Data analysis in spectroscopic STXM

Matthew A. Marcus1
1Advanced Light Source, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA

Tài liệu tham khảo

Henke, 1993, X-ray interactions: photoabsorption, scattering, transmission, and reflection at E= 50-30,000 eV, Z= 1-92, At. Data Nucl. Data Tables, 54, 181, 10.1006/adnd.1993.1013 CXRO, X-ray Interactions with Matter. 〈https://henke.lbl.gov/optical_constants/〉. Ravel, 2005, ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT, J. Synchrotron Radiat., 12, 537, 10.1107/S0909049505012719 Collins, 2012, Quantitative compositional analysis of organic thin films using transmission NEXAFS spectroscopy in an X-ray microscope, J. Electron Spectrosc. Relat. Phenom., 185, 119, 10.1016/j.elspec.2012.05.002 M.A. Marcus, STXM Reader software. 〈https://drive.google.com/drive/folders/1cPFyfENvWmtH4MBo0uuLz2IoW3QIPwG6?lfhs=2〉. Kilcoyne, 2003, Interferometer-controlled scanning transmission X-ray microscopes at the Advanced Light Source, J. Synchrotron Radiat., 10, 125, 10.1107/S0909049502017739 Guizar-Sicairos, 2008, Efficient subpixel image registration algorithms, Opt. Lett., 33, 156, 10.1364/OL.33.000156 Evangelidis, 2008, Parametric image alignment using enhanced correlation coefficient maximization, IEEE Trans. Pattern Anal. Mach. Intell., 30, 1858, 10.1109/TPAMI.2008.113 Van der Walt, 2014, scikit-image: image processing in Python, PeerJ, 2, 10.7717/peerj.453 Pedregosa, 2011, Scikit-learn: machine learning in Python, J. Mach. Learn. Res., 12, 2825 Cody, 2008, Quantitative organic and light‐element analysis of comet 81P/Wild 2 particles using C‐, N‐, and O‐μ‐XANES, Meteorit. Planet. Sci., 43, 353, 10.1111/j.1945-5100.2008.tb00627.x Le Guillou, 2018, XANES-based quantification of carbon functional group concentrations, Anal. Chem., 90, 8379, 10.1021/acs.analchem.8b00689 Manceau, 2002, Quantitative speciation of heavy metals in soils and sediments by synchrotron x-ray techniques, 49, 341 M.A. Marcus, X-ray photon-in/photon-out methods for chemical imaging, Trac Trends Anal.Chem. 29, 508–517. doi:10.1016/j.trac.2010.02.013. Von Der Heyden, 2014, Ubiquitous presence of Fe (II) in aquatic colloids and its association with organic carbon, Environ. Sci. Technol. Lett., 1, 387, 10.1021/ez500164v Chowdhury, 2022, Surfactant engineering and its role in determining the performance of nanoparticulate organic photovoltaic devices, ACS Omega, 7, 9212, 10.1021/acsomega.1c05711 McNeill, 2006, Nanoscale quantitative chemical mapping of conjugated polymer blends, Nano Lett., 6, 1202, 10.1021/nl060583w MANTiS - Multivariate ANalysis Tool for Spectromicroscopy. 〈https://spectromicroscopy.com/〉. Penrose, 1956, On best approximate solutions of linear matrix equations, in, Math. Proc. Camb. Philos. Soc., 17, 10.1017/S0305004100030929 Press, 1992, 1 Obst, 2009, Precipitation of amorphous CaCO3 (aragonite-like) by cyanobacteria: a STXM study of the influence of EPS on the nucleation process, Geochim. Cosmochim. Acta, 73, 4180, 10.1016/j.gca.2009.04.013 Foetisch, 2022, Identification and characterisation of individual nanoplastics by scanning transmission X-ray microscopy (STXM), J. Hazard. Mater., 426, 10.1016/j.jhazmat.2021.127804 Toner, 2009, Preservation of iron(II) by carbon-rich matrices in a hydrothermal plume, Nat. Geosci., 2, 197, 10.1038/ngeo433 Hoffman, 2018, Near-field iron and carbon chemistry of non-buoyant hydrothermal plume particles, Southern East Pacific Rise 15 S, Mar. Chem., 201, 183, 10.1016/j.marchem.2018.01.011 Alleon, 2021, Inherited geochemical diversity of 3.4 Ga organic