Methods & Tools Overview
Introduction
Thanks to rapid technological and methodological advances, neuroscience has made giant leaps in understanding the functions and inner workings of the brain. With cutting-edge neuroimaging and recording techniques, precise experimental manipulations, and a large dose of creativity, researchers continue on their quest to uncover some of the mechanisms deeply enclosed beneath our skulls. In many studies, these methods and tools are often combined to complement one another, multiplying perspectives to better capture the complexities of brain and behaviour. Though the brain guards its secrets well and much remains to be discovered, each breakthrough sheds new light on its inner processes and opens new paths for the testing of competing hypotheses. The following overview presents some of the key methods and tools used to investigate how the brain generates and shapes our conscious and unconscious perceptions, cognition and behaviour.
Neuroimaging and Recording
Neuroimaging and recording techniques allow scientists to visualise and measure the brain and its activity. These methods can be used to study the structure as well as the functions of its different regions. As many of these can now be used while subjects are busy engaging with a variety of tasks, they provide powerful and informative ways to study in real-time what happens when we perceive the world, reason or perform actions. By correlating the information obtained with real-life tasks, they enable the mapping between brain processes and their functions and reveal the dynamics of its activities. Widely used in neuroscientific research, many of these tools are also incredibly important in medical settings, where they are used for the diagnosis and further treatment of neurological disorders. ​
FMRI
Functional Magnetic Resonance Imaging, or fMRI, is a neuroimaging technique that indirectly maps brain activity by detecting changes in blood oxygenation within the brain. When a brain area is active, blood flows to supply the working neurons with oxygen. In the blood, the magnetic properties of haemoglobin change depending on whether or not it is carrying oxygen: fMRI is tracking that change. This technology can then generate images that highlight which regions of the brain are active when one is performing specific tasks.fMRI can reveal details a few millimetres in size. Activity can be measured up to several times per second, but fMRI remains limited by the natural delay of our biological processes. Indeed, it takes several seconds for blood vessels to respond to the activation of a brain area. Regardless, fMRI remains an incredibly precious neuroimaging tool for research and medicine. Its main strength resides in offering a non-invasive way to measure activity as people are awake and engaged in behavioural tasks. Plus, unlike classical MRI, it does not require the use of radioactive markers to function.
EEG
Electroencephalography (EEG) is a neuroimaging technique that records the brain's electrical activity by using electrodes directly placed on the scalp. It can detect minute electrical signals produced by the synchronized activity of large groups of neurons in the cortex. The neurons recorded are oriented in such a way that each of their signals adds up and their sum can be picked up as it reaches the scalp. EEG stands out in terms of temporal resolution: as it records neuronal activity directly, it can capture their dynamics in milliseconds. EEG is especially useful when studying fast cognitive processes: it can track and time the quick changes of activity, as information travels between different areas of the brain. However, the electrical signals become slightly distorted as they travel through the skull and scalp, which is impacting EEG's spatial resolution. EEG is widely used in research and clinical settings alike.
MEG
Magnetoencephalography (MEG), is in essence very similar to EEG: this non-invasive technique records neuronal activity from the outside of the skull with the help of highly sensitive sensors. While EEG records electrical signals produced by the neurons, MEG captures the small magnetic fields generated by these same currents. As a result, it shares EEG's high temporal resolution and activity can be recorded to the scale of milliseconds, allowing to track fast dynamics in brain activity. One advantage of MEG over its cousin, is that the magnetic signals recorded are not as distorted by the skull and the scalp. Still, its spatial resolution is not as high as with fMRI. The sensors needed for MEG further need to be shielded from the external magnetic noise of the environment by an alloy of nickel and iron and cooled down to -269°C with liquid helium! Only under such conditions, can it allow for the superconductivity necessary for it to function, and heavily reduce signal loss. MEG machines are thus bulkier and more expensive than those of EEG, which partly explains why EEG still remains most often used.
