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What is SMAK?

SMAK is Sam's Microprobe Analysis Toolkit,

a software package for x-ray microprobe data

It contains the basic functions for:

  • Importing ASCII fluorescence data and displaying as an image

  • Support for several colormaps and displays of scale legends

  • Ability to perform math operations on data channels, including basic addition, subtraction, multiplication,
    division, as well as smoothing and derivatives.

  • Production of correlation plots, with the ability to make arbitrary masks for regions of particular interest.

  • Display of tricolor RGB plots, with a selected channel representing a color.

  • Ability to combine data channels from multiple files.

  • Display of raw data from image by selecting data pixels, producing a line plot in x and y directions.

  • Recall of MCA data if data was saved at collection time.

  • Ability to rebin data to capture missed peaks.

  • PyMCA integration for advanced analysis of MCA data.

  • Pricipal component analysis routines on MCA data. Components can be saved back to image maps.
    Preliminary routine for using PCA to do EXAFS included as well.

  • XANES imaging fitting (SEE-XAS or sparse excitation energy XAS) routine to do linear least squares
    regressions given maps performed at several energies. User enters matrix of standards and gets the
    fitted proportions as a function of location on the sample.

  • Multi-modal image analysis between compatible image types (XRF, visible, FTIR, MS)


Data formats

Current data formats supported at this time are: 

  • SSRL Microscan files (HDF)

  • SSRL SCANE ASCII files (format for saved files)

  • SSRL MGScan ASCII files

  • SSRL Super grid files

  • SSRL Image Mosaics

  • GSE-CARS files (ASCII and HDF)

  • NSLS-II HDF5 files (XFM beamline)

  • PNC-CAT files (ASCII and HDF)

  • MAPS format h5 files

  • MRCAT files

  • CLS BIO-XAS image HDF files

  • Image and Stack files from AXIS2000 (XIM and NCB)

  • NSLS-II SRX HDF saved data format

  • SOLEIL data flyscan formats (NXS)

  • SOLEIL step scan formats (NXS)

  • ALS beamline 10.3.2 files

  • RGB files from Diamond

  • ESRF ROBL image files

  • ESRF EDF format

  • CHESS HDF5 data

  • Bruker, Agilent, Thermo (ENVI) FTIR image formats

  • Horiba text export micro-Raman

  • LA-TOF-MS formats in zip/vit format

  • LA-MS formats in laser log CSV format

  • MALDI-MS data in imzML format

  • SIGRAY Attomap data

  • JPG, TIFF, GIF, BMP, qTIFF image formats

Future ability to include other formats is planned, including possible plug-in type support.  A generic ASCII file loader to accommodate other file formats may be provided in the future.  The program is still in its VERY early stages of development, but all questions and particularly comments for improvement are welcomed.

How to Cite

Webb, SM (2011) The MicroAnalysis Toolkit: X-ray Fluorescence Image Processing Software.  Amer. Inst. Phys. Conf. Proc.1365196-199.  DOI: 10.1063/1.3625338.



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