und Mykologie, Ludwig-Maximilians Universität (MSB)
• Herbarium Senckenbergianum Frankfurt/M. (FR)
• Herbarium Senckenbergianum Görlitz (GLM)
• Herbarium Tubingense University of Tübingen (TUB)
• Institut für Botanik, Universität Hohenheim (HOH)
• Institut für Paläontologie, Museum für Naturkunde, Berlin, Germany (BHUPM)
• Martin-Luther-Universität (HAL)
• Staatliches Museum für Naturkunde Stuttgart (STU)
• Universität Göttingen (GOET)
• Universität Heidelberg (HEID)
• Willdenow Herbarium, Freie Universität Berlin (B-W)
• Herbarium, Trinity College, Dublin (TCD)
• Centro Studi Erbario Tropicale Università degli Studi di Firenze (FT)
• Museo di Storia Naturale dell'Università, Firenze (FI)
• Nationaal Herbarium Nederland, Leiden University branch (L)
• Nationaal Herbarium Nederland, Utrecht University branch (U)
• National Herbarium of The Netherlands (NHN)
• Wageningen UR (WAG)
• Department of Botany, University of Coimbra (COI)
• Herbarium LISU, Jardim Botânico Museu Nacional de História Natural Universidade de Lisboa (LISU)
• Instituto de Investigação Científica Tropical (LISC)
• Herbarium Russian Academy of Sciences - V. L. Komarov Botanical Institute (LE)
• Saint Petersburg State S. M. Kirov Forest Technology Academy- Borodin Herbarium (KFTA)
• Institute of Botany of Slovak Academy of Sciences (SAV)
• Herbari de la Universitat de València (VAL)
• Herbario AH - Universidad de Alcalá de Henares (AH)
• Herbario de la Escuela de Ingenieros de Montes de Madrid (EMMA)
• Herbario de la Universidad de Almería (HUAL)
• Herbario de la Universidad de Extremadura (UNEX)
• Herbario de la Universidad de La Laguna (TFC)
• Herbario de la Universidad de Salamanca (SALA)
• Herbario de la Universidad de Sevilla (SEV)
• Herbario de la Universidad Pablo de Olavide (UPOS)
• Herbario del Centro de Investigaciones Forestales de Lourizán (LOU)
• Herbario SANT - Universidade de Santiago de Compostela (SANT)
• Herbario VIT de plantas vasculares, Museo de Ciencias Naturales de Álava (VIT)
• Herbarium, University of Alicante (UA) (ABH)
• Institut Botànic de Barcelona (BC)
• Jardín Botánico Atlántico (JBAG)
• Real Jardín Botánico - CSIC (MA)
• Sociedad de Ciencias Aranzadi (ARAN)
• Universidad de León (LEB)
• The Bergius Foundation at the Royal Swedish Academy of Sciences (SBT)
• Lund University Botanical Museum (LD)
• Swedish Museum of Natural History Department of Botany (S)
• University of Gotenborg (GB)
• Conservatoire et Jardin botaniques de la Ville de Genève (G)
• Donetsk Botanical Garden of the National Academy of Sciences of Ukraine (DNZ)
• Institute of Ecology of the Carpathians Herbarium (LWKS)
• Ivan Franko National University of Lviv (LW)
• Museum of Natural History Herbarium, National Academy of Sciences of Ukraine (LWS)
• National Herbarium of Ukraine, M.G.Kholodny Institute of Botany, National Academy of Sciences of Ukraine (KW)
• V. N. Karasin National University Herbarium (CWU)
• Yuriy Fedkovych Chernivtsi National University Herbarium (CHER)
• Cambridge University Herbarium (CGE)
• Linnean Society of London (LINN)
• National Museums and Galleries of Wales Herbarium (NMW)
• Natural History Museum (BM)
• Royal Botanic Garden Edinburgh (E)
• Royal Botanic Gardens, Kew (K)
• Royal Horticultural Society (WSY)
• Academy of Science, Uzbekistan (TASH)

• Aim: The GPI seeks to digitise and make available plant type specimens and other holdings used by botanists every day.
• Abstract

The project funded digitisation equipment and staff in partner institutes. The funding is now finished. The sustainability model is based on subscriptions by users. Some data and low resolution images are freely available on the Global Plants website (plants.jstor.org). High resolution images and additional functionality including measuring tools are available to subscribers. The rights to the data and images are retained by the source institute and they are free to make the data and high resolution images freely available on their own websites or in other aggregators.