ECoG
Electrocorticography (ECoG), also referred to as intracranial EEG (iEEG), is a neuroimaging technique that measures the electrical activity of neurons by using electrodes that are placed directly on the exposed surface of the brain. Unlike EEG that uses electrodes placed on the scalp, ECoG requires a surgical procedure, and although it does not penetrate the actual brain, this makes it more invasive. The upshot of this intimate contact is a major improvement in resolution, as the signal does not have to travel through the skull and scalp to be recorded, and therefore distortion is minimized. ECoG is used in medical settings to identify the zones generating seizures in epileptic patients. Since such patients have to be recorded with ECoG for extended periods of time, they sometimes give consent to participate in research while the electrodes are in place. ECoG then offers real-time, high spatio-temporal resolution mapping of the dynamics of the brain as participants are engaged in a variety of perceptual, cognitive or motor tasks.
Calcium Imaging
Calcium imaging is a technique that allows the visualisation of cells by tracking changes in calcium levels. In neurons more specifically, activation triggers a rapid influx of calcium which can then be recorded to track their responses. The indicators used to bind with calcium can be either chemicals directly injected in the tissues, or genetically encoded proteins. When placed under a fluorescence microscope, these indicators light up and the light intensity is measured. Widely used in non-human animal studies, calcium imaging provides colourful maps of neuronal activity in real-time, shining light on the intricate connections and workings of neural circuits . While this technique allows for recording activity near the surface of the brain, reaching deeper structures remains a challenge.
Neuropixel
High-density probes bring a novel and powerful tool to the neuroscientific scene, allowing the direct recording of electrical neuronal activity from within the brain with exceptional spatio-temporal resolution. A widely used example of such probes is Neuropixel, a brand name that is thus often used to refer to the technique. While most neuroimaging techniques provide a general overview of regional brain activity, high-density probes allow researchers to monitor hundreds to thousands of individual neurons simultaneously. Each chip consists of a printed circuit board with a thin silicon tip probe which is directly implanted into the brain. This slender design enables the implantation of multiple probes at a time, increasing spatial coverage while minimizing tissue damage. Still, due to their invasive nature, such probes remain primarily used in non-human animal studies. Each probe carries 960 recording sites, of which a subset of 384 can be chosen for recording. The signals are then analysed with sophisticated computational tools, disentangling the activity of separate neurons and allowing insights into their responses, interconnectivity and coordination. Combined with manipulation techniques such as electrical stimulation or optogenetics (see below), high-density probes can participate to uncover causal links within neural circuits. They can record activity for weeks or months at a time, making them especially invaluable to study memory and learning processes.
Experimental Manipulations
While imaging, recording and measuring brain activity and behaviours can reveal important information, causal relationships are best tested and understood when researchers can actively manipulate them. Neuroscience provides a varied set of tools for this purpose, a selection of which are introduced below.
Optogenetics
Optogenetics is a groundbreaking technique that combines genetics with optics in order to control the activity of specific cells in living tissues. By using modified viruses, light-sensitive proteins are introduced into target neurons. Researchers can then activate or inhibit these neurons by using lasers of specific wavelengths, directing the light with thin optical fibres. This can be done with incredible precision, both spatial and temporal, reaching even individual neurons deep into the brain . When targeting neurons which are located deeper, an optical fibre then needs to be implanted directly inside the brain to be able to reach the area of interest. Optogenetics has allowed to move from recording correlations (using neuroimaging techniques) to looking into causality through manipulating precise neural circuits. The recent development of optogenetics has been a methodological breakthrough, allowing so far unequalled understanding of brain processes at the level of specific cell types and populations. Due to its invasive nature, optogenetics is primarily applied to non-human animal models. However, the method is also being tested in humans, in early clinical trial: its potential is explored to address vision loss in retinitis pigmentosa, a disease affecting the light sensitive retina of the eye (which is indeed a neuronal tissue).
Electrical Stimulation
Electrical stimulation techniques are used in order to directly modulate activity in specific regions of the brain by delivering small and targeted electrical currents, thus altering, inducing or disrupting conscious perception. Unlike purely observational neuroimaging techniques, electrical stimulation allows researchers to move beyond sole correlation and to identify, through manipulation, causal links between neural activity and behaviour. These techniques are often used in parallel with behavioural tasks, enabling comparison between stimulated versus normal brain activity. By manipulating neural activity, researchers can gain understanding on mechanisms involved in perception, cognition, awareness or behaviour, which shape our conscious experiences.
