Software implementation for fast speciation mapping

In a paper published today in the Journal of Synchrotron Radiation, to which I collaborated while a postdoc in IPANEMA, we developed a robust framework and software implementation for fast speciation mapping.

One of the greatest benefits of synchrotron radiation is the ability to perform chemical speciation analysis through X-ray absorption spectroscopies (XAS). XAS imaging of large sample areas can be performed with either full-field or raster-scanning modalities. A common practice to reduce acquisition time while decreasing dose and/or increasing spatial resolution is to compare X-ray fluorescence images collected at a few diagnostic energies. Several authors have used different multivariate data processing strategies to establish speciation maps.

In this manuscript, the theoretical aspects and assumptions that are often made in the analysis of these datasets are presented. A robust framework (algorithm) is developed to perform speciation mapping in large bulk samples at high spatial resolution by comparison with known references. We also provide two fully operational software implementations: a user-friendly implementation within the MicroAnalysis Toolkit software, and a dedicated script developed under the R environment. The procedure is exemplified through the study of a fossil sample.

Principle of the sparse excitation energy XAS (see-XAS) procedure developed in this paper to perform fast speciation mapping. In this schematic example, the see-XAS decomposition performed on X-ray fluorescence maps collected at 7 excitation energies allows mapping and distinguishing the two chemical species (e.g. two different oxidation states) composiing the sample.

The algorithm provides accurate speciation and concentration mapping while decreasing the data collection time by typically two or three orders of magnitude compared with the collection of whole spectra at each pixel. Whereas acquisition of spectral datacubes on large areas leads to very high irradiation times and doses, which can considerably lengthen experiments and generate significant alteration of radiation-sensitive materials, this sparse excitation energy procedure brings the total irradiation dose greatly below radiation damage thresholds identified in previous studies. This approach is particularly adapted to the chemical study of heterogeneous radiation-sensitive samples encountered in environmental, material, and life sciences.

Mapping of the two oxidation states of cerium in a well preserved ~100 million years old teleost fossil fish from Morocco (a) Photograph of the fossil. (b) Light microscopy image of the studied sample (origin: spot denoted by a star in a). (c) Corresponding [Ce(IV)]/[Ce(tot)] ratio (scan step: 2 µm x 2 µm, 6466 pixels). (d) Total cerium content [Ce(tot)] determined from post-edge spectral decomposition (5900 eV). (e) Csum(v, z) map. Note the similarity and improved signal-to-noise with respect to the cerium map in (d). (f) µXRF spectrum from a single spot and mean spectrum from the full map, calculated from subtraction of the spectra collected at 5726 eV from that collected before the edge at 5680 eV. The difference spectrum reveals the specific contribution of the excited fluorescence lines from cerium. (g) Kernel density estimates of the [Ce(IV)]/[Ce(tot)] distribution from areas corresponding, respectively, to fossilized muscles (black curve; 915 pixels, bandwidth: 0.009) and to bone (grey curve; 915 pixels, bandwidth: 0.006). Data collected at the Lucia beamline of the SOLEIL synchrotron.

Reference: Cohen S.X., Webb S.M., Gueriau P., Curis E. & Bertrand L. 2020. Robust framework and software implementation for fast speciation mapping. Journal of Synchrotron Radiation 27: 1049–1058. Find the article here