films from the Buck Reef Chert, South Africa, Commun. Earth Environ., 2, 1, 10.1038/s43247-020-00066-7 Lewis, 2022, Characterization of sea surface microlayer and marine aerosol organic composition using STXM-NEXAFS microscopy and FTIR spectroscopy, ACS Earth Space Chem., 6, 1899, 10.1021/acsearthspacechem.2c00119 Leinweber, 2007, Nitrogen K-edge XANES–an overview of reference compounds used to identify unknown organic nitrogen in environmental samples, J. Synchrotron Radiat., 14, 500, 10.1107/S0909049507042513 Le Guillou, 2014, Evolution of organic matter in Orgueil, Murchison and Renazzo during parent body aqueous alteration: in situ investigations, Geochim. Cosmochim. Acta, 131, 368, 10.1016/j.gca.2013.11.020 Wan, 2007, Organic carbon distribution, speciation, and elemental correlations within soil microaggregates: applications of STXM and NEXAFS spectroscopy, Geochim. Cosmochim. Acta, 71, 5439, 10.1016/j.gca.2007.07.030 Solomon, 2012, Micro-and nano-environments of carbon sequestration: multi-element STXM–NEXAFS spectromicroscopy assessment of microbial carbon and mineral associations, Chem. Geol., 329, 53, 10.1016/j.chemgeo.2012.02.002 Myneni, 2002, Soft X-ray spectroscopy and spectromicroscopy studies of organic molecules in the environment, 49, 485 Urquhart, 1997, Inner-shell excitation spectroscopy of polymer and monomer isomers of dimethyl phthalate, J. Phys. Chem. B, 101, 2267, 10.1021/jp963419d Dhez, 2003, Calibrated NEXAFS spectra of some common polymers, J. Electron Spectrosc. Relat. Phenom., 128, 85, 10.1016/S0368-2048(02)00237-2 Manceau, 2012, Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy, Geochim. Cosmochim. Acta, 99, 206, 10.1016/j.gca.2012.09.033 Van Aken, 2002, Quantification of ferrous/ferric ratios in minerals: new evaluation schemes of Fe L23 electron energy-loss near-edge spectra, Phys. Chem. Miner., 29, 188, 10.1007/s00269-001-0222-6 Von der Heyden, 2012, Chemically and geographically distinct solid-phase iron pools in the Southern Ocean, Science, 338, 1199, 10.1126/science.1227504 Szymanski, 2015, Shifts in oxidation states of cerium oxide nanoparticles detected inside intact hydrated cells and organelles, Biomaterials, 62, 147, 10.1016/j.biomaterials.2015.05.042 Vairavamurthy, 1993, Oxidation state of sulfur in thiosulfate and implications for anaerobic energy metabolism, Geochim. Cosmochim. Acta, 57, 1619, 10.1016/0016-7037(93)90020-W Fleet, 2005, XANES spectroscopy of sulfur in earth materials, Can. Mineral., 43, 1811, 10.2113/gscanmin.43.6.1811 Marcus, 2008, Classification of Fe-bearing species from K-edge XANES data using two-parameter correlation plots, J. Synchrotron Radiat., 15, 463, 10.1107/S0909049508018293 Fakra, 2018, Correlative cryogenic spectromicroscopy to investigate selenium bioreduction products, Environ. Sci. Technol., 52, 503, 10.1021/acs.est.5b01409 Manceau, 2012, Determination of Mn valence states in mixed-valent manganates by XANES spectroscopy, Am. Mineral., 97, 816, 10.2138/am.2012.3903 Tetef, 2021, Unsupervised machine learning for unbiased chemical classification in X-ray absorption spectroscopy and X-ray emission spectroscopy, Phys. Chem. Chem. Phys., 23, 23586, 10.1039/D1CP02903G Ueno, 2022, Measurement informatics in synchrotron radiation X-ray spectroscopy, Synchrotron. Radiat. News, 35, 3, 10.1080/08940886.2022.2112497 Kumar, 2014, Sequential electronic and structural transitions in VO2 observed using X‐ray absorption spectromicroscopy, Adv. Mater., 26, 7505, 10.1002/adma.201402404 Kumar, 2016, Direct observation of localized radial oxygen migration