Data analysis - X-ray fluorescence microscopy

Data analysis - XFM beamline

It is reasonable for inexperienced users to expect the beamline staff to assist with the first-round of the data analysis.  This will generally involve using either GeoPIXE or MAPS to fit the fluorescence data.  Here we describe this process in some detail.

Please also feel free to contact us if you want help to refine your output, once you have a good idea of what you want to display for publication.

Data acquired using the Maia detector

X-ray fluorescence data collected at XFM using the Maia and Vortex detectors can be analysed using the GeoPIXE software. GeoPIXE is essential for the complex and huge Maia data-sets, providing the necessary tools for spectral analysis, the projection of images using the Dynamic Analysis (DA) method for spectral deconvolution, and final exploration of the elemental image data. GeoPIXE has been developed by CSIRO and more information can be obtained from the GeoPIXE web-site. 

Access to GeoPIXE on MASSIVE is provided for all licensed users of GeoPIXE. To obtain a license for use at your home institution and on MASSIVE, send an email to [email protected]. A user guide to running GeoPIXE on MASSIVE is available for download here. 

Conversion of Parts per million to areal density 

GeoPIXE will typically report concentrations as ppm or wt%.  A percent sign is shown if the concentration is wt%, otherwise, it is ppm.  A common unit in XRF microscopy is areal density, typically specified as μg/cm2 or ng/cm2.

Recall that μg/g is ppm, so say for example a concentration is reported as 250 ppm or 250 μg/g, for a 10 μm thick sample having 1.1 g/cm3 density.The conversion to areal density is 

Areal density, μg/cm2  =  250 μg/g x 1.1 g/cm3 x 10 μm x 0.0001 cm/μm

                                = 0.275 μg/cm2

GeoPIXE assumes the sample is a uniform thickness, so both over-estimations and under-estimations in concentration are possible with deviations from 10 um specified thickness. The thickness, density and sample matrix (e.g., cellulose or quartz) are explicitly stated in the GeoPIXE Yield file setup.

 

Data acquired using the Vortex detector

If your data set was acquired using the Vortex detector then you may wish to view it using the MAPS analysis package that was likely used at the beamline.  If so you will need to:

  1. Download the IDL Virtual Machine. You can get this from the ITTVIS website here.  Download requires registration but is free.
  2. Get the MAPS program from: http://www.stefan.vogt.net/downloads.html
  3. Download the MAPS manuals from here (pdf, 629KB).

Overall it is likely to take several hours to install and debug IDL and MAPS; but once you have it running, it can be used for much of your data interrogation and visualisation.  Please let us know if you have any trouble.

Mining the metadata

If you wish to interrogate your data directly (in particular, the .mda file) then you may find Mark Rivers’ EPICS scan display routine useful.  You can search for it (and related programs) on the web, or download it from http://cars9.uchicago.edu/software/idl/epics_sscan_display.html