The Long Goodbye…

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3D scan, 3D scans, bones, Bradford, Hunterian, MOLA, news, palaeopathology, Royal college of Surgeons, Wellcome

As the year draws to a close it begins to dawn on us how quickly the Digitised Diseases project has progressed. It seems not long ago we had just begun the MOLA part of the project and it feels like only yesterday that the equipment was delivered and we were trained how to use the laser scanner.

Dismantling 140 kilos of steel table!

In the past year we have scanned a diverse and impressive cross-section of our archaeological collections covering all of the common and some of the more unusual pathological bone conditions we encounter in past populations. We have completed over 300 laser scans and taken over 17000 photos for overlaying.

Arrival at the Royal College of Surgeons

Andy installs the laser at the Royal College of Surgeons

But now it is time to say goodbye, the laser is already packed up and with more than a little help from Andy and Tom from Bradford, we have hauled the 140 kilo steel table from the MOLA offices to the Royal College of Surgeons to begin the next stage of the project.

This will involve the scanning of the well preserved clinical pathological specimens from the Wellcome and Hunterian Museum collections.

Both collections have played an important role in informing the medical world and continue to play a part in the education of surgeons today. The associated records, histories and diagnoses will provide a wealth of examples to add to the Digitised Diseases collection that will continue to provide a resource to help in the understanding, teaching and education of pathological conditions.

As with all happy endings, this is not actually goodbye but more au revoir as the MOLA team is privileged to continue to work with Carina, Martyn and Emmy at the RCS in the scanning of their collections and John who has kindly accommodated us in his photography studio. We look forward to sharing some of the fascinating and interesting examples we encounter in the New Year.

Don eager to start scanning

Definitely NOT Richard III

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3D scan, 3D scans, achondroplasia, bones, MOLA, palaeopathology, Richard III, Scoliosis

… but a fellow sufferer of scoliosis (bent spine) excavated from Chelsea Old Church post-medieval burial ground in London, by Museum of London Archaeology  Museum of London Archaeology (MOLA).

The image features the fused 9th to 11th thoracic vertebrae, as well as a fused right rib, from a mature adult female. It is taken from a high resolution 3D scan which has been rendered in gold to maximise visibility of the surface contours of the bones. She probably suffered from idiopathic scoliosis resulting in severe lateral (sideways) curvature of the spine.

The condition is thought to be congenital (genetic?) and usually manifests in childhood, so this woman would have been affected for several decades. The left sides of her vertebrae have fused together in an attempt to stabilise her spine. This image only shows a small section of her spine. When all her vertebrae are joined together (articulated), the spine forms an ‘S’-shape, which in life would have given her body an asymmetrical appearance with the right shoulder higher than the left.

This work forms part of the Digitised Disease project , a collaboration between the Biological Anthropology Research Centre (BARC) at University of Bradford, MOLA and the Royal College of Surgeons (RCS). It will provide a web based learning and reference resource for students, professionals and others. By scanning and reproducing examples of pathological lesions, both archaeological (BARC and MOLA) and from the collections at the Royal College of Surgeons, we plan to provide evidence of disease from populations who lacked antibiotics and other modern treatments and so present the full range of bone lesions that result from pathological conditions.

The two examples below illustrate 1. the scanned and 2. the textured 3D images of a right humerus of an individual from St Mary Spital medieval burial ground with achondroplasia, a form of dwarfism. On the first image, each colour represents a different ‘pass’ over the bone with the laser scanner. These are eventually aligned to form a single image. This is then used as a template on which to map photographic images of the bone in order to produce the final surface detail. This and further images can be found on MOLA Facebook, Twitter and blog pages.

Dr Keith Manchester appointed Honorary Visiting Professor of Palaeopathology at Bradford

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bones, news, palaeop, palaeopathology

Dr Keith Manchester, co-author (with Prof. Charlotte Roberts) of The Archaeology of Disease, has been appointed Honorary Visiting Professor in Palaeopathology at the University of Bradford.

