Thursday 27 December 2012

Manchester Museum

A couple of weeks ago the mobile team went to the beautiful Manchester Museum, I underline beautiful as there were many interesting things to see and we didn't have enough time to view it all;  as usual we were in a hurry to photograph as many types as possible!

Unfortunately there wasn't enough time  to record all the fossil types in the Museum (more than 200), so we had to prioritise the fossils to be recorded, a thing which is always better to avoid and we don't like doing!
We've taken lots of good picture of the Plesiosaur on display, the specimen is too big for our laser scanner and the exhibition display didn't make the access easy, as it is on the floor underneath a 70 cm tall glass! But we hope the photos will help us creating a decent 3 D photogrammetric model.

In the end we managed to scan most of the Buckman Ammonite Collection and photograph a good variety of plants, trilobites, bivalves, cephalopods, insects and fishes, only some bivalves and gastropods were left apart... Time is running out and we must be on the road again, and who knows, we can always come back!

Just one folklore note about this trip: as we looked for  accommodation near the Manchester Museum, we ended up next to the curry mile! Although it's true that life is not all about fossils, an entire week of curry dinners have heavily tested the team! Is there any real English food restaurant left in Britain?   

Michela Contessi
(GB3D Mobile Team)

A visit to Liverpool, and a large fossil!

World Museum, Liverpool

A little while ago  the JISC GB3D fossils team were at the World Museum, Liverpool. As well as the more "normal" sized fossils, a couple of fossils presented a little problem.....

Chirotherium storetonense

This is a specimen of Chirotherium storetonense (the "hand-beast" of Storeton) - it is currently on display in the geology gallery in the museum. The slab weighs over a tonne, so moving it for photography in the available time was out of the question. Additionally, the gallery is open to the public every day, so we would not be able to set up lights and tripods without disturbing access.

We hope to be able to solve this problem through the use of photogrammetry software, where we will use several photographs taken from different angles to create a model of the specimen - we will update this post when we have some results.

Simon Harris
(GB3D Mobile Team)

Cambridge University Museum of Zoology

The mobile digitalization team was in Cambridge on the 14th of November, visiting the Cambridge Zoological Museum. Only 11 types are held there, but some are very nice specimens: two of the most complete Lower Carboniferous reptiles and a Cretaceous turtle, with the skull completely and nicely preserved! Nothing the size of a dinosaur, but let’s say that we encountered some of its smaller ancestors!

Michela scanning a type in the University Museum of Zoology, Cambridge

Time is always running fast when you have only a day in Cambridge, but we managed to have a quick look through the Sedgwick Museum which is always fascinating to see (it was our lunchtime Mike, don’t worry, we worked as much as we could!), and we met the Cambridge digitisation team. Like us, Hilary (scanning) and Lindsey (photographing) are digitising the type collections of the Sedgwick Museum, the they showed us hundreds of boxes with types: it can seem an easy and quick job, but it is never as you would expected it! We also exchanged some useful information about common problems we had and tricks to solve them, I won’t reveal you the latter, you know we still have to keep a little mystery around the final product you will see on the website! 
Simon at work with the Canon EOS5D

Michela Contessi
(GB3D - Mobile digitization team)

Thursday 1 November 2012

And so what.......?

Ahead of a JISC Content Programme 2011-13 meeting in Bristol on 9th 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.....

Wednesday 31 October 2012

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: 

Museums Sheffield

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

Tuesday 18 September 2012

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 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 - . 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 ( ) 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.

Monday 17 September 2012

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.

Monday 27 August 2012

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  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 . 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:  . 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 . 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'?>
<title>Minimal VAXML example</title>
<name>Single Object</name>
<file>GSE  482.ply</file>

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:

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).

Sunday 26 August 2012

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  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]

Thursday 5 April 2012

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

Thursday 22 March 2012

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.

Geoscience Collections at BGS

In our first post, we should like to provide some background information about the British Geological Survey (BGS), the lead partner in the project.
Founded in 1835, the British Geological Survey (BGS) is the world's oldest national geological survey and the United Kingdom's premier centre for earth science information and expertise.
As a public sector organisation, BGS is responsible for advising the UK government on all aspects of geoscience as well as providing impartial geological advice to industry, academia and the public. We also undertake an extensive programme of overseas research, surveying and monitoring, including major institutional strengthening programmes in the developing world.
The BGS is part of the Natural Environment Research Council (NERC), which is the UK's main agency for funding and managing research, training, and knowledge exchange in the environmental sciences. Our annual budget is in the region of £52m, about 50 per cent of which comes from NERC's Science Budget, with the remainder coming from commissioned research from the public and private sectors. Further details may be found in our Annual Report.
The NGDC holds core and samples from approximately 24,000 boreholes and wells, both onshore and offshore (UK Continental Shelf) in a “state of the art” core store at Keyworth, Nottingham.
The BGS houses the National Geoscience Data Centre (NGDC), one of NERC’s seven data centres. The NGDC includes major digital holdings (e.g. digital geological maps, a wide range of images and scans, and numerous indexes), extensive records and maps collections, and probably the largest collection of British geosciences samples. These include onshore and offshore borehole and well samples, fossils, and mineralogy and petrology samples. The fossil collections include over 30,000 type, figured and cited fossils – of which the type fossils form a significant part of this project.
An enrolled trilobite, Calymene

GB/3D Fossil Types online: Database of type specimens of British fossil species