Visual Manipulations
Visual manipulations come in many forms, all designed to alter visual input and probe different aspects of visual perception and awareness. In backward masking experiments, for example, an image presented very shortly is immediately replaced by another, preventing conscious perception while still allowing for unconscious processing. With continuous flash suppression, an image shown to one eye can be rendered unconscious by flashing images in the other. Motion-induced blindness is an illusion in which unmoving dots seem to disappear when a larger pattern is moving in the background. Another exploited phenomenon is change blindness: when two similar scenes are presented one after the other, separated only by a brief interruption, significant changes tend to go unnoticed. Visual manipulations tools reveal the limits of our conscious awareness. When used along neuroimaging techniques, they allow researchers to explore which areas of the brain are involved in conscious versus unconscious perception. These methods can be used to test and compare different theories of consciousness which make different predictions about the neural activity linked to awareness.
Auditory Manipulations
Like with visual manipulations, auditory manipulations modify sound to study aspects of perception and awareness. Auditory masking can be used to hide the presence of a sound by playing another one either simultaneously of within a very short delay of time. In dichotic listening, different recordings (digits, syllables, words or even full sentences) are played simultaneously in each ear. Often times, signal played in the right ear is advantaged, as it is more strongly connected to areas of the brain involved in processing language. Sine-wave speech exploits another striking effect, where what seems to be meaningless noise can turn into recognizable words or sentences. Auditory manipulations are used to uncover how auditory information is perceived and interpreted by the brain. Combined with neuroimaging techniques, auditory manipulations allows researchers to learn more about brain functions and to test some of the predictions of competing theories of consciousness.
Video Games
Within neuroscientific research, video games offer a creative way to study brain function. They allow researchers to explore aspects of perception, attention and decision-making while participants are engaged in an immersive and dynamic visual or auditory environment under controlled experimental conditions. For example, scientists can investigate how the brain processes both seen and unseen information in the background while attention is focused on a demanding task. When video games are combined with neuroimaging techniques, it becomes possible to capture in real-time the brain's responses as the participants play. This method makes it possible to probe mechanisms of conscious awareness and to test specific hypotheses about what parts of the brain are involved when cues are noticed... or overlooked. Virtual reality games open new options to push these experiments further by increasing immersion and enabling the study of motor behaviour through body movement.
Hypnotic Suggestion
Hypnotic suggestion provides a unique window to investigate consciousness within neuroscientific research. This psychological process allows researcher to influence the conscious perceptions of those participants who are highly suggestible through hypnosis, by giving them carefully crafted verbal instructions before presenting them with various stimuli. This way, a person's felt experience can be altered without any corresponding change in the sensory inputs being received. Such induced changes in conscious perception can be particularly spectacular: a person might for instance be led to see happy faces as being sad, or vice versa. In consciousness research, hypnotic suggestion can be used to explore how sensory information processed by the brain and higher-cognitive functions interact, investigating how different brain regions and processes influence each other and ultimately shape what we consciously experience.
Other Measures
Other techniques, such as eye tracking and behavioural measures, can provide valuable insights into our conscious and unconscious processes. These are often combined with recording and visualizing techniques in order to get a broader picture of what is happening inside the head.
Eye Tracking
Eye tracking is a method that captures and measures the movements of the eyes, where the gaze is pointing, and even sometimes pupil dilatation, by using a family of specialized devices known as eye trackers. Researchers can record fixations (when the eyes remain steady) and saccades (the rapid movements between fixations). Eye tracking is used within a large variety of disciplines, from neuroscience, psychology, psycholinguistics, to medical and even marketing research. Used both in human and animal research, eye tracking helps with understanding how visual information is processed, and where, when, and how much attention is directed. In doing so, it provides insight about how we sample our environment, read or make decisions.
Behavioural Measures
Behavioural measures are a set of methods used in both human and non-human animals to observe, record and quantify various behaviours, often in response to specific sensory inputs or during the performance of a specific task. In detection tasks, for example, participants can report the precise moment at which they notice a stimulus by pressing a button. Other tasks can involve comparing different inputs: does one seem brighter, louder or clearer than the others? When working with mice or with primates, researchers can train them to report specific stimuli, such as images of faces or objects, by rewarding correct responses with food or juice. Behavioural measures are often combined with neuroimaging techniques in order to study the links between actions and brain processes, furthering our understanding on how we perceive and interact with the world.
Editorial
This Methods and Tools Overview was written by Lucie Cauwet in consultation with our researchers and content developers.
