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Simulations of the Human Brain


Fun fact, the human brain is weird. But weirder than you think. For about the first 12 years of my life I was a case study volunteer for two hospitals and one university. Every month or so I'd get a phone call, go over to the center, answer some questions, and have a bunch of electrodes stuck to my head. Or be placed in an MRI machine. It was fun, and I kind of understand how Homelander felt as a kid. But over the whole process I learned a few things about my brain I didn't really know. Such as, a good MRI technician can know when you are afraid by looking at where the activity is in your brain. Or how well the facial recognition part of my brain worked.

So I wanted to share some knowledge out of general interest. As well as the simulation technology around the human brain that is starting to be developed. Let's get started.

How Your Brain Works

Your brain is the center of your personality, thought, creativity, emotion, and movement. It is a network of billions of neurons and nerve endings to the rest of your body. In a split second, you can decide if you want ice cream, or if it's worth watching South Park for the 35th time.

Fun fact: the human brain doesn't fully mature till you are 25-30. So whatever you do to your brain between now and then really matters. It's also a very important reason to keep learning new things.......


So let's dive into different parts of the brain that can help you make those choices, and why you are who you are.

Your Brain's hemispheres are divided into four lobes:

  • Frontal Lobes: These control your thinking, planning, organizing, problem solving, short term memory, and movement.

  • Parietal Lobes: These control your sensory information. Such as taste, touch, and temperature.

  • Occipital Lobes: These control the images from your eyes and process visual information, and how it can be linked to other memories in your brain.

  • Temporal Lobes: These control your sense of smell, taste, and sounds. They also help to form new memories.

These lobes can be divided into even smaller and specific areas. One of these areas is called The Cerebrum.

The Cerebrum is the largest part of your brain. It is the outer layer of your brain and contains all the other parts inside of it. The outermost layer of the cerebrum is called the cerebral cortex. It is mostly made up of grey matter. The cerebrum is divided into two halves by a deep line. When you look at a picture of the brain from above, this is the line you see on the top. The two halves of the cerebrum communicate through a series of nerve paths. These paths are called the Corpus Callosum.

Next is The Cerebellum. The Cerebellum is located at the bottom and at the rear of your brain. It combines all the sensory information from your body's sensors. These include the eyes, ears, and your overall muscles.

One of the most important areas of the brain is The Brainstem. The brainstem connects the brain to the spinal cord. It controls your heart rate, blood pressure, sleep, and breathing. If you damage this area of the brain, you die.

Another system in your brain is called The Limbic System. You can think of it as a twin element in your brain. Each structure of the limbic system is mirrored on either side of your brain. It is made up of four main parts:

  • The Thalamus: This part controls the messages passing between the cerebral hemispheres and spinal cord.

  • The Hypothalamus: This part controls emotions, your body's temperature, and "urges." Whether that be sexual, eating, or sleeping.

  • The Hippocampus: This part sends your memories to different parts of the brain. Then tells you to recall them when needed.

  • The Amygdala: This part attaches emotions to your memories, and your associations and responses to them.

The Peripheral Nervous System is next. This system connects all the nerves in your body. Minus the ones in your brain and spine. It makes sure your brain is communicating with the other parts of your body. So if you feel something hot, this nervous system let's your brain know that maybe touching this object isn't a great idea.

So after reading about those key areas of your brain, we should probably talk about the little messengers that travel through all these systems. These are Nerve Cells, or Neurons. These carry all the information you need around your brain.  As cells, they have two main branches coming off them. You can kind of picture them as an input and an output. Dendrites are the inputs, and they receive messages from other cells, and Axons are the outputs. They carry the messages to other cells. All neurons operate on electrical impulses. When these impulses travel through a neuron, they travel to the tip of an axon, and cause it to release a bunch of neurotransmitters. Then these transmitters pass through any synapses (gaps between brain cells), and attach themselves to the dendrites on the next cell.

So that was a lot of information. Now we can break into the fun stuff. But before we move on, keep this in mind. (No pun intended.)

Studying the anatomy of the human brain is called Neuroanatomy. But if you study the functions of the brain, that is considered neuroscience.


A Quick History of Simulations in Neuroscience 


Scientists have been using a variety of ways to study and image the human brain for years. Traditionally, they have used microscopes to capture close up glimpses of animal and human specimens. As well as rare and extreme cases of brain injuries to achieve insight into functions in each part of the brain. But recently, tools such as neuroimaging, and electroencephalography (EEG) recordings have emerged. These play a huge role in studying brain functions. 

Simulations are also creating a huge role on how we view brain behavior. Simulation science is a huge advantage in this field, because it allows for experiments to take place in a controlled environment, with no risks to patients. They are also a lot cleaner, and are more forgiving as scientists do not have to cut into actual flesh, and think before they cut.

