Neuron Laboratory

'Sapere aude'

Blue Brain

The brain seems like a challenging enough object of study. This section collects my ideas of the operation of the neurons in the brain to answer this one question:

What process in the brain allows us to participate in the moment ?

Neuroscience has a pretty good idea of how long term memories are created and stored in the brain (Donald Hebb's Fire together/Wire together), but this function requires an actual growth of interconnections in the brain and requires long periods of time - days to weeks to complete. Learning to play a passage on the piano is this type of learning.

Short term or working memory is being studied but there doesn't seem to be an agreement on the mechanical apparatus that does the work. Remembering a list of numbers read to you five minutes ago is an example of this type of learning.

This may be the answer - I think that STDP and possibly Synfire Chains give us the ability to live 'In the moment - the last 100 mSec or so? I can think of no other set of mechanisms that work in milliseconds and could be responsible for the range of processing needed to keep us aware of the world.

I want to understand the processes that allow us to be aware of our surroundings in the tens of milliseconds time frame. No one seems to have an idea on this, or at least I haven't run across it yet. Needless to say - its complex.

Yes Its Very Complex

The complexity in the brain is by far in excess of the complexity of any other thing humans have confronted. And this is a very hard and painful pill to swallow for scientists, when you're trying to understand something that has so much complexity.

And let me give you a sense of how complex it is.

In a technique like functional magnetic resonance imaging, where the brain is divided into voxels-- little cubic points of data that's related to blood flow-- the grain of that image is about one cubic millimeter per voxel. And that still gives rise to a million voxels in a brain. So, there's a huge amount of data in fMRI images.

If we take one of those cubic millimeter voxels and ask, how much resolution do we need to see all these synapses in that voxel? We need about 2,000 terabytes of data-- 2 petabytes per cubic millimeter.

So, if we wanted to do a whole human brain, we would deal with like 2 million petabytes of data-- 2 million, million terabytes-- which is comparable to the digital content of the world.

It's an extraordinarily large number and much more than will fit on my laptop.

Prof. Jeff Lichtman - Harvard

Along the way, I wanted to present what I have found in a format that is accessible to others like myself - interested in the subject but not expert in it. I decided publish my learning process as well in near real time and this web site is the result. It will be continuously updated as I work on the project.

I made the decision to move toward an understanding of the neuron using simulations rather than a exhaustive accounting of all neuron actions, bits and pieces. For this reason, the synapse topics like neural transmitters, RDNA, re-uptake, etc are all ignored. They are completely covered in endless detail in other well written books and on-line classes many of which I used in this quest.

I don't consider my effort will result in a solution to the question only a way for me to gain an understanding using the tools I have at hand.

Development notes: I try to keep a running notebook of ideas, tests, failures as I work on the Neuron project. You can access it here:

During this process I used several books and made use of on-line classes:


  • Principles of Neural Scence - Kandle and Schwartz
  • Neuroscience - Bear, Conne and Paradiso
  • Neuroscience - Purvis et. al
  • Dynamical Systems in Neuroscience - Izhikevich
  • How to Build a Brain - Ellasmith
  • The NEURON Book - Carnevale and Hines
  • From Neuron to Brain - Wallace
  • Theoretical neuroscience - Dayan and Abott

On-Line Classes

  • Computational Neuroscience - U. Washington via Coursera
  • Simulation Neuroscience - EdX
  • Medical Neuroscience - Duke via Coursera
  • Fundamental Neuroscience - Johns Hopkins via Coursera
  • Fundamentals of Neuroscience 1,2 and 3 - Harvard Online
  • Cellular Mechanisms of Brain Function EPFlx via BrainX
  • Circuits and Electronics - MIT via MITx
  • Neuroscience - School of Physics, University of Sydney (
This project consists of:
  1. The Cell and Ions - Description of the cell membrane and its chemical makeup. The movement of charged ions across the lipid bilayer and what is an ion channel.
  2. Neuron Time Constant - The electrical calculations of time and the effect of opening an ion channel
  3. NeuronLab Simulator - Description and download link for the simulator along with videos for installation and basic operation. The simulator is for Windows only.
  4. Dendrites - The organization of the dendrite tree and the calculations of the charge in the compartments. This includes a setup on the simulator for close in understanding.
  5. Soma - The makeup of this vital part of a neuron and a simulator setup that illustrates the generation of the action potential using Izhikevich neuron calculations.
  6. Axon - Transmission of action potential down the axon compartments.
  7. Neuron - The complete operation of a simulated neuron with Dendrites, Soma and Axons all firing.
  8. Neuron Papers - A collection of publications on the subject

My Brain with neurons firing.

... yes that is my actual brain

Would you want to live in a world like this?

Guess What - its your world

Dendrites 'growing' a memory


NEXT - Cells and Ions