Mapping the Human Brain

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When you think about all the things humans have put their minds to, it’s impressive. We built and landed robots on Mars to learn more about space. We conjured up theories about how the universe works and then prove them right we sequenced the human genome to paint a complete picture of our DNA. But as for the minds that made this all possible we still don’t know much about how those actually work. Scientists have been trying to navigate the mechanics of our large complicated brains for hundreds of years. What would be really helpful is, if we had a map in order to get one of those we are going to need some brave scientists and very advanced technology. So how close are we to mapping the human brain?

Why Mapping the Human Brain is Necessary?

If we could build a complete map of our brain and translate it imagine what we could do. We think maybe that will give us clues as to the causes of various forms of mental illness, learning difficulties, diseases of aging. If that might better allow us to figure out are their treatments or prevent the onset of some of those illnesses. Mapping the human brain could even help us understand other scientific mysteries like the origins of consciousness.

Our brain is so powerful that if we understood how it worked we might be able to create smarter robots and computers. A map of the human brain is seen as so valuable that multiple efforts across the world are underway to get us there. Aside from some big projects in the US, the European Commission is funding a hundred universities to create a detailed computer model of the human brain. China also announced a project to map the brain and so has Japan. There are even several private projects focused on this goal. So, what do we mean when we say “Mapping the Human Brain”. Specifically, we are talking about creating something called a “CONNECTOME”.

What is Connectome?

A complete catalog of all the structures in the brain and how they connect. Scientist and researchers typically think of there being both a structural and a functional connectome. The structural connectome is the white matter fibers that connect different parts of the brain or the synapses that connect neurons. And researchers call that structural because there’s a physical synapse that they can measure and look at. They are kind of making more of a roadmap of connections among brain regions.

C-elegans-Mapping the Human Brain
C-elegans (Caenorhabditis elegans)

But there is also what they call functional connections in the human brain which have to do with kind of coordination and function across brain regions. That means identifying parts of the brain that work together but don’t necessarily touch. We don’t have any fully mapped functional connectomes yet. And the only structural connectome we have fully mapped is of C-elegans (Caenorhabditis elegans). A transparent nematode about one millimeter in length.  That lives in temperate soil environments. It is the type species of its genus. The name is a blend of the Greek caeno- (recent), rhabditids (rod-like) and Latin elegans (elegant).

Obstacles faced in mapping the human brain

Even though scientist have been able to do that, it’s still a complex organism and there’s still a lot of work to be done to understand how the interactions, give rise to even the relatively simple behaviors that the C-elegans can accomplish. The connectome of the C-elegans brain identifies 302 neurons and if researching and building that connectome was complicated imagine how exponentially more difficult it is to do the same with human brains, who have somewhere in the region of a hundred billion neurons. This is probably the first obstacle scientists have to overcome in mapping the human brain.

The sheer size and daunting complexity. So, they have to start small and I mean really small. The samples they are studying are the size of a grain of sand. Inside that small grain of sand, there are about a hundred thousand neurons and form about 1 billion connections. Now your brain is more than a million times bigger than this grain of sand. So, you can see how many units are compressed in such a small space. And the brain is always changing which makes it even more difficult to study. When we are born the brain grows over the course of development it builds new neurons. We are learning and interacting with the environment and that’s also shaping brain connections and how different parts of the brain work together. But then it also starts to change as we get older and we move into later in life.

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To tackle these challenges the Obama administration started the brain initiative in 2014. Bringing several scientific institutions together to understand and treat the human mind. As part of that coalition, the Allen Institute is analyzing mouse brain samples to count catalog and connect as many different cell types as a foundation for eventually doing the same for the human brain. Using electron microscopy, the team imaged billions of tiny synaptic connections in a cubic millimeter of mouse neocortex.

How they are planning to do it?

Mapping the brain at least at the resolution that scientist do is difficult because many things have to go right in a series preparing the sample has to be perfect. Scientists had to section the grain sized brain sample into 25,000 pristine slices 40 nanometers wide. For reference, a strand of hair is five times as thick as that. Then those slices were distributed over six electron microscopes to be photographed. It took them about five months to take all the pictures of that millimeter cube. They don’t have the final tally but there are certainly hundreds of millions of those. This type of data gathering took exhaustive, dedicated work around the clock. When all the images were collected, researchers could then segment every single neuron and create a 3d wiring diagram. Step one towards that complete structural connectome, which the team estimates will take five years to finish.

Brain Mapping Neurons - Mapping the Human Brain

In terms of data storage was about two petabytes of data. That’s about two million gigabytes from just a millimeter. To eventually work with the bigger human brain samples, something about this process will have to change. As it will eventually be the largest data set ever collected about anything in the world. Researchers think substantial, advances on sample preparations and sample sectioning. And above all, the storage of such will be immense. Either technology will have evolved in a way that such storage is available or their thinking will have to evolve in ways that they can compress the information that they want to extract from it.

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We will also need forms of technology that aren’t as invasive as this so we can study live human brains too. And to develop a really robust map, we are going to need to work with more than just one single brain. We will need to study young brains, old brains, male brains, and female brains. Scientist collected a pretty interesting and unique sample of 1200 individual. The human connectome project, led by the NIH, is using non-invasive tools to study human brains now.

MRI -Mapping the Human Brain
MRI Scanner

So, the main tool the scientist uses to start out is an MRI machine. If they are looking at the structural connectome, they typically use something called diffusion imaging. It’s looking at the diffusion of water along with these white matter connections in the brain. If you have a nice strong connection going in a certain direction between two parts of the brain they can measure that.

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They do something pretty different though when they look at the functional connectome in the human brain. So, they still use an MRI scanner, but they use a different kind of sequence. It’s looking actually at blood flow that they think happens after there has been neural activity in the brain. If you are looking at brain activity in a brain region going up and down over time, you can say “Are there other brain regions that show that same pattern?”. And if the patterns are very similar over time, they call those functionally connected brain regions.

Brain Mapping of Cerebral Cortex

So far, the human connectome project has made a lot of advances in this area of mapping the human brain. In 2016, they released the most detailed map of the cerebral cortex to date. Discovering 97 new brain regions in addition to confirming the existence of 83 others. Scientist understands much more now about how different brain regions kind of wire up together to form networks. They are starting to get a good sense of how those networks relate to which types of behaviors. Where scientist think they still have work to do is understanding exactly how those contribute or are changed by the experience of illnesses, how different kinds of environmental factors might have an impact.


This challenge is immense. It will push our technology and creativity to their furthest limits. But so, did send robots to Mars and sequencing the human genome. And we did all that. So, how close are we to mapping the human brain? The biggest barriers keeping the researchers for building a highly detailed human connectome is really technology. Even in their scientific lifetime, the progress has been exponential. They wouldn’t be surprised in 10 or 20 years if they had a sort of dramatic leap in their understanding. They may never have a map of every connection in the human brain in the sense of understanding exactly how they interact together to give rise to exactly all the humans behavioral and cognitive and emotional abilities.

That’s a tall order and they are not entirely convinced that they will ever be there. Looking at the shape that those neurons, they are beautiful they make them happy. Scientist and researchers are the first ones to see such detail at such scale on the brain like the old explorers when they arrived at the new continent. They are going into a territory where things are new.

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