And so what.......?

Ahead of a JISC Content Programme 2011-13 meeting in Bristol on 9^th November 2012, we have been asked consider the “value” of our project –“and so what?”

British palaeontologists have been active since the early days of the subject, and the great range of rock types present in Britain has resulted in large collections of type fossils (the reference specimen(s) that define species and subspecies) in many of the museums across the country. The Museum of Practical Geology, Jermyn Street, London (1851 – 1935) was one of such museums.

 Museum of Practical Geology, Jermyn Street, London

The project has involved the location and digitising (high-resolution images, stereo-anaglyphs, 3D digital models and locality / taxonomic metadata) of type fossil specimens in the partner institution collections, and at numerous other museums around the country. We have produced thousands of good quality photographs of type specimens, and already many hundreds of 3D digital models. We have improved the quality of much of the specimen metadata and have imaged many of the specimen labels. Making this information available through the web to the world is the natural extension of the work that museums have always done.

The project will ensure that palaeontologists working anywhere in the world can easily and rapidly track down the type specimens they need to view. This will improve their efficiency and the quality of their research. In some cases, the images and digital models will be sufficient, thus reducing personal travel or risk to specimens while being accessed and loaned. Type specimens underpin taxonomy, and without a consistent, accurate taxonomy, studies of biodiversity are impossible. This is particularly important now that we are relating changes in biodiversity to changes in climate.

The images and models are also being used in the development of OERs, which will hopefully inspire not only the next generation of palaeontologists, but also the public at large. There could even be many parents, grateful that their children have collections of virtual fossils, rather than dusty rock-filled shoeboxes under their beds.....

OERs - Open Educational Resources

ESTA - The Earth Sciences Teachers Association met at BGS Keyworth on the 28th - 30th September and the GB/3D team ran a demonstration of  laser scanning and 3D fossil models.

The project will produce an "OER" or Open Educational Resource using the 3D models and images. This is intended to be a "proof of concept", and the hope is that others will use the models and images to produce many other OERs. We are not sure yet whether our OER will be aimed at primary, secondary or higher education - or if there is sufficient interest, we might produce one for each sector.

We have already recruited some volunteers to help guide the work, including some at the ESTA meeting, but we are looking for one or two more any level. The work will be mainly via email and the web, but might include an odd trip to BGS Keyworth. If you have a suitable background and are interested in becoming part of an exciting project, please email me through the BGS website at:  http://www.bgs.ac.uk/staff/profiles/3858.html 

Museums Sheffield

The GB/3D Fossil Types digitisation team recently paid a visit to the stores of Museums Sheffield

(link: http://www.museums-sheffield.org.uk/), to image the type specimens held there. One of the most interesting specimens was the holotype of Dentalium sorbii, pictured below. 

Even just the name of the fossil tells us many things:

·         Dentalium, the name of the Genus, is taken from the latin Dentis, for tooth, as the fossils are shaped like teeth, even though they are actually a kind of mollusc!

·         sorbii, the species name, is named after Henry Clifton Sorby (link: http://en.wikipedia.org/wiki/Henry_Clifton_Sorby), who presented this specimen to the museum. Sorby was born near Sheffield in 1826, and went on to become a geologist and metallurgist of some significance. He was once ridiculed for wanting to “examine mountains with microscopes”, yet his work examining rock slices ground so thin that light could pass through them led to the establishment of the field of thin-section petrography, nowadays considered a standard analytical technique. Metalurgically, he was the first person to realise the contribution made by a small amount of carbon to the properties of steel, and who has not, at some time, used a blade with the words “Sheffield Steel” engraved upon it?

·         Finally, we know that the species was described by William King in 1850 – the rules for naming new species state that it is not allowed to name a fossil after oneself. Therefore King was able to name this shell after Sorby, in his honour. Roughly translated then, the name means “Henry Sorby’s tooth shaped shell”. 

Simon Harris,

GB/3D mobile team 

Dust off your fossil types..... the JISC funded GB/3D type fossils online project would like to visit you

The following call has gone out by the Geological Curators' Group to all curators and managers of geological collections across the UK:

The Geological Curators’ Group is a partner in the JISC funded project GB/3D type fossils online (JISC was previously known as the Joint Information Systems Committee, and it runs the JANET computer network to which all .ac.uk domains belong).

