Robust framework and software implementation for fast speciation mapping

Cohen, Serge X.; Webb, Samuel M.; Gueriau, Pierre; Curis, Emmanuel; Bertrand, Loïc

doi:10.1107/s1600577520005822

Title: Robust framework and software implementation for fast speciation mapping

Journal Article · Tue Jun 16 00:00:00 EDT 2020 · Journal of Synchrotron Radiation (Online)

DOI:https://doi.org/10.1107/s1600577520005822· OSTI ID:1647024

^[1];

^[2];

^[3];

^[4];

^[1]

Univ. Paris-Saclay, Saint-Aubin (France). CNRS, Ministere de la Culture, UVSQ, IPANEMA
SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
Univ. Paris-Saclay, Saint-Aubin (France). CNRS, Ministere de la Culture, UVSQ, IPANEMA; Synchrotron SOLEIL, Gif-sur-Yvette (France); Univ. of Lausanne (Switzerland)
Univ. Paris Descartes, Paris (France). Lab. de Biomathematiques; Hopital Saint-Louis, Assistance Publique Hopitaux de Paris (France)

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. In this work, several authors have used different multivariate data processing strategies to establish speciation maps. Furthermore, the theoretical aspects and assumptions that are often made in the analysis of these datasets are focused on. A robust framework is developed to perform speciation mapping in large bulk samples at high spatial resolution by comparison with known references. Two fully operational software implementations are provided: 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 cross section of a typical fossil specimen. Additionally, 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.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE); Horizon 2020

Grant/Contract Number:: AC02-76SF00515; 654028; ANR-l1-EQPX-0034; 20141143

OSTI ID:: 1647024

Journal Information:: Journal of Synchrotron Radiation (Online), Vol. 27, Issue 4; ISSN 1600-5775

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 3 works

Citation information provided by
Web of Science

References (46)

