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).

Leicester Literary and Philosophical Society (Section C: Geology) and Warwickshire Geological Conservation Group Visit – 11th August 2012

Two local geological societies, the Leicester Literary and Philosophical Society and the Warwickshire Geological Conservation Group, visited the Geological Collections at BGS on a sunny Saturday in August. In the morning, Dr Phil Wilby showed them the work that BGS has been doing on the Ediacaran (Neoproterozoic, Precambrian) fossils of Charnwood Forest. This work centres around new sets of moulds and casts that BGS has produced, in conjunction with GeoEd and Natural England. At one locality, approximately 140m² of casts have been made, making it probably the largest exercise of its type anywhere in the world. Studying the casts under controlled lighting in the laboratory provides much more information than can be seen at outcrop.

Viewing one of the three core storage halls at BGS. This one contains material from 15,000 onshore boreholes.
 [Photo: Mike Clarke]

I then showed the societies round other parts of the Collections, including the GB/3D scanning and imaging lab. Here they donned 3D glasses and enjoyed some of the delights of the BGS type fossil collections, while I explained how laser scanning works. There was a lot of interest in the digital models and I offered to make a selection of models available for download before the official launch of the main project website next year.

 

The Warwickshire and Leicester groups put their 3D glasses on to view some of the digital models.

 

After lunch out in the sun, the group then viewed the recently open Geological Walk http://www.bgs.ac.uk/contacts/sites/keyworth/geologicalWalk/home.html  and endeavoured to identify the many different rocks – before receiving copies of the guide. Then, after the group photograph in front of the James Hutton building, which forms part of the walk, everyone dispersed.



Members of the two societies pose for the group photograph in front of the James Hutton building. The wall behind the group represents Hutton’s unconformity at Siccar Point, Berwickshire, Scotland, where gently sloping beds of Devonian to lower Carboniferous sandstone  overlie near vertical beds of Silurian grewacke. [Photo: Mike Clarke]

JISC OER Networking Day - 26th March 2012

An enrolled trilobite, genus Calymene

On Monday 26th March, some 70 or so delegates made their way to Dexter House, just opposite the Tower of London, for an Open Educational Resorces (OER) networking day. The participants came from a range of JISC funded projects, but all were involved in developing OERs.

The morning sessions, run by David Mossley of JISC, used two techniques new to me: "Open Space Activity" and "World Cafe Activity". The first involved splitting into groups of three, with the members in turn acting as interviewer, interviewee and notetaker, with the latter tasked with recording identified challenges to the development of OERs on individual "post-it" notes. Adjacent groups then attempted to classify the identified "post-it" challenges into categories, and derive questions representative of the challenges.

The World Cafe activity then had groups listing their main questions on flip charts, and everyone then voted on which of the questions they considered the most important.The  popular questions were then allocated to individual tables and delegates migrated to their table of choice for a discussion.

After lunch, delegates broke into three groups according to their type of project. My own group (JISC Content) then split into three - I followed the discussions on Collaboration and partership around OERs. There were some really helpful discussions, but probably the most important outcomes of the day were the contacts that I had made.

On the way home I reflected on the educational opportunities that the web is providing. From its earliest days, the British Geological Survey and its sister organisations have been involved involved in public education, but the OERs of today are far removed from the public lectures of 150 years ago.....

Professor Owen lecturing at the Museum of Practical Geology, 1857

Vacancy for two project staff - closing date 28th March 2012

Anaglyph image of ammonite, produced by SpiersView from digital model. View with red-cyan glasses

Are you interested in helping to make important national fossil collections available on the web as digital models, photographs and stereo anaglyph images?

A vacancy has arisen at the British Geological Survey for two highly motivated and enthusiastic Digitisation Staff, working on a high-profile JISC (Joint Information Standing Committee) funded 3D fossil project at our headquarters in Keyworth, Nottingham.
Your role will be working as part of a flexible team and will be working partly at Keyworth, and partly offsite at museums and collections around Britain. Duties include:
• Operating digital SLR camera, photographing type fossil specimens, including production of stereo pairs
• Operating NextEngine HD laser scanner to produce digital models of selected fossils
• Enter and retrieve information into PalaeoSaurus database
• Post-processing of images to add scales and produce anaglyph stereo images
• General data management, ensuring model and image metadata is correctly recorded according to the Data Management Plan
The closing date is 28th March 2012
Link for further information.