Other partners include:

·         British Geological Survey

·         National Museum, Cardiff

·         Oxford University Museum of Natural History

·         Sedgwick Museum, Cambridge

Other collaborating organisations to date include the Natural History Museum, London and a number of local museums.

The ICZN and the International Code of Nomenclature for algae, fungi and plants require that every species or subspecies of organism (living & fossil), should have a type or reference specimen to define its characteristic features. These specimens are held in collections around the world and must be available for study. Many of the UK type fossil specimens were first described over a century ago, and with the passage of time and the transfer and amalgamation of collections, their present location is uncertain.                                                                                                                                                                          

The project partners are busy photographing all their UK macro-fossil type specimens, including close-ups and labels. In most cases they are also taking stereo-pairs for anaglyph production. They are laser scanning about 10% of the specimens to produce downloadable digital models. Please see the project blog for the background to the project and for some free downloadable digital models - http://gb3dtypefossils.blogspot.co.uk/ . Next year a web portal will be released, linking all the fossil registration details (including identification, locality, age, registration number, repository, etc.) to the images, stereo-anaglyphs and 3D digital models.

The Geological Curators’ Group is now trying to track down the UK type macro-fossils held in other collections and museums around the country. We would like to visit as many collections as possible with our mobile cameras and laser scanner to photograph and record all the available types, and make them available through the web portal. All the material will be clearly badged with the holding institution’s logo, which will link to contact details and access information, thereby helping to open up the collection for worldwide study. At a time when collections are being increasingly required to justify their existence, this is a good way of raising their profile and demonstrating the international scientific importance of material they hold. All collections will be provided with copies of the photographs and digital models of their material to do with as they wish; the images and models on the web portal will be available for free download under a Creative Commons  – Attribution – NonCommercial – ShareAlike licence.

We would like to hear from any museums and collections interested in joining the project. We also have a budget available to help cover the cost of the collection staff involved (£200 per day, on a first-come first-served basis). Please email me (GB3D-Fossils@bgs.ac.uk ) with information about the types you hold, including the approximate number of specimens, or if you wish to receive further information. Where a collection has just a few types, and they are considered safe to travel, we would ask you to consider loaning the material to BGS for the work to be done in Keyworth.

Please consider joining what is becoming a very exciting development.

Kind regards,

Mike Howe

Project leader & Chairman GCG.

Simon Harris joins the project team

The JISC fossil digitisation team at Keyworth has recently welcomed a new member. Simon Harris joins us as a photographer who has specialised in photographing objects in museums and historic houses for several years. 

Simon Harris using one of the project's Canon EOS5D MkII's

Simon commented:

"I have spent a number of years working with varied historic collections across the UK, and have been interested in fossils since my childhood, so the opportunity to work with historically and scientifically significant fossil collections is a very exciting prospect for me."

"I also have training in engineering and object conservation - it's surprising just how often these different disciplines come in handy when working in a museum!"

"The nature of the collection we are working with here means that a lot of the specimens are quite small and we really need to utilise the capabilities of the equipment that we have. For instance, the live view facility on the camera is invaluable for checking focus and depth of field, and we can check the final image for any problems, like camera shake or under exposure, instantly. It was never that easy when we used film!"

We will bring you some fossil photographs in a future blog posting.

Fossil Digital Model Preview

The laser scanning of fossil type specimens at BGS and our partner organisations in the JISC funded project is progressing well, with some stunning results. BGS now has several hundred specimens completed, in addition to those being scanned by our partner organisations.

Michela Contessi, one of the project team, operating the NextEngine HR Laser Scanner

 

Whilst the formal launch of the project website, with the database and portal to all the type specimen data, images, 3D anaglyphs and 3D digital models, is still almost a year away, I thought it would be useful to make a selection of digital models available for users to download, experiment with and comment on.

Please note: All the digital models are licensed under a Creative Commons Attribution-non Commercial-ShareAlike license.

