Journal Highlight: Multivariate analysis of extremely large ToFSIMS imaging datasets by a rapid PCA method

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  • Published: Oct 12, 2015
  • Author: spectroscopyNOW
  • Channels: Chemometrics & Informatics
thumbnail image: Journal Highlight: Multivariate analysis of extremely large ToFSIMS imaging datasets by a rapid PCA method
The new random vectors method of singular value decomposition has been applied to ToFSIMS data, increasing the speed of calculation by a factor of several hundred to make PCA of these datasets practical on desktop PCs for the first time.

Multivariate analysis of extremely large ToFSIMS imaging datasets by a rapid PCA method

Surface and Interface Analysis, 2015, 47, 986-993
Peter J. Cumpson, Naoko Sano, Ian W. Fletcher, Jose F. Portoles, Mariela Bravo-Sanchez and Anders J. Barlow

Abstract: Principal component analysis (PCA) and other multivariate analysis methods have been used increasingly to analyse and understand depth profiles in X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES) and secondary ion mass spectrometry (SIMS). These methods have proved equally useful in fundamental studies as in applied work where speed of interpretation is very valuable. Until now these methods have been difficult to apply to very large datasets such as spectra associated with 2D images or 3D depth-profiles. Existing algorithms for computing PCA matrices have been either too slow or demanded more memory than is available on desktop PCs. This often forces analysts to ‘bin’ spectra on much more coarse a grid than they would like, perhaps even to unity mass bins even though much higher resolution is available, or select only part of an image for PCA analysis, even though PCA of the full data would be preferred. We apply the new ‘random vectors’ method of singular value decomposition proposed by Halko and co-authors to time-of-flight (ToF)SIMS data for the first time. This increases the speed of calculation by a factor of several hundred, making PCA of these datasets practical on desktop PCs for the first time. For large images or 3D depth profiles we have implemented a version of this algorithm which minimises memory needs, so that even datasets too large to store in memory can be processed into PCA results on an ordinary PC with a few gigabytes of memory in a few hours. We present results from ToFSIMS imaging of a citrate crystal and a basalt rock sample, the largest of which is 134GB in file size corresponding to 67 111 mass values at each of 512 × 512 pixels. This was processed into 100 PCA components in six hours on a conventional Windows desktop PC.

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