The LUCIA beamline at SOLEIL Vantelon, D.; Trcera, N.; Roy, D. Journal of Synchrotron Radiation, Vol. 23, Issue 2 https://doi.org/10.1107/S1600577516000746	journal	February 2016
Trends in hard X-ray fluorescence mapping: environmental applications in the age of fast detectors Lombi, E.; de Jonge, M. D.; Donner, E. Analytical and Bioanalytical Chemistry, Vol. 400, Issue 6 https://doi.org/10.1007/s00216-011-4829-2	journal	March 2011
Three-dimensional imaging of chemical phase transformations at the nanoscale with full-field transmission X-ray microscopy Meirer, Florian; Cabana, Jordi; Liu, Yijin Journal of Synchrotron Radiation, Vol. 18, Issue 5 https://doi.org/10.1107/S0909049511019364	journal	July 2011
Leaf metallome preserved over 50 million years Edwards, N. P.; Manning, P. L.; Bergmann, U. Metallomics, Vol. 6, Issue 4 https://doi.org/10.1039/C3MT00242J	journal	January 2014
Development and trends in synchrotron studies of ancient and historical materials Bertrand, Loïc; Cotte, Marine; Stampanoni, Marco Physics Reports, Vol. 519, Issue 2 https://doi.org/10.1016/j.physrep.2012.03.003	journal	October 2012
Synchrotron-Based X-ray Absorption Spectroscopy for Art Conservation: Looking Back and Looking Forward Cotte, Marine; Susini, Jean; Dik, Joris Accounts of Chemical Research, Vol. 43, Issue 6 https://doi.org/10.1021/ar900199m	journal	June 2010
Application of the Ce anomaly as a paleoredox indicator: The ground rules German, Christopher R.; Elderfield, Henry Paleoceanography, Vol. 5, Issue 5 https://doi.org/10.1029/PA005i005p00823	journal	October 1990
Cerium Anomaly at Microscale in Fossils Gueriau, Pierre; Mocuta, Cristian; Bertrand, Loïc Analytical Chemistry, Vol. 87, Issue 17 https://doi.org/10.1021/acs.analchem.5b01820	journal	August 2015
Phytoremediation of heavy metals and study of the metal coordination by X-ray absorption spectroscopy Gardeatorresdey, J.; Peraltavidea, J.; Delarosa, G. Coordination Chemistry Reviews, Vol. 249, Issue 17-18 https://doi.org/10.1016/j.ccr.2005.01.001	journal	September 2005
Nanoscale Hard X-Ray Microscopy Methods for Materials Studies Holt, Martin; Harder, Ross; Winarski, Robert Annual Review of Materials Research, Vol. 43, Issue 1 https://doi.org/10.1146/annurev-matsci-071312-121654	journal	July 2013
Robust framework and software implementation for fast speciation mapping Cohen, Serge X.; Gueriau, Pierre; Bertrand, Loïc Zenodo https://doi.org/10.5281/zenodo.3611251	dataset	January 2020
Elemental and chemical-state imaging using synchrotron radiation Kinney, John; Johnson, Quintin; Nichols, Monte C. Applied Optics, Vol. 25, Issue 24 https://doi.org/10.1364/AO.25.004583	journal	January 1986
Quantitative, chemically specific imaging of selenium transformation in plants Pickering, I. J.; Prince, R. C.; Salt, D. E. Proceedings of the National Academy of Sciences, Vol. 97, Issue 20 https://doi.org/10.1073/pnas.200244597	journal	September 2000
Mitigation strategies for radiation damage in the analysis of ancient materials Bertrand, Loïc; Schöeder, Sebastian; Anglos, Demetrios TrAC Trends in Analytical Chemistry, Vol. 66 https://doi.org/10.1016/j.trac.2014.10.005	journal	March 2015
Advanced Synchrotron Characterization of Paleontological Specimens Gueriau, Pierre; Bernard, Sylvain; Bertrand, Loïc Elements, Vol. 12, Issue 1 https://doi.org/10.2113/gselements.12.1.45	journal	February 2016
X-ray Absorption Near-Edge Structure (XANES) Spectroscopy Henderson, G. S.; de Groot, F. M. F.; Moulton, B. J. A. Reviews in Mineralogy and Geochemistry, Vol. 78, Issue 1 https://doi.org/10.2138/rmg.2014.78.3	journal	January 2014
TXM-Wizard : a program for advanced data collection and evaluation in full-field transmission X-ray microscopy Liu, Yijin; Meirer, Florian; Williams, Phillip A. Journal of Synchrotron Radiation, Vol. 19, Issue 2 https://doi.org/10.1107/S0909049511049144	journal	January 2012
