Near infrared spectroscopy is based on molecular overtone and combination vibrations. Such transitions are forbidden by the selection rules of quantum mechanics. As a result, the molar absorptivity in the near IR region is typically quite small. One advantage is that near infrared can typically penetrate much farther into a sample than mid infrared radiation. Near infrared spectroscopy is therefore not a particularly sensitive technique, but it can be very useful in probing bulk material with little or no sample preparation.

For medical research, near infrared spectroscopy can be accompanied by other modalities such as magnetic resonance imaging (MRI) or computerized tomography (CT). For example, infrared thermal imaging can be used for non-invasive assessment of the brain function through an intact skull in human subjects by detecting changes in blood hemoglobin concentrations associated with neural activity. This application is sometimes called optical topography (OT) in which infrared thermal imaging is used for functional mapping of the human cortex. The term optical tomography is used when infrared thermal imaging is applied to obtain slices of Sectional images of tissue or structure.

In the case of optical topography or tomography, the accessibility of the blood sample from the brain prohibits the absolute initial calibration procedures used in non-mapping infrared thermal imaging assays mentioned above. However, optical topography or optical tomography systems do have the ability to monitor oxygen content change by comparing two channels from two different light sources with different wavelengths.

Near infrared spectroscopy is starting to be used in pediatric critical care, to help deal with cardiac surgery post-op. Indeed, the infrared thermal imaging trend has been shown to correlate with the SVO2. This SVO2 is the venous oxygen saturation, which is determined by the cardiac output, as well as other parameters (FiO2, hemoglobin, oxygen uptake). Therefore, following the infrared thermal imaging can give critical care physicians a notion of the cardiac output.

Near infrared spectroscopy is also currently being used in branches of Cognitive psychology as a partial replacement for fMRI techniques. Infrared imaging can be used on infants, where fMRI cannot, and infrared imaging cameras are much more portable than fMRI machines. However, Infrared thermal imaging cannot fully replace fMRI because it can only be used to scan cortical tissue, where fMRI can be used to measure activation throughout the brain.

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