Measuring brain activity, from one neuron to the whole brain

Before starting

The pathway assumes a basic knowledge of neurons and action potentials; Cells of the brain, How the brain works and the glossary cover the terms used. Each step uses one tool and asks what it can and cannot show.

The answers are kept in this browser only and are not sent to GloNeuro. At the end they form a worksheet that can be saved or printed. Other pathways are listed on Learning pathways.

1. Where to look

Open the 3D brain atlas at the chapter on movement and find the primary motor cortex, then the hippocampus in the chapter on memory. Note where each region lies and how deep it is below the skull.

The two regions, where each lies and what each does Why the depth of a region matters for the choice of a recording method This step is complete

2. One neuron

In the patch-clamp simulator, inject steps of current into the model neuron and watch its membrane potential. Whole-cell patch clamp records the voltage or the current of a single cell with a resolution well below a millisecond, usually in a brain slice or in cultured cells. The patch-clamp guided experiment follows the procedure on a real rig.

What happened as the injected current increased, and what the channel blockers changed What a recording from one cell cannot tell about the circuit it belongs to This step is complete

3. Many neurons

A silicon probe records the spikes of many neurons at once from outside the cells, and spike sorting assigns each spike to a neuron. Run the spike-sorting simulator, where the true assignment is known, or the silicon-probe guided experiment.

The sorting errors you found, such as merged or split neurons How such errors could change a conclusion about the neurons This step is complete

4. A population, by imaging

In the calcium-imaging simulator, compare the fast and the slow indicator and change the frame rate. Calcium imaging shows which cells are active and where they are, but the indicator reports calcium, not the spikes themselves, and it rises and falls more slowly than they do.

What changed with the indicator and the frame rate Why a calcium signal is not a direct count of spikes This step is complete

5. The whole human brain

EEG records the summed activity of large populations of neurons through the scalp, with millisecond timing but poor localisation; the EEG simulator shows how averaging many trials reveals the P300. fMRI measures the BOLD signal, which follows changes in blood oxygen and flow and peaks several seconds after the neural activity; the fMRI simulator shows how the timing of a design affects what can be detected.

What EEG and fMRI each measure, and their timing and spatial detail Why neither method records the activity of single neurons This step is complete

6. Choosing a method

A group asks whether a drug changes the response of the motor cortex during a simple finger movement, first in mice and then in people. No single method answers every part of the question.

The method or methods for each part of the question, with the reason What is given up with each choice: detail in space or time, invasiveness, species What would remain unanswered This step is complete

The worksheet

The answers above form the worksheet. It can be saved as a text file in Markdown format or printed. A completed worksheet is a record of the reasoning, not a grade or a certificate.

Notes for supervisors

Suited to a module on neurophysiology or neuroimaging methods; about two to three hours, in one session or two.

For bachelor’s students, steps 1 to 5 can be set as independent work and step 6 discussed in class. Master’s students can be asked in step 6 to name the controls, the sample size and the main sources of bias for each method chosen.

Discussion points: what each signal measures directly, the difference between recording activity and showing that activity causes behaviour, and why results from mice and people are compared with care.