Keith has worked in Archaeological Sciences for many years, contributing to teaching and research, particularly in the field of leprosy and infectious diseases.

Keith is also the Bradford based clinical advisor for Digitised Diseases. He was previously a general practitioner in Bradford and is the author of numerous papers and books on palaeopathology.

(Image courtesy of Dr. Rebecca Storm)

New team members!

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3D scans, bones, cemetery to clinic, new staff, news

Today we were delighted to welcome two new team members. Pawel Eliasz (who was one of the texturers from the first project) and David Keenan are full time texture technicians and will be based in Visual Computing.

They are responsible for filling in holes in the scan data and texturing the 3D models with high resolution photographs.

They popped over to Archaeological Sciences this morning to meet the team, including some of the more famous BARC skeletons. We thought it was important that they actually see a skeleton, so they can understand the realtive size of elements and experience bone colour and texture in real life, rather than just seeing lots of photographs.

Pawel and David meet Chichester 88

They also got to meet the laser scanner. Andy Holland talked them through some of the finer points of scanning bones.

David, Pawel and Andy talk 3D laser scanning

Welcome to the team guys!

The specimen selection process

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BARC, bones, syphilis, treponemal

The major aim of this project is the digitisation of pathological type specimens. A type specimen is a particular example that is the classic manifestation of a particular condition. A good example is Pott’s disease of the spine for Tuberculosis.

As we can’t scan everything in the collections (the BARC alone has over 4000 individuals), we have to choose the best possible examples for scanning.

We start the specimen selection process by pulling together the various teaching lists that are used to plan labs for our own MSc students on the Human Osteology and Palaeopathology course as well as the Palaopathology Short Courses.

These lists are all slightly different and have evolved over the years, but cover the range of pathological conditions in the collections.

Four different teaching lists, photo log, skull ring, highlighters and and iPad

I use these lists to find examples of pathologies in the collection and photograph the lesions. This means finding all the examples on the list.

We have Drawer Specimens, which are kept in the lab and are used extensively for teaching. These specimens are usually single or associated elements rather than the remains of an entire individual. The Drawer Specimens are sorted by pathology type (i.e trauma, infectious disease, metabolic disease).

The majority of skeletal material in the BARC is curated in a climate controlled store.  There are over 4000 individuals curated by the BARC. Each individual is stored in a box labelled with the site and skeleton number. The store is arranged by site – so everything from a particular site is stored together. The skeletons are sorted by skeleton number, which makes it easy to find a specific individual. You can find out more about the BARC Human Remains Policy, including curation and access here.

BARC Store at Bradford

So after I photograph the lesions I collate a document. This goes to Dr. Jo Buckberry and Dr. Keith Manchester who make the decisions on what will be scanned. We have a category system – from A to C – A being an excellent type specimen that must be scanned to category C – a specimen that may have an ambiguous diagnosis or extensive taphonomic damage not suited to scanning.

I photographed all the examples of Treponemal disease and non-specific infection in the collection last week. I took 439 photographs in total. Below is Blackfriars 77. This is an example of Treponemal disease (syphilis) in a young adult female.

Blackfriars 77, a young adult female showing caries sicca on the frontal bone

If this individual looks familiar you may have seen heron the cover of Donald Ortner’s Identification of Pathological Conditions in Human Skeletal Remains.

Dr. Rebecca Storm and Dr. Keith Manchester then take the specimens in category A and write clinical descriptors and lay descriptions. These descriptions will accompany the finished scan on the Digitised Diseases website.

Last week’s activities

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3D scan, bones, gout, training

Well, last week was a week of meetings. Very useful meetings.

On Wednesday (11 Jan) we met with Prof Peter Hartley, an e-learning expert from the University’s Centre for Educational Development. We talked about the outcomes from this project, and how we can maximise access to a wide audience and how we can measure how successful our efforts have been, which is something JISC, as our funding body, are keen for us to do.

