This is my article which was shortlisted for the Max Perutz Science Writing Award 2012 – an annual competition to encourage MRC-funded scientists to communicate their research to a wider audience. You can also read the winning article, published in The Metro, here.

Rodrigo Braga at the Max Perutz Award Ceremony

The human brain is the most complex object in the known universe. With it we have built entire civilisations and harnessed the power of nature. Yet despite their amazing complexity, all brains begin life as a tiny bundle of cells that divide, migrate and miraculously wire themselves up into the thinking machines that make us who we are. The fact that it happens at all is almost as astounding as the finished product itself, but it doesn't always work out as Mother Nature intended.

Tucked up in her crib at the Neonatal Imaging Centre of Hammersmith Hospital, newborn baby Eliza is sleeping through another magnetic resonance imaging (MRI) scan. Around her head, the scanner machinery wails and screams with high-pitched ululations, but she sleeps peacefully, ears protected by tiny muffs. Eliza was born prematurely and her doctors are making sure that her little brain is growing normally. In her short 10 week life, she has been inside the scanner more times than most of us ever will. But today is different. Today we are using a new technique called Diffusion Tensor Imaging (DTI) to help unravel the mysteries of brain development. And that is a huge task.

The human brain contains 1,000 trillion connections between 86 billion neurons (neurons are what we really mean when we say 'brain cells'). Each neuron has a long thin arm called an 'axon' that it uses to send messages to other neurons that could be on opposite ends of the brain. Connecting them all means criss-crossing the brain with axons.

To give you a sense of the resulting confusion, imagine a planet (let's call it 'Braintopia') that is packed with ten times more people than planet Earth. Imagine that every Braintopian has to make regular long distance calls to an overbearing mother on the other side of the planet. On Earth this would be easy, but Braintopians haven't discovered mobile phones or landlines yet. Instead, all they have are those cup and string phones that children play with here on Earth. Each Braintopian carries their own paper cup, and trails along a string that stretches around the globe to mum. Simple!

It might seem absurd, but this is actually how neurons communicate, through a direct physical connection. In order that you can wriggle your toes, a daring axon made the journey from the top of your brain to the bottom of your spinal cord to pass the message on to your legs. Now if a single Braintopian trailing a string like an umbilical cord sounds ridiculous, picture the mess that a whole city-full of them would make, strings tangling through the streets like a Great Spaghetti Monster. Or worse, imagine the chaos of an entire planet-full of intercontinental strings. The resulting ball of yarn would be monolithic!

The brain has a similar connection problem, but it maintains order by packing the axons heading in the same direction together into thick fibres called 'white matter tracts'. Recent research suggests that the normal development of white matter is an important indicator that a baby's brain is healthy. If a white matter tract doesn't develop properly, the brain regions connected by that tract cannot communicate with each other. This can lead to serious physical and learning disabilities. If doctors could assess a baby's white matter early on, they could check the connections are healthy and in place, and give special attention to the infants that need it. But doing this when the brain is sealed inside a baby's head is extremely challenging. Luckily, this is where DTI comes in.

Back in Hammersmith, Eliza's scan is almost done. The DTI procedure uses the MRI scanner's powerful magnets to spin the atoms in Eliza's brain on the spot, like pirouetting ballerinas. Atoms spin frantically anyway, but when placed inside a magnet they align their spin with the direction of the magnetic field. And so the ballet begins. In this synchronised dance, each atomic twirl sends out a tiny radio signal that the scanner uses to work out where the atom is. From this, we can find atoms that are attached to water molecules and trace them as they float around Eliza's brain. The brain is 70% water, and white matter tracts act like miniature hosepipes, channeling water along them. By following the movement of water we can therefore visualise exactly where the white matter tracts lie. Using this principle we have created a white matter atlas for babies, to help doctors recognise abnormal brain development.

Eliza continues to sleep while the scanner diligently chugs away. This short 20 minute scan will produce a beautiful map of her own Braintopia without hurting her in any way. By comparing Eliza's map to our atlas, doctors can tell if her fibres are healthy, and give her the best possible start in life.