Medical Physics and Biomedical Engineering


Functional optical signal analysis (fOSA)

fOSA is a software package for the processing and analysis of functional neuroimaging data using Near Infrared Spectroscopy (NIRS). The software description and operation manual is provided in the package. The current version of the software is 2.2. 

fOSA is a suite of Matlab functions and it requires Matlab (Release 13 or later) to operate.

Download fOSA

License Agreement

fOSA is made available to the scientific community as a useful tool for the analysis of general optical topographic data. This software is distributed as copyright freeware under the terms of the GNU General Public Licence.

The developer is convinced that there are some remaining bugs in the software and there will be no guarantee that the software is free of errors. Please help to report any bugs here.

In particular, fOSA is supplied as is. No formal support or maintenance is provided or implied.


Near-infrared optical imaging has been shown to provide an effective and non-invasive approach to monitor the cerebral haemodynamics response during functional activation. Optical topography (OT) relies on near infrared light to make simultaneous spectroscopic measurements at multiple brain sites and provides a spatial map of the brain activity from the surface of the head. The optical data will inevitably include haemodynamic signals arising from systemic physiological changes and other fluctuations which can exhibit a temporal pattern of amplitude change that is similar to that of the evoked neurovascular response. In order to interpret the observed response it is necessary to pre-process the highly diffused NIR signal without affecting the activation-induced response. Statistical comparisons can then be applied to infer the neurovascular signal changes between different experimental conditions.

The functional Optical Signal Analysis (fOSA) software offers a range of processing tools to facilitate the analysis of multi-channel OT data. This Matlab based program provides a flexible and adaptable approach to perform real-time analysis of the OT data using algorithms which incorporate both a range of standard libraries as well as additional plug in options for user defined processing procedures. This open source software is well-suited for the processing of OT data from “continuous-wave” OT systems and includes a list of pre-defined formats for analysing data coming from a range of different commercial and research OT systems and for a variety of measurement optode geometries.

In addition to offering itself as a data processing tool for the analysis of spatially resolved OT data, fOSA incorporates statistical inference capabilities about the distribution of brain activity both spatially and temporally, and by experimental condition. It does this by mapping the optical signals into a standard functional neuroimaging analysis software, Statistical Parametric Mapping (SPM), and forms, in effect, a new SPM toolbox specifically designed for the NIR signals in an OT configuration. The software that was developed, SPM-OT has been incorporated into fOSA which allows the OT data processed in fOSA to be subsequently analysed in the SPM environment. The SPM-OT approach offers the flexibility to model the varying haemodynamic changes, specifically the concentration changes of oxy-haemoglobin and deoxy-haemoglobin and to take into consideration the spatial influence of neighbouring measurements by estimating the smoothness of the spatially extended OT data. The application of fOSA and SPM-OT has been shown to be suitable for analysing the spatially resolved optical imaging data.