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)

Digitised Diseases Visits America

Last week, project Co-I Dr Jo Buckberry attended the annual meetings of the Paleopathology Association and theAmerican Association of Physical Anthropologists in Portland, Oregon, USA. On Saturday she presented our poster “From Cemetery to Clinic: 3D digitised pathological data from archaeological leprous skeletons”. This gave us a fantastic opportunity to spread the word about our 3D digitisation projects. Jo reports:

The poster (click here to download a copy), designed by Tom Sparrow, was really striking, and was a real draw. Plus I had a great location, in a quiet corner of the room with a table (useful for stashing all my stuff), but very close to the morning coffee! Better still, I was equipped with my laptop and the project iPad, and was able to showcase a selection of 3D scans to anyone who stopped by (I did pounce a few times!). This worked as a great hook, capturing people’s interest, and facilitating discussion about how the images were captured, the texturing process, and comparing greyscale raw scans with textured images. It was also great to be able to compare the high resolution scans in the full version of Meshlab with the lower resolution scans using the ipad. One response I heard over and over again was “wow…”!

Overall, delegates were impressed by the project and many indicated that they would be visiting our website and downloading a few scans to investigate further. There was some mild consternation that we couldn’t get WiFi in the area of the venue we were stood in, so it wasn’t possible to download the meshlab app and get going straight away… The opportunity to use the scans for teaching was seen as a clear benefit to the anthropological community (especially with North Americans who rarely have a skeletal collection at their institution). The outputs from Digitised Diseases are clearly going to be extremely useful in this regard – one palaeopathologist jokingly commented ‘I am teaching leprosy and TB next week – any chance you can upload your TB scans by Monday?’… The clinical radiographs were also recognised as a particularly valuable teaching and research resource.

Over the course of the two conferences there were several podium presentations and posters about 3D scanning, using a variety of different techniques and each project had different aims. It was a great opportunity to discuss approaches, share problems and bounce around ideas. Throughout the Paleopathology Association conference I used the meshlab app on my iphone to show off a few scans whenever I told anyone about the project – a great way to advertise our poster on the Saturday, and to pass on information to delegates who weren’t able to stay all week.

Many people asked me if we were going to have scans of a normal skeleton, which could be used for comparison. Sadly this is outside the scope of the current project (we have a target of 1800 scans and many, many pathologies to cover), but it is certainly an area we are investigating. At present ‘From Cemetery to Clinic’ uses a series of line drawings and photographs, to illustrate the location of the affected bones and their normal appearance respectively. Some of our early scans of metabolic disease were for the You Are What You Ate exhibition “The Dark Side of Eating”, which David and Pawel developed into video renders – often using stills to indicate where the scanned bone came from (in the case of cranial bones affected by scurvy), or articulating and then opening out two knee joints affected by osteoarthritis. This is an area that we really hope to be able to develop further.

Some screen shots of finished 3D models

The project is well under way now here in Bradford and at MOLA. It is an exciting time, as we are now seeing the first finished textured bones of this project. The finished models will be up at the Digitised Diseases webpage in the coming weeks.

Below is a selection of some of the bones that have been textured. The resolution is much higher in the real thing!

Specimen Selection: Metabolic Disease

The next stage of the project is scanning bones affected by metabolic diseases. Rather than being a specific disease, metabolic diseases are a range of conditions that may affect bone. Our project specific disease classification breaks down metabolic disease into three categories:

1. Deficiency: Scurvy (Vitamin C deficiency); Anaemia (iron deficiency, also including Thalassaemia and Sickle Cell); Rickets (Vitamin D deficiency); Osteomalacia; Porotic Hyperostosis; Osteoporosis

2. Excess: Gout; Fluorosis; Hypervitaminosis; Urinary calculus

3. Dysfunction: Paget’s Disease

The BARC collection at Bradford has numerous examples of these conditions. With so many examples to choose from, the Osteology team has to pick the examples that are classic manifestations of these various conditions.

The gallery below has a few examples of some of the specimens that may be scanned.

Chichester 215, severe anaemia

Gout, 1st metatarsal

Severe Rickets in a tibia and fibula.

Rickets, subadult femur

Porotic Hyperostosis

Severe Cribra orbitalia.

Chichester 30 – Osteoporosis

Gloucester Gambier Parry Lodge 572

Kingsholm 217 – healed Cribra orbitalia

An update from MOLA – completed scan of achondroplastic humerus

Our colleagues at MOLA have been getting to grips with the Faro Quantum laser scanner that arrive just before Christmas.

Don Walker scanning an acondroplastic humerus

Using the scanner takes a while to get used to, but the resulting scans look great, as you can see below.

MOLA's first completed scan: An achondroplastic humerus

Achondroplasia is an inherited disorder in which the upper and lower limbs fail to grow to  normal size due to defects in bone and cartilage. The result is a form of dwarfism characterised by short limbs with a normal sized head and body (description from Oxford Concise Medical Dictionary).

Thanks to Natasha Powers for photographs

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!

“Digitised Diseases” Press Release

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media, news, press release

University of Bradford safeguarding skeletons using 3D digitisation

24 November 11

The University of Bradford has secured almost £750K to safeguard skeletons from world-renowned collections based in Bradford and London.

The project, funded by the ‘Joint Information Systems Committee’ (JISC), will use 3D laser scanning, CT scans and high resolution photography together with new clinical descriptions and historical illustrations to create a web-accessible archive of photo-realistic digital 3D models of pathological type-specimens.  The skeleton collections used in the project will be from internationally renowned collections that have restricted access and are therefore usually only seen by students and researchers.

The project will create a unique educational tool that will appeal to various disciplines including clinicians, medical trainees, medical historians, archaeologists, osteologists and palaeopathologists, as well as enriching the public understanding of anatomy and medical science.

Project leader Dr Andrew Wilson, lecturer in Archaeological Sciences at the University of Bradford, said: “The project will also play a crucial role in conserving a resource that is otherwise under threat from damage. Pathological specimens are often the most handled bones within skeletal collections and yet they are also the most fragile.

“Archaeological and historical skeletal collections are important because they offer the opportunity to observe pathologies in an era before effective therapy. The University of Bradford, Museum of London Archaeology and Royal College of Surgeons of England house internationally important skeletal collections and will each be providing pathological type-specimens for the project.”

Paola Marchionni, programme manager at JISC, said: “Digitised Diseases builds on the successful JISC-funded pilot digitization From Cemetery to Clinic, where the University of Bradford experimented with 3D digitisation of bones affected by leprosy. The team has now taken this approach further by setting up new partnerships, broadening the scope of the collections to include other chronic diseases and experimenting with innovative ways of delivering the models online.

“This project promises to have a wide-ranging impact by opening up access to material that has been so far the preserve of bona fide researchers.  The opportunity for pathologists to look back in time at archaeological remains in order to make assertions about future illness will, we hope, prove invaluable.”

The project is a collaboration between Archaeological Sciences and the Centre for Visual Computing at the University of Bradford and project partners Museum of London Archaeology and the Royal College of Surgeons of England.  The project began in November and will be completed in July 2013.
The funding follows on from the successful JISC-funded pilot project entitled “From Cemetery to Clinic” which saw the rapid digitisation of bone lesions caused by leprosy (Hansen’s Disease) from individuals excavated from the Medieval leprosarium of St James & St Mary Magdalene in Chichester in conjunction with Chichester District Museum.

You can follow the project on Twitter: @digidiseases, or keep up-to-date via the project blog. You can also see examples from the pilot project, including this video!