Fortunately for us, our brains are well contained and protected inside of our skulls, unfortunately, this makes studying the brain extremely difficult. The simplest way to study the brain is postmortem, after a person has died the brain can be dissected, easily labelled, and viewed under powerful microscopes. Obviously this has major drawbacks, if we want to monitor how a disease progresses in a person it can be difficult to do if we can only examine the brain postmortem.
Molecules that build up in the brain can be examined in living people by withdrawing cerebrospinal fluid (CSF), a fluid found surrounding the brain and spine, but this can only be used to determine general levels, not locations within the brain where the molecule may be building up. However, a link between Alzheimer's disease (AD) and a molecule known as beta-amyloid was shown by examining beta-amyloid levels within CSF.
In humans, many imaging techniques have been developed to examine the brain while it's functioning. Functional magnetic resonance imaging (fMRI) uses the different magnetic properties of hemoglobin, the oxygen carrying molecule in the blood, to monitor brain activity in real time by monitoring changes in oxygenation, and by extension activity, during various activities. This only gives a very broad idea of regional activity of the brain.
Another technique, called positron emission tomography (PET), can give more precise information on the brain by using specifically labelled (safe) radioactive molecules that can be examined as the radioactive molecule decays and gives off a signal. Different molecules can be designed to look at different areas of the brain or different targets. PET is often used to diagnose dementia (such as AD)and was also used to demonstrate the link between AD and the beta-amyloid mentioned above.
New techniques are being developed all the time to better examine the living brain. In mice there are even techniques that surgically add a window to the mouse's skull for live imaging of mice brains during certain activities. Of course between the difficulty of examining the brain in living people, and the incredible complexity of the human brain, it's difficult to definitively link any condition to specific causes.
I've added a link to a NPR podcast below about brain imaging being used to examine the link between AD and sleep which may be interesting to you.
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