SYNTHESYS3 : synthesis of systematic resources.
Date: 2016-02-01
Institutions: Directorate-General for Research and Innovation
Subjects: botany, digital technology, digitisation, life sciences, museum, research project, scientific cooperation, scientific research, virtual library, zoology

SYNTHESYS3
Synthesis of systematic resources

Zoological specimens in one of the storage rooms at the Darwin Centre of the Natural History 

Museum, London. © The Trustees of the Natural History Museum, London

Natural  history  collections  are  an  invaluable  resource  for  scientists,  enabling  them  to  study  examples  of  the  rich 
diversity of life around the globe and across the ages. SYNTHESYS3, a network of prominent institutions across Europe, 
strives to ensure that these collections can realise their full potential to support outstanding research. It offers funded 
opportunities to study specimens on site and supports the creation of new types of digital collections. The project is 
also exploring innovative ways to make the partners’ material available online through the development of digitisation 
tools and services.

Networking for natural history 

“The  main  objective  is  to  open  up  our  collections  and  to 
make them more accessible,” says project manager Dr Kristina 
Gorman  of  the  Natural  History  Museum,  London.  “We  now 
have 21 partners, most of which are natural history museums 
or  botanical  gardens.  These  include  the  largest  collection-
holding institutions across Europe.”

Together, these partners curate a total of 390 million specimens 
ranging  from  the  fossilised  remains  of  the  earliest  forms  of 
life  to  high-definition  videos  of  recently  discovered  micro-
organisms.  SYNTHESYS3,  which  builds  on  the  outcomes  of 
two predecessor projects, enables participating institutions to 
identify and exchange best practice, harmonise their approach 
to  managing  natural  history  collections  and  jointly  address 
common research challenges.

A gateway to leading institutes around Europe

As  one  of  its  main  priorities,  the  SYNTHESYS3  consortium 
operates  a  transnational  access  programme,  which  enables 
scientists to apply for funds to visit participating institutes and 
conduct  research  on  site.  Visiting  researchers  are  welcomed 
at  11  taxonomic  access  facilities,  which  jointly  cover  the 
network’s  combined  collection.  More  than  11  000  user  days 
will be funded through this programme.

The  transnational  access  programme  helps  tackle  the  key 
challenge of conducting research involving specimens that may 

Image of collection of Lepidoptera, illustrating variation. Only the four in the 
bottom left corner are butterflies, the rest are unusually colourful moths. 
 © The Trustees of the Natural History Museum, London

be located hundreds or thousands of kilometres away from the 
researchers that need them. One part of the project’s strategy for 
solving this problem is to share extensive information about the 
partners’ collections along with associated multimedia material. 
This  move  also  helps  to  preserve  these  unique  resources  for 
the  future  by  ensuring  that  rare  and  potentially  irreplaceable 
specimens are not handled unnecessarily. 

Innovative techniques for virtual collections

The  consortium  has  thus  launched  a  multifaceted  joint 
research activity to speed up the digitisation of collections. One 
strand of this activity is dedicated to the automated capture 
of  data  from  digital  images.  More  specifically,  SYNTHESYS3 

SYNTHESYS3
Synthesis of systematic resources

researchers are developing software that can detect and capture 
image properties, recognise and classify depicted specimens, and 
ultimately  generate  descriptions  of  properties  like  their  colour, 
size and shape. Not only will this automation make the digitisation 
process  quicker,  but  it  makes  the  digitial  surrogates  of  these 
specimens more useful to researchers and easier to find through 
online portals. 

Specialised 3D techniques are another priority. The aim is to create 
digital objects that can be viewed and inspected in detail from all 
angles, just like the specimens themselves. The project partners 
are  assessing  and  upgrading  existing  3D  techniques  to  rapidly 
digitise specimens that have a range of sizes, shapes and surface 
structures. They are also developing models and workflows for the 
use of micro-computed tomography to facilitate the digitisation 
of collections so these 3D tomograms are available online.

State-of-the-art  digitisation  and  automatic  data  capture 
techniques  open  up  exciting  possibilities,  but  building  virtual 
extensions of entire collections remains a daunting task. A third 
activity  within  the  joint  research  programme  is  dedicated  to 
developing a platform that will enable the wider community to 
collect  data  about  digitised  specimens.  SYNTHESYS3  is  hoping 
for  support  from  expert  communities  to  classify  previously 
unidentified specimens from images. The project will also engage 
the general public to transcribe handwritten information, such as 
scans of specimen labels or catalogue cards, and to correct text 
extracted via optical character recognition software.

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Scanning electron microscope image of Scyphosphaera apsteinii, 
an equatorial coccolith. 
© The Trustees of the Natural History Museum, London

Further work focuses on managing and providing access to an 
integrated European digital collection. The partners are looking 
into ways to ensure that the images and metadata produced by 
SYNTHESYS3 are publicly available via open access platforms. They 
are also assessing the feasibility of a “digitise on demand” service 
by  which  users  could  order  the  images  of  the  specimens  they 
require, which would then also be added to the digital collection, 
helping to enrich it progressively. 

“Natural history collections essentially represent a physical model 
of  the  natural  world,”  says  Gorman.  They  are  used  in  research 
on  topics  as  varied  as  assessing  the  impact  of  climate  change, 
identifying new food crops and improving human health. With 
the  help  of  SYNTHESYS3,  they  will  soon  be  in  an  even  better 
position to support outstanding science. 

Project acronym: SYNTHESYS3
Funding scheme (FP7): Integrating Activities (IA)
EU financial contribution: €8 million
EU project officer: Anna Maria Johansson
Duration: 48 months
Start date: 1 September 2013
Completion date: 31 August 2017
Partners: Natural History Museum (UK) 
Royal Botanic Gardens Kew (UK) 
Royal Botanic Garden Edinburgh (UK) 
Muséum national d’Histoire naturelle (FR) 
Københavns universitet (DK) 
Agencia Estatal Consejo Superior de Investigaciones Cientifícas (ES) 
Real Jardín Botánico (ES)
Naturhistoriska riksmuseet (SE) 
Stichting Naturalis Biodiversity Center (NL) 

Freie Universität Berlin (DE) 
Museum für Naturkunde — Leibniz-Institut für Evolutions- und 
Biodiversitätsforschung an der Humboldt-Universität zu Berlin (DE) 
Naturhistorisches Museum (AT) 
Magyar Természettudományi Múzeum (HU) 
Institut royal des Sciences Naturelles de Belgique (BE) 
Musée royal de l’Afrique centrale (BE) 
Národní Muzeum — National Museum NM (CZ) 
Vizzuality SL (ES) 
Stichting VU-VUmc (NL) 
Hellenic Centre for Marine Research (EL)
Senckenberg Gesellschaft für Naturforschung (DE)
Staatliches Museum für Naturkunde Stuttgart (DE)
Coordinator: Vincent Smith, v.smith@nhm.ac.uk
Project webpage:  http://www.synthesys.info

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© European Union, February 2015 — Reproduction is authorised provided the source is acknowledged