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Virtual Journal for Biomedical Optics

Virtual Journal for Biomedical Optics


  • Editors: Andrew Dunn and Anthony Durkin
  • Vol. 8, Iss. 5 — Jun. 6, 2013

A Fast, Automated, Polynomial-Based Cosmic Ray Spike-Removal Method for the High-Throughput Processing of Raman Spectra

H. Georg Schulze and Robin F.B. Turner

Applied Spectroscopy, Vol. 67, Issue 4, pp. 457-462 (2013)

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Raman spectra often contain undesirable, randomly positioned, intense, narrow-bandwidth, positive, unidirectional spectral features generated when cosmic rays strike charge-coupled device cameras. These must be removed prior to analysis, but doing so manually is not feasible for large data sets. We developed a quick, simple, effective, semi-automated procedure to remove cosmic ray spikes from spectral data sets that contain large numbers of relatively homogenous spectra. Although some inhomogeneous spectral data sets can be accommodated—it requires replacing excessively modified spectra with the originals and removing their spikes with a median filter instead—caution is advised when processing such data sets. In addition, the technique is suitable for interpolating missing spectra or replacing aberrant spectra with good spectral estimates. The method is applied to baseline-flattened spectra and relies on fitting a third-order (or higher) polynomial through all the spectra at every wavenumber. Pixel intensities in excess of a threshold of 3× the noise standard deviation above the fit are reduced to the threshold level. Because only two parameters (with readily specified default values) might require further adjustment, the method is easily implemented for semi-automated processing of large spectral sets.

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Vol. 8, Iss. 5 Virtual Journal for Biomedical Optics

H. Georg Schulze and Robin F.B. Turner, "A Fast, Automated, Polynomial-Based Cosmic Ray Spike-Removal Method for the High-Throughput Processing of Raman Spectra," Appl. Spectrosc. 67, 457-462 (2013)

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