But where would you even start when attempting to build a simulation of a brain? Sure, modeling one might be easier, but how do you copy someone's consciousness and actions digitally? 

Let's start from the beginning.

The first research into neuroscience started a few centuries ago. It was pure experimental research based on observation, measurement and experimentation. As computers only were created less than a century ago, (1943) these observations were all done by hand, and through practical application.

About 475 years ago, one of the first person to study the brain was a man called Andreas Vesalius. He was a Flemish anatomist, and is responsible for discovering white matter and grey matter in the brain. As well as being considered the founder of modern human anatomy. He mostly studied corpses.


For anyone wondering, white matter is responsible for learning, and sending messages around your brain. It contains all nerve fibers and neutrons. Grey matter is responsible for processing all the information your white matter generates. It also is responsible for your motor skills.

  • Then in about 1719, vessels in the brain were observed for the first time. Up until this point, the brain was just thought to be a fleshy mass. These were first discovered by Antonie van Leeuwenhoek, also thought to be the father of Microbiology. 

  • In 1858, nerve cells started to be classified into pyramidal cells, small and irregular or granular cells and spindle-shaped cells. This started the study of cytoarchitectonics.

  • In 1867, cortical layers and cell function were observed for the first time in brains as well.

  • In 1891 neurons were discovered by German anatomist Wilhelm Waldeye, by using current diagrams of cell theory at the time.

There were a lot more discoveries, but for the sake of this article, I am keeping the list short.

Through these observations, two main phases of research have emerged. These are experimental and theoretical phases. These are important to consider when mapping the human brain. These forms of research have three distinct paths.


  • The first being neuronal mapping. Neuronal mapping attempts to classify and catalog different types of cells in the brain. 


  • The second is connectivity mapping. This aims to map connectivity between individual neurons traveling through the brain. Neurologists have primarily used topographic maps of major nerve tracts between brain regions to map brain connections. But now they are starting to use physiological maps of connections between individual neurons. 


  • Then finally, functional mapping. Functional mapping tries to relate brain function and behavior to the structure of the brain. Generally, stereotypes of human behavior have been used to map brain behavior. Which has then helped to better understand the overall function of the organ.

With all of these functions combined together, suddenly it becomes fairly simple for anyone to get a good starting point to understand the thinking structure of the brain. This is where simulations take the experimental and theoretical approaches listed above, and try to achieve a digital reconstruction. The goal of simulation neuroscience is to build a complete digital copy of the brain. However, still to this day, that goal has not been achieved. 

But this doesn't mean scientists aren't trying. They know in theory that the digital copy should contain synthesized principles of cellular structure of all the neurons and glial cells. It should also demonstrate a good molecular organization and interaction of how ion channels and receptors work in the brain. As well as synaptic connectivity, show how the brain regions are connected, and how the brain attaches itself to the rest of the human body. Just as you might guess, this is rather hard to do. Both from an observational perspective, and a technical one.


Diffusion MRI (dMRI), Functional Magnetic Resonance Imaging (fMRI), and regular MRI techniques have greatly improved the observational process. MRI machines were first developed in 1977, while dMRI was invented in 1991, and then fMRI in 1990. All of these are slightly different imaging techniques, but they have provided a huge leap of information into the brain.

  • A regular MRI is a medical imaging device that uses magnetic fields and radio waves to generate images.

  • Functional magnetic resonance imaging systems involves the same process as a regular MRI, but measures brain activity by detecting changes associated with blood flow.

  • Diffusion MRI systems involve diffusing water solutions into the brain tissue, and then observing any changes under an MRI.

As you can see, there are many methods of observations that scientists are using to copy the human brain. One other one that they use is a bit different. It is called Single-cell staining. It is currently the only available way to study neural circuits at microscale. It involves isolating a neutron in the brain, injecting it with a micro-electrode to simulate it's firing, and then observing it's behavior.

As of today, imaging and gathering information about the brain is fairly easy. But what are the challenges of building one?

Well there are a few.

One of the major issues for creating a brain simulation is creating the simulated Nano-connections. There are a huge number of neurons in the human brain, well over 85 billion. With our current technology it would take 10 million years to map all the synapses in a single human brain. The second issue is the storage and processing power it would take to hold memory data. Currently, the most recent EM data suggests our brains run on the equivalent of a few gigabytes per minute. This pushes the limits of our current computing power, as a computer would need to be capable of executing one quadrillion operations per second to mimic the human brain.

Creating a biologically similar simulation also poses a bit of a challenge. The simulation would need any almost limitless set of parameters, and attributes to draw information from. So the amount of randomness and possibilities to program into a model would be almost impossible. The speed that a computer would also need to mimic synapses firing is currently not readily available. Only a quantum computer could have this ability.

