For the analysis of NIRS data acquired with our ISS OxiplexTS frequency domain, multidistance tissue spectrometer, we have developed a NIRS data processor that automatically applies a multistage pipeline and saves data in Excel^{TM} files. Specifically, the software proceeds through the following steps:
 First, it applies the movement artifact removal algorithm from the NIRS Analysis Package (NAP), to remove spikes (i.e., nearinstantaneous signal inflections much larger in amplitude than the typical amplitude of the hemodynamic signal) and correct discontinuities (i.e., baseline shifts). This algorithm uses piecewise loworder polynomial interpolation to reconstruct data segments affected by movement artifacts.
 Second, it removes the verylow and high parts of the frequency spectrum by applying a thirdorder Butterworth filter, with bandpass settings of 0.008 and 0.5 Hz. This step is intended to remove oscillations due to heart pulsations (i.e., 2 Hz or higher during exercise) and respiration (i.e., 0.5 Hz or higher during exercise).
 Third, it applies the denoising algorithm of Feuerstein et al. The goal of this algorithm is to separate the noise from the signal given their differences in amplitude (assuming that the noise has larger amplitude than the underlying hemodynamic signal). The algorithm first calculates the difference between the original signal and a smoothed signal resulting from a quadratic SavitzkyGolay filter and then uses a histogram of this signal difference to iteratively seek the filtering threshold that minimizes the variance overlap between the presumed signal and the presumed noise.
 Fourth, for each timeseries, it fits a linear regression through the O_{2}Hb and HHb data segments representing the "baseline" period and then expresses all O_{2}Hb and HHb data points as changes from this baseline.
 Finally, it divides each timeseries representing exercise periods into segments and calculates the median value of O_{2}Hb and HHb for each segment. These median values are then used to calculate the Tissue Oxygenation Index and the [O_{2}Hb] – [HHb] difference (ΔHbDiff) that is used in statistical analyses.
Illustrative Publications

Jones, L., & Ekkekakis, P. (2019). Affect and prefrontal hemodynamics during exercise under immersive audiovisual stimulation. Journal of Sport and Health Science, 8(4), 325338. [DOI] [PubMed]