Data and Analysis XFM

Owned by Microscopy Cluster (Unlicensed)

Last updated: Jul 23, 2024 by AS Microscopy Wiki

3 min read

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 GeoPIXE to fit the fluorescence data.

Please 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 or Vortex detector

X-ray fluorescence data collected at XFM using the Maia and Vortex detectors can be analysed using GeoPIXE software. GeoPIXE has been developed by CSIRO and more information can be obtained from the GeoPIXE web-site.

GeoPIXE Data Analysis Workshop videos

Please visit the Workshop recordings on the Microscopy Group workshop page.

Also see the GeoPIXE help page for more information.

XFM users have free access to analyse their XFM data on GeoPIXE via web browser on the Australian Synchrotron’s ASCI computing platform.

XANES Analysis

Popular packages for data reduction include Athena and Artemis for data analysis. Further information and downloads (incl Athena, Artemis, and Hephaestus) can be found here: https://bruceravel.github.io/demeter/

A recent XANES analysis alternative is Larch. https://millenia.cars.aps.anl.gov/xraylarch/

Online XANES Workshops and Tutorials

Helpful tutorials can be found online to assist with XAS data analysis. For example:

Software help with Athena/Atemis: https://bruceravel.github.io/demeter/
IFEFFIT mailing list: https://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit/
A webpage sponsored by the International XAFS Society with a wealth of resources: https://xafs.xrayabsorption.org/
Online Bruce Ravel XAS courses here: https://vimeo.com/search?q=bruce+ravel+xas+course
and here: https://vimeo.com/channels/exafs

Shelly Kelly et al. (2008) Soil Science Society of America, Methods of Soil Analysis. Part 5. Mineralogical Methods. Analysis of soils and minerals using X-ray Absorption Spectroscopy, Chapter 14.
Available online here: https://www.semanticscholar.org/paper/Analysis-of-Soils-and-Minerals-Using-X-ray-Kelly-Hesterberg/8e4c088837e9c0cf8d5d96d6c1b528ff23b9c1c9
EXAFS for Everyone (2013) by Scott Calvin

Downloading Data

Visit https://asci.readthedocs.io/en/latest/index.html to learn how to download your data.

You can access ASCI at: https://asci.synchrotron.org.au logging in with your Australian Synchrotron user portal credentials.

Getting started on ASCI: https://asci.readthedocs.io/en/latest/index.html

This has information on how to download your data from ASCI.

Your data at XFM is organised in the following manner.

above: Data folders shown in Windows File Explorer

‘/data/XFM/data/<Round>/<User_EPN#>/’

where <Round> is the year and round number. e.g., <2020r3>

and <User_EPN#> is e.g., <Harland_16496>

within the experiment’s <User_EPN#> directory are the subdirectories:

raw	with '/detector' subdirectories (e.g. ‘/384D22/', ‘/FX5/’, '/eiger’) This is where raw detector data is stored. Once the experiment has ended, the raw data directory is write protected to prevent accidental deletion. contains a useful scan Summary file outlining all the scans
	‘/metadata’ subdirectory contains further scan log files in ‘/logs’ subdirectory ‘after_scan_images’ contains an image taken by the active camera at the end of each scan
analysis	Where analysed data goes. The format should mimic ‘/raw’, with ‘/analysis' replacing '/raw’
help	Contains many help files for GeoPIXE analysis and ASCI setup - VERY USEFUL!
docs+ images	location to place experiment specific documents and images
scripts	contains the Excel spreadsheets used to setup the XFM scans
mda, mda_52	contains some beamline metadata, generally not used by users anymore

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 equivalent to 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, quartz, pyrite) are explicitly stated in the GeoPIXE Yield file setup.

Data retention policy

Information on user data retention on the Australian Synchrotron’s scientific storage can be found here.