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]