Coupled X-ray Fluorescence and X-ray Absorption Spectroscopy for Microscale Imaging and Identification of Sulfur Species within Tissues and Skeletons of Scleractinian Corals Farfan, Gabriela A.; Apprill, Amy; Webb, Samuel M. Analytical Chemistry, Vol. 90, Issue 21 https://doi.org/10.1021/acs.analchem.8b02638	journal	October 2018
3D elemental sensitive imaging using transmission X-ray microscopy Liu, Yijin; Meirer, Florian; Wang, Junyue Analytical and Bioanalytical Chemistry, Vol. 404, Issue 5 https://doi.org/10.1007/s00216-012-5818-9	journal	February 2012
The MicroAnalysis Toolkit: X-ray Fluorescence Image Processing Software Webb, S. M.; McNulty, Ian; Eyberger, Catherine THE 10TH INTERNATIONAL CONFERENCE ON X-RAY MICROSCOPY, AIP Conference Proceedings https://doi.org/10.1063/1.3625338	conference	January 2011
Submicrometer Hyperspectral X-ray Imaging of Heterogeneous Rocks and Geomaterials: Applications at the Fe K-Edge De Andrade, Vincent; Susini, Jean; Salomé, Murielle Analytical Chemistry, Vol. 83, Issue 11 https://doi.org/10.1021/ac200559r	journal	June 2011
An assessment of the resolution limitation due to radiation-damage in X-ray diffraction microscopy Howells, M. R.; Beetz, T.; Chapman, H. N. Journal of Electron Spectroscopy and Related Phenomena, Vol. 170, Issue 1-3 https://doi.org/10.1016/j.elspec.2008.10.008	journal	March 2009
Full-Field Fluorescence Mode Micro-XANES Imaging Using a Unique Energy Dispersive CCD Detector Tack, Pieter; Garrevoet, Jan; Bauters, Stephen Analytical Chemistry, Vol. 86, Issue 17 https://doi.org/10.1021/ac502016b	journal	August 2014
A new method for the determination of CeIII/CeIV ratios in geological materials; application for weathering, sedimentary and diagenetic processes Takahashi, Y. Earth and Planetary Science Letters, Vol. 182, Issue 3-4 https://doi.org/10.1016/S0012-821X(00)00250-8	journal	November 2000
In situ chemical mapping of a lithium-ion battery using full-field hard X-ray spectroscopic imaging Wang, Jiajun; Chen-Wiegart, Yu-chen Karen; Wang, Jun Chemical Communications, Vol. 49, Issue 58 https://doi.org/10.1039/c3cc42667j	journal	January 2013
Methods for Investigating Trace Element Binding in Sediments Linge, Kathryn L. Critical Reviews in Environmental Science and Technology, Vol. 38, Issue 3 https://doi.org/10.1080/10643380601174780	journal	March 2008
Transmission and emission x-ray microscopy: operation modes, contrast mechanisms and applications Kaulich, Burkhard; Thibault, Pierre; Gianoncelli, Alessandra Journal of Physics: Condensed Matter, Vol. 23, Issue 8 https://doi.org/10.1088/0953-8984/23/8/083002	journal	February 2011
Elemental and Chemically Specific X-ray Fluorescence Imaging of Biological Systems Pushie, M. Jake; Pickering, Ingrid J.; Korbas, Malgorzata Chemical Reviews, Vol. 114, Issue 17 https://doi.org/10.1021/cr4007297	journal	January 2014
Three-dimensional mapping of nickel oxidation states using full field x-ray absorption near edge structure nanotomography Nelson, George J.; Harris, William M.; Izzo, John R. Applied Physics Letters, Vol. 98, Issue 17 https://doi.org/10.1063/1.3574774	journal	April 2011
Chemical Speciation and Bioavailability of Selenium in the Rhizosphere of Symphyotrichum eatonii from Reclaimed Mine Soils Oram, Libbie L.; Strawn, Daniel G.; Möller, Gregory Environmental Science & Technology, Vol. 45, Issue 3 https://doi.org/10.1021/es1029766	journal	February 2011
Quantitative compositional analysis of organic thin films using transmission NEXAFS spectroscopy in an X-ray microscope Collins, Brian A.; Ade, Harald Journal of Electron Spectroscopy and Related Phenomena, Vol. 185, Issue 5-7 https://doi.org/10.1016/j.elspec.2012.05.002	journal	August 2012
Synchrotron x‐ray fluorescence microprobe: Quantification and mapping of mixed valence state samples using micro‐XANES Sutton, S. R.; Bajt, S.; Delaney, J. Review of Scientific Instruments, Vol. 66, Issue 2 https://doi.org/10.1063/1.1145942	journal	February 1995
