How Scientists’ are Studying the Brain: A Multi-Method Review

by ljammers

Neuroscience is expanding rapidly. US President Barack Obama is launching a new initiative called ‘Brain Research through Advancing Innovative Neurotechnologies (BRAIN)’, estimated to receive up to $3 billion dollars in investment, it is clear that President George Bush’s ‘decade of the brain’ has left a lasting imprint. So what exactly are scientists doing to try to understand the most complex organ known to exist? There are many technological advances, practically every week, that even as someone within the field it is hard to keep track. Here I broadly break down and explain the different approaches to mapping and understanding the brain, linking biological and cognitive approaches.

 N.B. I do not by any means pretend this is an exhaustive list! It simply reflects an account of my own research into this area, which will hopefully give readers a flavour of the different approaches, and scale of development and innovation in this field.

Post-mortem Dissection

Historically studies of the human body were derived from post-mortem dissections. This approach is still used in most anatomy teaching, including neuroanatomy, and has proved invaluable. My experience of brain dissection is that whilst it was a little ghoulish and odd, seeing and feeling a real 3D brain was really helpful in putting textbook based information into context. However, it of course only allows us to examine at a level visible to the naked eye, and within a dead organism. These two factors are obviously extremely limiting when studying the brain, which is commonly estimated to contain approximately 100 billion neurons (brain cells), and particularly when trying to link structure to function.


A new technique developed in Brazil by Dr Suzana Herculano-Houzel has tried to get a more accurate estimate of the number of neurons in the human brain. Her research team took the brains of four neurologically healthy men and turned them into what has been described as a ‘brain soup’. The method involved dissolving the cell membranes of neurons, and then taking a sample of the soup, allowing one to count the number of neuron cell nuclei within the sample. This figure is then scaled up to calculate an estimate of the overall number of neurons in the brain. Whilst to many this may be a deeply disturbing idea, the scientists were able to reach a more precise estimate, of 86 billion neurons. Furthermore, it also dealt with the issue of different brain regions having more or less dense neuronal packing. The soup created a homogenous sample of neurons from a range of brain regions.

So postmortem brain dissection and research is alive and kicking, but now comes in all kinds of weird and wonderful forms!

Histological Studies

Histology refers to study of cells and tissues of plants and animals under a microscope; this is achieved by sectioning and staining cells and tissues, and examining them under a microscope to reveal the microscopic level of anatomy.


Cytoarchitectonics refers specifically to the study of the arrangement of neuronal cells bodies in the brain and spinal cord. Studying the microscopic level of the human cerebral cortex (a thick layer of neuronal tissue that covers most of the brain and is associated with human evolution) is credited to the Viennese psychiatrist Theodor Meynert (1833-1892). In 1867 he noticed regional variations in the histological structure of different parts of the grey matter in the cerebral cortex.

! For non-neuroscience folks !

The brain is made of both grey and white matter. The cerebral cortex is comprised of grey matter consisting of neurons. The white matter lies in a layer below the grey matter, and consists of the axons and dendrites, which connect neurons with one another and other parts of the central nervous system.

Korbinian Broadmann was a German anatomist who studied the cytoarchitectuaral organisation of neurons in the cerebral cortex. In 1909 Brodmann published maps of different cortical areas in humans. He used the cytoarchitecture of cells to distinguish brain regions from one another, and his map continues to be used widely in psychology and neuroscience when studying structural localization of cognitive functions. Whilst his work was extremely impressive, technological advances have superseded those available to him at that time; better stains and more powerful microscopes are available, allowing scientists to study the brain in even more detail.


Moreover, Broadmann’s maps were based on visual analysis of the cells using a microscope. Recently scientists have begun to use statistical analysis and developed quantitative criteria to redefine regional boundaries. These quantitative criteria involves measurement of cell density within the grey matter, and also patterns between the surface of the cortex and the white matter layer. This information is taken into account to create a sliding window procedure, where boundaries are defined where the cytoarchitectonic structure changes maximally.

See Amunts, Schleicher & Zilles (2007) for a more detailed read!


This technique examines the density of neurotransmitter receptors within different layers of the cortex, which can be useful for telling us about the structure of cortex at a molecular level. Changes in receptor density can provide new criteria for a more detailed mapping of the human brain than can be achieved by cytoarchitectonics alone (Zilles et al., 1995). The density of neurotransmitter receptors varies significantly between different locations in the human brain, and this has been linked to both cytoarhcitectonic or structurally defined boundaries, and to the functional organisation of the cortex (Zilles et al., 2002). Zilles et al (2002) compared data from various methods, including both cytoarchitectonic and post-mortem studies of the human brain, and found that areas of similar function show similar ‘receptor fingerprints’, and differ from those with other properties.

