Accounting for Poisson noise in the multivariate analysis of ToF-SIMS spectrum images. Keenan, M. R and Kotula, P. G Surf Interface Anal, 36(3):203–212, Wiley Online Library, 2004.
Accounting for Poisson noise in the multivariate analysis of ToF-SIMS spectrum images [link]Paper  doi  abstract   bibtex   
Recent years have seen the introduction of many surface characterization instruments and other spectral imaging systems that are capable of generating data in truly prodigious quantities. The challenge faced by the analyst, then, is to extract the essential chemical information from this overwhelming volume of spectral data. Multivariate statistical techniques such as principal component analysis (PCA) and other forms of factor analysis promise to be among the most important and powerful tools for accomplishing this task. In order to benefit fully from multivariate methods, the nature of the noise specific to each measurement technique must be taken into account. For spectroscopic techniques that rely upon counting particles (photons, electrons, etc.), the observed noise is typically dominated by 'counting statistics' and is Poisson in nature. This implies that the absolute uncertainty in any given data point is not constant, rather, it increases with the number of counts represented by that point. Performing PCA, for instance, directly on the raw data leads to less than satisfactory results in such cases. This paper will present a simple method for weighting the data to account for Poisson noise. Using a simple time-of-flight secondary ion mass spectrometry spectrum image as an example, it will be demonstrated that PCA, when applied to the weighted data, leads to results that are more interpretable, provide greater noise rejection and are more robust than standard PCA. The weighting presented here is also shown to be an optimal approach to scaling data as a pretreatment prior to multivariate statistical analysis.
@Article{keenan04accounting,
  author    = {Keenan, Michael R and Kotula, Paul G},
  title     = {Accounting for Poisson noise in the multivariate analysis of ToF-SIMS spectrum images},
  journal   = {Surf Interface Anal},
  year      = {2004},
  volume    = {36},
  number    = {3},
  pages     = {203--212},
  abstract  = {Recent years have seen the introduction of many surface characterization instruments and other spectral imaging systems that are capable of generating data in truly prodigious quantities. The challenge faced by the analyst, then, is to extract the essential chemical information from this overwhelming volume of spectral data. Multivariate statistical techniques such as principal component analysis (PCA) and other forms of factor analysis promise to be among the most important and powerful tools for accomplishing this task. In order to benefit fully from multivariate methods, the nature of the noise specific to each measurement technique must be taken into account. For spectroscopic techniques that rely upon counting particles (photons, electrons, etc.), the observed noise is typically dominated by 'counting statistics' and is Poisson in nature. This implies that the absolute uncertainty in any given data point is not constant, rather, it increases with the number of counts represented by that point. Performing PCA, for instance, directly on the raw data leads to less than satisfactory results in such cases. This paper will present a simple method for weighting the data to account for Poisson noise. Using a simple time-of-flight secondary ion mass spectrometry spectrum image as an example, it will be demonstrated that PCA, when applied to the weighted data, leads to results that are more interpretable, provide greater noise rejection and are more robust than standard PCA. The weighting presented here is also shown to be an optimal approach to scaling data as a pretreatment prior to multivariate statistical analysis.},
  doi       = {10.1002/sia.1657},
  file      = {KeenanEtAl_PoissonNoiseMVASIMSImages_SIA_2004.pdf:2004/KeenanEtAl_PoissonNoiseMVASIMSImages_SIA_2004.pdf:PDF},
  optmonth  = mar,
  owner     = {purva},
  publisher = {Wiley Online Library},
  timestamp = {2015.11.28},
  url       = {http://onlinelibrary.wiley.com/doi/10.1002/sia.1657/abstract},
}
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