Peter was very enthusiastic about the project and seemed genuinely impressed when we showed him some of the models from “From Cemetery to Clinic”.

On Friday (13th!!) we had a Bradford project team training day, that ran from 10.00 – 17.00.

Andy Holland and Tom Sparrow took the team through the bespoke management database they have produced for this project. I was blown away – they really have thought of everything! Andy Holland is also an experience Forensic Archaeologist and Anthropologist, something I think has been invaluable as he understands the needs of the Osteologist was well as the needs of a database to manage this kind of project. Tom and Andy have also written in QA mechanisms, so you can be sure that when you view a finished, textured 3D model and read the clinical descriptors (written by Drs Rebecca Storm and Keith Manchester), you know they have passed quite a rigorous QA process before going live on the web.

Andy explaining the database table structure

We also had a business meeting where we discussed more formal academic outputs and submitted an abstract for the Digital Humanities Symposium – Virtualisation and Heritage to be hosted at the University of York next month. Fingers crossed they accept our submission! Andy Holland is first author and will present the methods we used for “From Cemetery to Clinic”.

The last part of the day we all had training using the FARO Quantum laser arm. As a group we scanned a fantastic example of gout from the BARC teaching collection.

Scanning is a lot harder than it looks! We were pretty excited about our first group efforts (see below).

Gouty toe (1st metatarsal) from Lincoln

And our attempt. The different colours represent different scan passes.

Our group attempt to scan a pathological bone

If this was a real scan, it would now go on for post-processing. More about that later in the project.

From Cemetery to Clinic

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3D scans, bones, cemetery to clinic, palaeopathology

The From Cemetery to Clinic project, funded by JISC,  was the pilot from the larger Digitised Diseases project. It was set up to create a unique interactive resource on the pathological manifestations of leprosy (Hansen’s disease) in skeletons excavated from the Medieval leprosarium of St. James and St. Mary Magdalene, Chichester in Southern England in 1986-87 and 1992 by Chichester District Archaeological Unit.

The leprosarium was founded circa 1118 AD to care for eight leper brethren and was used as a leprosarium until at least 1418. Of the 384 individuals excavated a minimum of 75 individuals show skeletal lesions which are likely to have been due to leprosy. The Chichester collection is the only large scale excavated and published archaeological assemblage of leprosarium patients in the UK, and one of a handful worldwide. None of the child skeletons from Chichester had definitive skeletal evidence for leprosy, and therefore this archive is only concerned with adult skeletal material.

The chronic infectious disease leprosy is a devastating and debilitating condition involving pathological changes to the upper jaw (rhino-maxillary syndrome), resorption of bones of the hands and feet (including knife-edge remodelling of metatarsals and concentric remodelling of phalanges), secondary infectious involvement of the tibiae and fibulae (periostitis), and remodelling of the hand phalanges caused by fixed flexion of the fingers (volar grooves due to claw-hand deformity). As a treatable condition it has largely been eliminated in the developed world. A digitised archive of 400 historic clinical x-radiographs taken of living leprous patients in Ethiopia 30 years ago provides additional context.

The video below is an example of a textured 3D model of an individual with the characteristic changes associated with rhino-maxillary syndrome.

By combining new clinical descriptions alongside the 3D data, this resource offers the opportunity to inspire an emotional response, understand past human experiences, and offer people the chance to come face-to-face with the realities of the disease and how people in the past may have responded to the social stigma of the disease. The following 3D digital archive preserves fragile dimensional information that is otherwise under threat from attrition through handling and is aimed as a virtual training and research tool for clinicians, human osteologists, archaeologists and the wider public.

See the project website here

At the moment the website is still under construction with reduced functionality. In the new year it will migrate to the new server, and with this move we should have a much more user friendly site.

What do you think of the models? Did you find the software easy to use? Let us know in the comments!