!Key definition!

Neurotransmitters are chemicals that transmit signals from a neuron to a target cell across a synapse. These chemicals are packaged into synaptic vesicles

 A synapse is a gap between two cells; pre- and postsynaptic. In a chemical synapse electrical activity in the presynaptic neuron is converted into the release of a chemical (neurotransmitter ) that binds to receptors located in the postsynaptic cell.

The neurotransmitter then initiates either an electrical response or a secondary messenger pathway, which either excites or inhibits activity in the postsynaptic cell.

Patient Studies

Research studying individuals with neurological and neurodevelopmental conditions, or in those who suffer brain injury after a stroke or accident has provided a cornerstone of modern psychology and neuroscience. By investigating the resulting deficits in such individuals, and linking this with the area of damage to the brain, broad localization of different neurological functions has been possible. Before neuroimaging (see section below) techniques were developed, work of this nature was particularly important.

One particularly seminal case is that of patient “Tan”. Pierre Paul Broca (1824-1880) was a French physician, surgeon and anatomist. He is best known for his research on Broca’s area, a region of the frontal lobe that was named after him. In 1861, Broca met a patient, who had a 21-year history of progressive loss of speech. The patient was able to understand, but not to produce language, and was otherwise mentally competent. He was nicknamed “Tan” due to his inability to clearly speak any other words (Broca, 1861). When he died some days later Broca performed an post-mortem, and found that he had a lesion in the frontal lobe of the left cerebral hemisphere. Broca went on to find post-mortem evidence from 12 more cases in support of the localisation of articulated language (Broca, 1861; Fancher, 1979).

Another classic neuropsychological case is that of “Phineas Gage”, an American railroad construction foreman – ask any psychology or neuroscience undergraduate, and they will no doubt be sick to death of hearing about this rather unfortunate fellow! On the 13th September in 1848 Gage became instantly famous for surviving a horrible accident in which a large iron rod was driven completely through his head, destroying much of his brain’s left frontal lobe. To the astonishment of the men Gage was working with, he was able to speak within a few minutes of the incident and to walk without assistance. Whilst he survived the injury, and initially seemed to have got away scot-free, it later emerged that there were profound changes to his personality and behavior over the next twelve years.

This often quoted passage from Dr John Martyn Harlow (who attended to his immediate care following the injury and subsequently published research papers about his recovery) highlights the scale of change observed:

“ The equilibrium or balance, so to speak, between his intellectual faculties and animal propensities, seems to have been destroyed. He is fitful, irreverent, indulging at times in the grossest profanity (which was not previously his custom), manifesting but little deference for his fellows, impatient of restraint or advice when it conflicts with his desires, at times pertinaciously obstinate, yet capricious and vacillating, devising many plans of future operations, which are no sooner arranged than they are abandoned in turn for others appearing more feasible. A child in his intellectual capacity and manifestations, he has the animal passions of a strong man. Previous to his injury, although untrained in the schools, he possessed a well-balanced mind, and was looked upon by those who knew him as a shrewd, smart businessman, very energetic and persistent in executing all his plans of operation. In this regard his mind was radically changed, so decidedly that his friends and acquaintances said he was “no longer Gage”.”

This was the first time that changes to personality and behavior had been linked to brain damage.


Neuroimaging is a relatively new discipline within medicine, psychology and neuroscience. It includes the use of various techniques to either directly or indirectly image the structure, functions and connectivity of the brain.

Structural – MRI and CT

Structural imaging of the brain is typically achieved using magnetic resonance imaging (MRI). It allows us to visualise the internal structures of the body in detail – rather like an x-ray allows one to visualise bone. It provides good contrast between soft tissues, so is particularly useful when imaging the brain. Structural imaging is widely used in medicine for the diagnosis of large intracranial disease such as tumours, or brain injury.


An MRI scanner is a huge device, in which a person lies with a large and very powerful magnet. The magnetic field is used to align the magnetization of nuclei in the body. Radio frequency magnetic fields are applied to systematically alter the alignment of this magnetization, causing the nuclei to produce a rotating magnetic field. The magnetic field gradients cause nuclei in different locations to precess at different speeds, which allows spatial information to be recovered that is detectable by the scanner. This information is recorded and then a construction of an image of the scanned area of the body is created. By using different combinations of gradient, 2D or 3D volumes can be obtained (Squire & Novelline, 1997).

Click here for information on CT (an alternative form of structural imaging)!