Microscale Imaging and Identification of Fe Speciation and Distribution during Fluid–Mineral Reactions under Highly Reducing Conditions Mayhew, L. E.; Webb, S. M.; Templeton, A. S. Environmental Science & Technology, Vol. 45, Issue 10 https://doi.org/10.1021/es104292n	journal	May 2011
Robust framework and software implementation for fast speciation mapping Cohen, Serge X.; Gueriau, Pierre; Bertrand, Loïc Zenodo https://doi.org/10.5281/zenodo.3748752	dataset	January 2020
XANES micro-imaging and tomography Rau, Christoph; Somogyi, Andrea; Bytchkov, A. International Symposium on Optical Science and Technology, SPIE Proceedings https://doi.org/10.1117/12.452851	conference	January 2002
X-ray photon-in/photon-out methods for chemical imaging Marcus, Matthew A. TrAC Trends in Analytical Chemistry, Vol. 29, Issue 6 https://doi.org/10.1016/j.trac.2010.02.013	journal	June 2010
Speciation mapping of environmental samples using XANES imaging Etschmann, Barbara E.; Donner, Erica; Brugger, Joël Environmental Chemistry, Vol. 11, Issue 3 https://doi.org/10.1071/EN13189	journal	January 2014
The new ID21 XANES full-field end-station at ESRF Fayard, B.; Pouyet, E.; Berruyer, G. Journal of Physics: Conference Series, Vol. 425, Issue 19 https://doi.org/10.1088/1742-6596/425/19/192001	journal	March 2013
Chemical contrast in X-ray microscopy and spatially resolved XANES spectroscopy of organic specimens Ade, H.; Zhang, X.; Cameron, S. Science, Vol. 258, Issue 5084 https://doi.org/10.1126/science.1439809	journal	November 1992
Visualization of electrochemically driven solid-state phase transformations using operando hard X-ray spectro-imaging Li, Linsen; Chen-Wiegart, Yu-chen Karen; Wang, Jiajun Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms7883	journal	April 2015
Microfluorescence and Microtomography Analyses of Heterogeneous Earth and Environmental Materials Sutton, S. R.; Bertsch, P. M.; Newville, M. Reviews in Mineralogy and Geochemistry, Vol. 49, Issue 1 https://doi.org/10.2138/rmg.2002.49.8	journal	January 2002
Micro-XANES: Chemical contrast in the scanning transmission X-ray microscope Zhang, X.; Ade, H.; Jacobsen, C. Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, Vol. 347, Issue 1-3 https://doi.org/10.1016/0168-9002(94)91922-4	journal	August 1994
Applications of Synchrotron-Based X-ray Microprobes Bertsch, Paul M.; Hunter, Douglas B. Chemical Reviews, Vol. 101, Issue 6 https://doi.org/10.1021/cr990070s	journal	June 2001
Soft X-ray spectroscopy from image sequences with sub-100 nm spatial resolution Journal of Microscopy, Vol. 197, Issue 2 https://doi.org/10.1046/j.1365-2818.2000.00640.x	journal	February 2000
Cluster analysis of soft X-ray spectromicroscopy data Lerotic, M.; Jacobsen, C.; Schäfer, T. Ultramicroscopy, Vol. 100, Issue 1-2 https://doi.org/10.1016/j.ultramic.2004.01.008	journal	July 2004
Robust framework and software implementation for fast speciation mapping Cohen, Serge X.; Gueriau, Pierre; Bertrand, Loïc Zenodo https://doi.org/10.5281/zenodo.3611252	dataset	January 2020

Similar Records

Reduced As Components in Highly Oxidized Environments: Evidence from Full Spectral XANES Imaging using the Maia Massively Parallel Detector

Journal Article · Fri Jan 01 00:00:00 EST 2010 · American Mineralogist · OSTI ID:1647024

Etschmann, B; Ryan, C; Brugger, J; +6 more

Dynamic X-ray diffraction sampling for protein crystal positioning

Journal Article · Sun Jan 01 00:00:00 EST 2017 · Journal of Synchrotron Radiation (Online) · OSTI ID:1647024

Scarborough, Nicole M.; Godaliyadda, G. M. Dilshan P.; Ye, Dong Hye; +10 more

JBlulce Data Acquisition Software for Macromolecular Crystallography

Software · Tue Jun 01 00:00:00 EDT 2010 · OSTI ID:1647024

Stepanov, Sergey; Makarov, Oleg; Hilgart, Mak; +1 more

Related Subjects

47 OTHER INSTRUMENTATION
synchrotron imaging
software
chemical speciation
X-ray absorption spectroscopy
heterogeneous materials

Title: Robust framework and software implementation for fast speciation mapping

Citation Formats

References (46)

Similar Records

Related Subjects