However, we do know through single cell recording techniques that specific brain functions are localized in certain populations of cells. These cells are considered to be "complex cells" with specifically oriented receptive fields. Such as “place cells” in the hippocampus and “face cells” in the superior temporal sulcus that respond selectively to faces. This is great because we can recreate these cells and their location with their proper functions. Currently, whole-brain cell atlases are being built, which will provide insights into cellular organization. The first dynamic 3D cell atlas for a whole mouse brain has recently been achieved. This model was able to provide insight into the densities and positions of all excitatory and inhibitory neurons, astrocytes, oligodendrocytes and microglia in each of the 737 brain regions of a mouse. So doing this for a human is very possible, we just have to develop the technology to achieve it.

On the up side, we have already created some very useful human neural simulations. One in particular can simulate up to 4 million neurons of the brain's visual system. Another is a simulation of a rat brain, (as previously mentioned above) and is a construction of 31,000 cortical neurons, comprising 207 cell types, and is connected by 36 million synapses. 

Scientists are also trying to combine top-down and bottom-up models of the brain in simulations. As well as creating digital tools out of these  models so they can be proceduralized.

The Human Brain Project

This is probably the biggest current project in helping develop a working simulation of the human brain. The Human Brain Project is a 10 year long research project started in 2013 to achieve deeper knowledge into neuroscience, computing, and brain-related medicine. By using exascale supercomputers they are hoping to build a fully accurate model of the brain over the next few years. They use a mix of  Neuroinformatics, High Performance Analytics and Computing, Neurorobotics, and Neuromorphic Computing to accomplish their goals. Currently, they employ over 500 scientists at more than 100 universities across Europe.  


You can check out their website HERE.

The Human Brain Project also hopes that through their research into brain simulations they can reduce the need for animal experiments, study diseases in-silico experiments, and improve the validation of data and experiments with computers.

So far between October 2013-March 2020 they have achieved the following:

  • Generated data-driven models of CA1 microcircuits and full-scale networks.

  • Generated data-driven models of hippocampal synapses.

  • Generated detailed models of hippocampal pyramidal cells.

  • Demonstrated that the adult hippocampal has membrane conductance.

  • Established a workflow for data-driven modelling of hippocampal neurons and circuits.

Houdini, Brains, and MRI Data

So, I'd love to say it's possible to make a copy of your brain, map it inside Houdini, and let your digital self run wild. Honestly, it would be my preferred final form as a Houdini artist. However, we just aren't at that point in reality. But there are some other cool things you can consider doing with the software.

Entagma, (I'm sure you've heard of them) has a great tutorial where they explore MRI data inside of Houdini, and create a brain scan effect out of it. They've done a great setup for bringing in data sets into Houdini, and turning the MRI data into VDBs. You can check out the tutorial HERE.

On a little bit of a different topic. SIGGRAPH has been showcasing some pretty amazing advancements on brain biometric systems. One being a Brain Modulyzer. This is an interactive exploration tool for exploring functional magnetic resonance imaging fMRI scans. As well as allowing analysis of correlations between different brain regions when resting or when performing mental tasks. The Brain Modulyzer also uses heat maps, node link diagrams, and anatomical views to better show brain activity.

Virtual reality is also being used to input stimulus into users so Brain-Computer Interfaces can be developed. By doing this scientists can analyze brain responses to visual input and real-time reactions. Then they can pinpoint the areas of electrical activity, and see the relationship between external stimuli and brain activity.


Brain Models and Simulation:

The four biggest challenges in brain simulation:

The Human Brain Project Hasn’t Lived Up to Its Promise:

Simulation of a Human-Scale Cerebellar Network Model on the K Computer:

This Attempt to Simulate the Human Brain Fell Amazingly Flat:

Will we ever… simulate the human brain?:

Understanding what counts:The key to make brain simulation feasible.:

The Crucial Role of Brain Simulation in Future Neuroscience:

There’s an algorithm to simulate our brains. Too bad no computer can run it:

A Brief History of Simulation Neuroscience:

ViSimpl: Multi-View Visual Analysis of Brain Simulation Data:

A Brief History of Simulation Neuroscience:

Physics Simulations and Simulating the Human Brain:

Importing an MRI Scan as VDB Volume:

Brains and Blocks: Introducing Novice Programmers to Brain-Computer Interface Application Development

A Survey on Brain Biometrics

Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity

The Brain Matters: A 3D Real-Time Visualization to Examine Brain Source Activation Leveraging Neurofeedback

Do men and women have different brains?:

Brain Maturity Extends Well Beyond Teen Years:,maturity%20until%20the%20age%2025.

Adolescent Maturity and the Brain: The Promise and Pitfalls of Neuroscience Research in Adolescent Health Policy:

Why is 18 the age of adulthood if the brain can take 30 years to mature?:

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