Bench modeSteps, parts, and safety only. Big type for a phone at the bench.
Microvolt
Phase 4

The brain behind the signal

The neuroscience and the models, now that every equation points at something you have measured.

You have spent three phases treating the brain as a signal source. Now the biophysics, the circuits, and the models. Hodgkin and Huxley's equations are more interesting after you have heard a spike. The forward problem is more interesting after you have wondered why your alpha showed up on every electrode.

This is the phase where the theory finally gets to go first, because you have earned it. You know what a spike sounds like, what alpha looks like, and how blurry a scalp map is. Now you find out why.

The projects here are mostly software: neuron models from the equations up, a forward model of the head and an attempt at inverting it, and simulators of what the two most successful neural prostheses deliver. Neuromatch Academy, the summer after this phase or during it, is the best three weeks you can spend.

Reading

Kandel a chapter a week is the backbone. Dayan and Abbott for the modelling. Sterratt for a gentler on-ramp. The reading thread has an order that matches the projects.

Projects

Choose one. Do a second if hooked.
Project

Project A: Neurons from the equations up

Hodgkin–Huxley in Python from the four equations, then leaky integrate-and-fire, then Izhikevich, then a spiking network in Brian2. You heard a spike in Phase 1; now you make one.

Two weekends$0Tier 0Project

Project B: The forward and inverse problems

Put a dipole in a head model and compute the scalp potentials. Then try to go backward. Compare to the spatial map you measured on the phantom. The physics of why scalp EEG is blurry, done by you.

Two weekends$0Tier 0Project

Project C: Prosthesis simulators

A cochlear implant vocoder that turns your recorded voice into what a 12-channel implant delivers, and a phosphene simulator that turns a webcam into what a retinal implant delivers. Software only, and the fastest way to understand what a neural prosthesis actually transmits.

One weekend$0Tier 0Project

Project D: Neuromatch Academy

Free, online, three weeks in July: the best crash course in computational neuroscience there is, with a project and an alumni network that is real. What it is, how to get in, and how to arrive ready.

Three weeks in July, plus a month of preparation$0 (fee waivers available)Tier 0Project

Project E: Large-scale neural data

Hundreds of neurons recorded at once from a mouse's visual cortex, downloaded free. Spike sorting, quality metrics, tuning curves, and the population view that Phase 3's decoders were pointing at.

Two to three weekends$0Tier 0

Explainers

Theory that attaches to what you just built. Read after doing.
Explainer

Neuron biophysics

Nernst and Goldman, the cable equation, dendrites, myelin, and conduction velocity. The physics underneath the four Hodgkin–Huxley equations you just integrated.

16 minExplainer

Synapses and plasticity

How one neuron changes another, how the connection strengthens or weakens with use, and why that is the mechanism behind a BCI user learning to control a cursor and a stroke patient recovering.

12 minExplainer

Neural coding

Rate codes, temporal codes, population codes, tuning curves, and low-dimensional manifolds. The theory that says what a decoder can and cannot read from a set of neurons.

14 minExplainer

Where oscillations come from

Pacemaker cells, excitation-inhibition loops, thalamocortical circuits, and why aligned pyramidal neurons make a field the scalp can see. The mechanisms behind alpha, spindles, slow waves, and gamma.

14 minExplainer

Motor cortex and the systems BCIs target

Primary motor cortex, premotor and parietal areas, the hand knob, the speech motor area, and why intracortical BCIs go where they go. The anatomy behind every cursor and every decoded sentence.

12 minExplainer

Sleep neuroscience

Stages and their circuits, the two-process model, replay and memory consolidation, and what closed-loop stimulation is trying to do. The biology behind the hypnogram your band drew.

12 minExplainer

Sensory systems as prosthesis targets

Cochlea to auditory nerve, retina to optic nerve, skin to somatosensory cortex, the vestibular organs. Where each sensory prosthesis connects, why hearing succeeded first, and what touch feedback for a prosthetic hand requires.

12 min

Reference

Look-up pages.
Reference

A reading order for Kandel

Principles of Neural Science is 1,600 pages. Here is which chapters to read in which order so that each one lands on something you have already built, one a week for about a year.

One chapter a week

Ready for Phase 5 when

Checks save on this device

What an interviewer would ask

If you can answer these, you are done here
  1. Why does a Hodgkin–Huxley neuron have a refractory period? Point to the variable responsible.
  2. What can MEG see that EEG cannot, and vice versa?
  3. What does a cochlear implant actually transmit, and why do users struggle with music?
  4. How would you tell a rate code from a temporal code in a recording?