Talk: 3D fossils and digitising collections

As part of the Lyme Regis Fossil Festival, I was invited to give a talk on 3D fossils and digitising collections.



Digitising Collections - images, anaglyphs and 3d digital models

I am particularly interested in promoting access to collections and information through digitisation and web delivery – an area in which the British Geological Survey is a world leader. We have delivered photographs via the web for many years – e.g. the National Building Stone Collection (4300 images) . Use of the JP2 (JPEG 2000) format allows web access to high resolution images, and has been used for several collections including UK continental shelf hydrocarbon well core samples (See for example ). It has also been used for the Historical maps of the Geological Survey of Great Britain and Ireland and Magnetograms . We have recently used it for high resolution fossil images, including stereo anaglyphs in the GB3D fossil types online project , and high resolution images of petrological thin sections (30 µ thick rock slices) – or search the database . The ultimate form of specimen digitisation is the 3d digital model. The GB3D project has captured several thousand such models.

For digitisation to make a difference, it needs a critical mass. The UK hydrocarbon core photographs total 125,000 and the rock thin sections represent 100,000 rocks.

For further details, my Presentation may be downloaded from ftp.bgs.ac.uk/pubload/mhowe/


Launch of the development (beta) version of the website - www.3d-fossils.ac.uk

 

 

 

 

One of the main reasons for attending the Lyme Regis Fossil Festival, as well as having the opportunity of talking to lots of the public about the fossil scanning and photography work that we have been doing, and of course some walks along the beach......

The beach and cliffs to the east of |Lyme Regis

....  was to launch the development (beta) version of the 3d-fossils website. So far there is only a relatively small small number of images, scans and information entries, but we are hoping for suggestions on how to improve the layout and function of the site.



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Please go to www.3d-fossils.ac.uk and try out the site. You can view stereo anaglyphs  (you will need red - cyan glasses), and view and download 3d digital models, which you can store on your computer and view with programs such as MeshLab (which can be downloaded from the web for free).

Lyme Regis went well...

The GB3D fossil team had a most enjoyable time at the Lyme Regis fossil festival in early May, demonstrating laser scanning and 3d-printing fossils to parties of schoolchildren on the Friday, and many hundreds of families over the Saturday and Sunday. My thanks are due to David Bailey and Paul Witney for the following photographs.

The Festival marquee on the beach

The festival marquee on the shingle was packed for most of the opening hours...

A school part enjoying 3d fossils

and another party collecting fossil cards .....

The stand after closing time 

Another view of the stand after closing - the only time you could photograph the displays.

News flash - from the Booth Museum, Brighton

The GB3D project's mobile team is currently working at the Booth Museum, Brighton.
Visit the Royal Pavilion and Brighton Museum's blog at  http://rpmcollections.wordpress.com/2013/05/15/the-booth-museum-stars-in-a-new-fossil-project/ to see the team at work. More information to follow.....

Mike Howe

The photographer's workbench: a guided tour

We thought you would like to see how we obtain most of the images for the project. This photograph shows you the typical working setup. 

1. Camera - we use a professional digital SLR and a range of macro lenses. The lens hood is very important - as well as protecting the front of the lens, it cuts down on flare from the light.

2. Copy stand - we can quickly move the camera up or down without moving it in any other direction. Trying to do this with a tripod would be far too time consuming.

3. Light - we use a bank of fluorescent tubes positioned at the ten o'clock position to provide standardised lighting for the specimen. Heat output from the lights is minimal, as is the UV component of the light.

4. Assorted reflectors, small weights, foam pads etc. - we use the foam blocks to position the specimen, and reflectors to fill the shadows before we take the photograph.

5. Tipping stage - by tipping the specimen by 4° either side of the horizontal position, we obtain a pair of images which can later be assembled into an anaglyph. White copier paper provides a cheap and easily replaced background, and the grey scale allows us to record dimensions and check colour balance at the same time.

6. Cable release - allows us to release the shutter without shaking the camera and ruining the picture. We are also able to use the camera tethered to a laptop to control it.

7. Brushes and blower - we can use these to carefully remove loose dust from the surface of the specimen and the background.

8. Type catalogues and other reference material - we like to refer to previously published material wherever possible to check details as we work.

9. Notepad and pencil - for recording information, it is preferable to use a pencil in museums, as there is no ink to risk staining valuable records or objects.

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Simon Harris

JISC 3D Fossil Types Project Photographer

Reconstructing a 3D surface from stereo pairs

The JISC 3D Fossils Project Team has been experimenting with the use of a simple piece of photogrammetry software to reconstruct a three-dimensional surface from a pair of stereo images. The software uses the difference in the position between certain points on the two images to construct a polygon mesh, which is then "draped" with an image file to provide the texture.

We start with two images, taken at a tilt of 4 degrees left and right from the horizontal plain. The images shown are of GSE 5568, a syntype of Sigillaria strivelensis. We can construct a red-cyan anaglyph from these, using a 

variety of pieces of software.

 

Next we feed the images into AgiSoft Stereoscan (a free download from http://www.agisoft.ru/products/stereoscan/) and allow it to reconstruct the 3-dimensional surface and texture, a process which takes no more than a couple of minutes using the powerful processors inside modern desktop computers. 

Finally we can export the model in OBJ format and use MeshLab to modify it as required. We find that there are some drawbacks to this method, for example:

·         The software can only reconstruct points which are visible in both photographs – this can result in some holes or defects in parts of the model

·         The resulting mesh is only single sided – much like a 'bracket scan' from the laser scanner

However, despite the drawbacks, for a number of specimens this provides a quick and effective way to visualise surface relief. 

Simon Harris

These fossils are NOT real!

In the JISC GB3D fossils project lab we have just received a parcel containing some fossils...

Only these are not millions of years old, they are just a few days old! They are in fact some of the first 3D printed copies of the laser scans we have been producing.

3D printing is now commonly used in industry, and some people are calling this the “second Industrial Revolution”, where everyone is able design or download objects and print them in-house. Our fossils were printed using inkjet bound powder based technology, which means that the colour data that we captured during the scanning phase is also printed.

Visitors to the lab who have seen the models have been very impressed, and it is easy to imagine the scientific and educational potential that a large repository of models will create.

Simon Harris