built around an object-oriented framework of Matlab classes and namespaces. AtlasViewer AtlasViewer allows fNIRS data to be visualized on a model of the brain. In addition, it also allows the user to design probes which can eventually be placed onto a subject. Application Brain–computer interface fNIRS has been successfully implemented as a control signal for brain–computer interface systems. Hypoxia & altitude studies With our constant need for oxygen, our body has developed multiple mechanisms that detect oxygen levels, which in turn can activate appropriate responses to counter hypoxia and generate a higher oxygen supply. Moreover, understanding the physiological mechanism underlying the bodily response to oxygen deprivation is of major importance and NIRS devices have shown to be a great tool in this field of research. Brain mapping Functional connectivity fNIRS measurements can be used to calculate functional connectivity. Multi-channel fNIRS measurements create a topographical map of neural activation, whereby temporal correlation between spatially separated events can be analyzed. Functional connectivity is typically assessed in terms correlations between the hemodynamic responses of spatially distinct regions of interest (ROIs). In brain studies, functional connectivity measurements are commonly taken for resting state patient data, as well as data recorded over stimulus paradigms. The low cost, portability and high temporal resolution of fNIRS, with respect to fMRI, have proven to be highly advantageous in studies of this nature. Cerebral oximetry NIRS monitoring is helpful in a number of ways. Preterm infants can be monitored reducing cerebral hypoxia and hyperoxia with different patterns of activities. It is an effective aid in Cardiopulmonary bypass, is strongly considered to improve patient outcomes and reduce costs and extended stays. There are inconclusive results for use of NIRS with patients with traumatic brain injury, so it has been concluded that it should remain a research tool. Diffuse optical tomography Diffuse optical tomography is the 3D version of Diffuse optical imaging. Diffuse optical images are obtained using NIRS or fluorescence-based methods. These images can be used to develop a 3D volumetric model which is known as the Diffuse Optical Tomography. fNIRS cap fNIRS electrode locations can be defined using a variety of layouts, including names and locations that are specified by the International 10–20 system as well as other layouts that are specifically optimized to maintain a consistent 30mm distance between each location. In addition to the standard positions of electrodes, short separation channels can be added. Short separation channels