Functional – fMRI and PET

 Functional MRI (fMRI) uses MRI technology that measures brain activity by detecting associated changes in blood flow (Huettel, Song & McCarthy, 2009). The assumption underlying this technique is that cerebral blood flow and neuronal activation co-occur; when a region of the brain is in use, blood flow to that area also increases. The procedure is similar to MRI but uses the change in magnetization between oxygen-rich and oxygen-poor blood as its measures. The resulting brain activation is typically presented graphically by colour-coding the strength of activation across the brain or region of interest.

fMRI has become a commonly used technique in brain research because it is safe and easy to use. fMRI scanners allow research participants to be presented with different visual images or sound stimuli, to which they can respond by pressing a button or moving a joystick. Consequently, fMRI can be used to reveal brain structures and processes associated with perception and cognition. It has good spatial resolution – it is accurate to about 2-3 millimeters at present. However, it is limited by its poor temporal resolution – as there is a time-lag in the increased blood flow response to neural activity.

In neuroscience research fMRI has largely replaced positron emission topography (PET). PET produces a 3D image or picture of function processes in the body using short acting radioactive tracers. PET, retains the significant advantage of being able to identify specific brain receptors associated with particular neurotransmitters through its ability to image radiolabelled receptor “ligands” (receptor ligands are any chemicals that stick to receptors). As cerebral bloodflow can be disrupted in many different types of brain pathology using fMRI can be difficult in a clinical setting. Thus, PET tends to be used more widely in the clinical domain.


Click here for more information on PET!

See my article ‘Neuromarketing: The Future’  for neuroethical concerns about the potential applications of fMRI!

Connectome – DTI

Whilst most neuroscientific research has focused on identifying specific regions for functions, increasing attention is being placed on brain connectivity, and thus the flow of information within and between regions. A new type of MRI called diffusion tensor imaging (DTI) is allowing the network of fibres, or white matter, to be systematically examined, allowing for an analysis of the connections between different cortical regions, composed of grey matter.

DTI uses information generated by the MRI scan to establish the directional flow of fibre orientations. These are the displayed in 2D images by assigning one colour to each orthogonal axis, creating a detailed map of the whole brain network. Using mathermatical theories it is then possible to establish how strongly connected different regions are to one another.

DTIIts main clinical application has been in study and treatment of neurological disorders. For instance, Professor Sachdev et al., have found that with ageing there is a reduction in the efficiency of these networks. Furthermore, they identified that this is related to cognitive function, including decreased information processing speed, and was correlated with performance on tests of executive functions (such as attention and concentration), and visuospatial skills (navigating in space) (Wen et al., 2011)

Its ability to reveal abnormalities in white matter fibre structure and provide models of brain connectivity is a major breakthrough for neuroscience. Since, its invention in 1985 a range of similar techniques have been and are being developed, including diffusion weighted imaging and diffusion spectrum imaging.



Amunts, K., Schleicher, A., & Zilles, K. (2007). Cytoarchitecture of the cerebral cortex—more than localization. Neuroimage, 37(4), 1061-1065.

Broca, P. “Remarks on the Seat of the Faculty of Articulated Language, Following an Observation of Aphemia (Loss of Speech)”. Bulletin de la Société Anatomique, Vol. 6, (1861), 330–357.

Fancher, R., E. Pioneers of Psychology, 2nd ed. (New York: W.W. Norton & Co., 1990 (1979), pp. 72–93.

Huettel, S. A.; Song, A. W.; McCarthy, G. (2009), Functional Magnetic Resonance Imaging (2 ed.), Massachusetts: Sinauer,

Squire LF, Novelline RA (1997). Squire’s fundamentals of radiology (5th ed.) Harvard University Press. P. 36.

Wen, W., Zhu, W., He, Y., Kochan, N. A., Reppermund, S., Slavin, M. J., … & Sachdev, P. (2011). Discrete neuroanatomical networks are associated with specific cognitive abilities in old age. The Journal of Neuroscience, 31(4), 1204-1212.

Zilles, K., Palomero-Gallagher, N., Grefkes, C., Scheperjans, F., Boy, C., Amunts, K., & Schleicher, A. (2002). Architectonics of the human cerebral cortex and transmitter receptor fingerprints: reconciling functional neuroanatomy and neurochemistry. European neuropsychopharmacology, 12(6), 587-599.

Zilles, K., Schlaug, G., Matelli, M., Luppino, G., Schleicher, A., Qü, M., … & Roland, P. E. (1995). Mapping of human and macaque sensorimotor areas by integrating architectonic, transmitter receptor, MRI and PET data. Journal of anatomy, 187(Pt 3), 515.