Instructions for downloading and viewing models

1.       The models are available for downloading from the BGS FTP server. Go to ftp://ftp.bgs.ac.uk/pubload/mhowe/GB3D_TypeFossils/  and download as many as you like. All the models are in “.PLY” format. This format is known as the “Polygon File Format” or “Stanford Triangle Format” and is a particularly simple and space efficient way of storing 3D scanned data.

 

2.       Each model is numbered with its specimen registration number. To obtain the metadata for each specimen (i.e. identification, locality, age, etc), visit the BGS PalaeoSaurus database at http://www.bgs.ac.uk/palaeosaurus/home.cfm . Enter the registration number into the appropriate box on the search form (the bottom box). Registration numbers consist of one or more letters followed by a number. DO NOT leave a space between the letters and the numbers and ensure you enter the correct case (upper or lower case - capital or small letters).

 

3.       I recommend either MeshLab or SpiersView for viewing the models. Both are easily available as free downloads from the web.

4.       MeshLab can be downloaded from:  http://meshlab.sourceforge.net/  . MeshLab is a particularly useful tool for viewing and improving models and changing file formats.  It can also be used to measure distances between points of the displayed meshes and to export planar sections of a mesh in SVG format. 

MeshLab screen showing GSM 49299: the ammonite Xipheroceras binodulatum from Lyme Regis, Dorset

5,      SpiersView can be downloaded from http://spiers-software.org/ . SpiersView is particularly useful for viewing models as coloured anaglyphs, i.e. they appear in full 3D when viewed through red – cyan glasses. SpiersView needs a VAXML file for each .PLY file.

 

Cut and paste the following into a basic text editor:

<?xml version='1.0'?>

<vaxml>

<header>

<version>2</version>

<title>Minimal VAXML example</title>

</header>

<objects>

<object>

<name>Single Object</name>

<file>GSE  482.ply</file>

<material>

<colour>

<red>255</red>

<green>255</green>

<blue>255</blue>

</colour>

</material>

</object>

</objects>

</vaxml>

Replace the file name (in this case GSE  482.ply) with the name of the file you wish to view and save with the file name suffixed with .vaxml (eg. GSE 482.vaxml).  When running SpiersView, you should then open the .vaxml file to open the corresponding .ply file. The advanatages of vaxml are explained on the SpiersView Site.

 

 

SpiersView stereo anaglyph view  of digital model of an ammonite

Feedback on the models is welcomed and should be sent via the email link at: http://www.bgs.ac.uk/staff/profiles/3858.html

Adam Smith moves to Wollaton Hall Museum

Adam Smith, who joined the project team in May, has just moved on to become Collections Access Officer [Natural Sciences] with Nottingham City Council, based at Wollaton Hall Museum. This is a permanent curatorial post, and I congratulate Adam on his success.

Adam setting up the NextEngine HR Laser Scanner on a type fossil from the BGS Collections

 

Adam commented, just before he left the project team:

“I’ve always been fascinated by fossils and wanted to be a palaeontologist from an early age. I completed degrees in palaeontology at Portsmouth and Bristol and then continued my studies in Dublin, where I conducted a PhD project specialising on plesiosaurs. Plesiosaurs are extinct marine reptiles that inhabited the ocean during the age of the dinosaurs.

I am pleased to have been part of the JISC digitisation project, working with fossils every day. The 3D models and photographs we are producing will be a valuable scientific and educational resource for everyone from academic researchers to school children. I’m sure I’ll use them myself!”

The other member to join the team at the same time as Adam was Michela Contessi, who is just completing a PhD at the University of Bologna on vertebrate ichnofossil assemblages in the Tataouine basin (South Tunisia). She has considerable experience on a number of laser scanners, including the NextEngine and has put her expertise to good use in the project.

The project lab, showing the two Canon EOS5D cameras in the fore-  and mid- ground and one of the NextEngine HR Laser Scanners at the back, being operated by  Michela. Note the “see-saw” on the camera copy stand for taking stereo photographs, and the greyscale. The cameras are controlled by computers and the digital images are transferred directly to the BGS SAN (Storage Area Network = corporate disc storage).