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How are X-rays used to produce those amazing 3D images of

In The Skull in the Rock we speak about the application of technology to the study of
Australopithecus sediba.  One of the neatest technologies we apply to fossils today are
the various applications of x-rays.  From plain x-rays just like the ones found in hospitals
and used to image a broken bone, to computed tomography machines (CT), to the most
sophisticated and expensive particle accelerators like a synchrotron, all these devices
emit x-rays of varying power and intensity and all of them are used to study these
important fossils.  

With sediba, we wanted to preserve some of the rock that surrounds the fossils for future
scientists to study, so we went to great lengths to try and not take too much rock away
while exposing the bones.  Luckily modern technology came to the rescue.  When I first
saw the tiny piece of the face of sediba coming out of the rock during the course of
preparation, I rushed it over to the local hospital to have it CT scanned (my wife Jackie is
luckily a Radiologist and let us use her machine at work).  One of the first images we saw
was this!  It was very exciting because never before in history had any scientists seen
what looked like a nearly complete skull in a rock!

Preparing more of the skull from the rock took months, and in that time we began to
realize that not only was the skull beautifully preserved, but that there might be very
important and fragile information in the rock that contained sediba – like soft tissue parts
and plant remains – that we wished to preserve.  That’s when we decided to really use
technology to prepare the specimens from the rocks so that we could preserve as much
of this information as possible.

The first thing we did was to take the CT scans and prepare them out.  This took highly
trained scientists months and months to do.  Each individual scan is about ½ a millimetre
in thickness, so there are literally thousands of them produced when we scan something
as big as a skull.  Each little digital pixel has to be examined to separate the fossil bone
from the fossil rock (although we are working hard on automating parts of this process –
watch this space!).   After hundreds of hours of work, we were finally able to see the
preserved skull in the rock and it looked like this.  

See how we can now make the rock transparent and the bone solid?

Once we have the skull digitally “segmented”, we can then tell the computer to extract
everything we have identified as bone. Now we take all the other pieces of the skull and
scan them with CT as well.  Then, using the same software that movie animators use to
make digitally animated movies, we move each piece into its correct anatomical position.  
Sometimes we color the bones differently so that other scientists know what parts we
moved about and what parts were part of the original.  We do this so others can check
our work and see if they agree.Finally, we mirror image missing parts and add them to the
model.  Because humans are pretty bi-laterally symmetrical (we are almost the same on
our right and left sides), we can do this with some confidence.   The end result is a nearly
complete skull.  

From this point we can start to play with the CT images.  Because CT don’t only look at
the outside, but also record the inside of the skull, we can make the internal anatomy
visible and the external anatomy transparent.  This allows us to see things like the
erupting molars of sediba and even the shape of the outside of the brain.

In this case, we can recreate the outside shape of the brain by taking the patterns of the
brain that are found on the inside of the skull.  During his life, every time Karabo’s heart
beat and while his skull was growing, it was impressing  itself against the inside of his skull
and this makes a sort of mould of the brain.  We call this an endocast.  By creating a
digital copy of these impressions, and then having the computer fill them, we end up with
a cast of his brain!  

Medical CT scans are certainly very valuable, but recently we have had even more
powerful tools available to us.  Micro-CT scanners can create scans that are only microns
thick (to about 1/20th the width of a human hair!), and synchrotrons can make images
even smaller suing energy millions of times more powerful than a medical scanner!  We
took Karabo to the synchrotron facility at Grenoble France and produced one of the most
precise scans of a skull and skeleton ever made.  The first results looked like this.

With this data, scientists around the world can now examine microscopic parts of Karabo’s
anatomy without touching the specimen and see things that we only dreamed of a few
years ago.  This sort of powerful X-ray technology is literally creating new fields science in

Posted May 13th 2012