in functioning tantalum oxide memristors, Adv. Mater., 28, 2772, 10.1002/adma.201505435 Geng, 2017, Ca L2,3-edge near edge X-ray absorption fine structure of tricalcium aluminate, gypsum, and calcium (sulfo) aluminate hydrates, Am. Mineral., 102, 900, 10.2138/am-2017-5670 Ogliore, 2020, Q-gases in a late-forming refractory interplanetary dust particle: A link to comet Wild 2, Geochim. Cosmochim. Acta, 271, 116, 10.1016/j.gca.2019.11.033 Zhou, 2008, Assignment of polarization-dependent peaks in carbon K-edge spectra from biogenic and geologic aragonite, J. Phys. Chem. B, 112, 13128, 10.1021/jp803176z Zhu, 2015, Individual titanate nanoribbons studied by 3D-resolved polarization dependent X-ray absorption spectra measured with scanning transmission X-ray microscopy, J. Phys. Chem. C, 119, 24192, 10.1021/acs.jpcc.5b08539 Ueno, 2017, Quantitative magnetic-moment mapping of a permanent-magnet material by X-ray magnetic circular dichroism nano-spectroscopy, AIP Adv., 7, 10.1063/1.4975043 DeVol, 2014, Oxygen spectroscopy and polarization-dependent imaging contrast (PIC)-mapping of calcium carbonate minerals and biominerals, J. Phys. Chem. B, 118, 8449, 10.1021/jp503700g Moffet, 2010, Automated chemical analysis of internally mixed aerosol particles using X-ray spectromicroscopy at the carbon K-edge, Anal. Chem., 82, 7906, 10.1021/ac1012909 Fraund, 2017, Elemental mixing state of aerosol particles collected in Central Amazonia during GoAmazon2014/15, Atmosphere, 8, 173, 10.3390/atmos8090173 Knopf, 2022, Micro-spectroscopic and freezing characterization of ice-nucleating particles collected in the marine boundary layer in the eastern North Atlantic, Atmos. Chem. Phys., 22, 5377, 10.5194/acp-22-5377-2022 Lerotic, 2004, Cluster analysis of soft X-ray spectromicroscopy data, Ultramicroscopy, 100, 35, 10.1016/j.ultramic.2004.01.008 Lerotic, 2005, Cluster analysis in soft X-ray spectromicroscopy: finding the patterns in complex specimens, J. Electron Spectrosc. Relat. Phenom., 144, 1137, 10.1016/j.elspec.2005.01.158 Mak, 2014, Non-negative matrix analysis for effective feature extraction in X-ray spectromicroscopy, Faraday Discuss., 171, 357, 10.1039/C4FD00023D Lee, 1999, Learning the parts of objects by non-negative matrix factorization, Nature, 401, 788, 10.1038/44565 Goulon, 1981, On experimental attenuation factors of the amplitude of the EXAFS oscillations in absorption, reflectivity and luminescence measurements, J. De. Phys., 42, 539 Hanhan, 2009, Optimization of analysis of soft X-ray spectromicroscopy at the Ca 2p edge, J. Electron Spectrosc. Relat. Phenom., 173, 44, 10.1016/j.elspec.2009.04.010 Bécares, 2012, Detector dead time determination and optimal counting rate for a detector near a spallation source or a subcritical multiplying system, Sci. Technol. Nucl. Install., 2012, 10.1155/2012/240693 Marcus, 2021, Ptychography reduces spectral distortions intrinsic to conventional zone-plate-based X-ray spectromicroscopy, Microsc. Microanal., 27, 1448, 10.1017/S1431927621012733 A.P. Hitchcock, (2022). aXis 2000 - Analysis of X-ray Images and Spectra. 〈http://unicorn.mcmaster.ca/axis/aXis2000-download.html〉. The IDL Virtual Machine. 〈https://www.l3harrisgeospatial.com/Support/Self-Help-Tools/Help-Articles/Help-Articles-Detail/ArtMID/10220/ArticleID/17309/The-IDL-Virtual-Machine〉. LabVIEW Run-time Engine. 〈https://www.ni.com/en-us/support/downloads/software-products/download.labview-runtime.html#460613〉. Lerotic, 2014, MANTiS: a program for the analysis of X-ray spectromicroscopy data, J. Synchrotron. Radiat., 21, 1206, 10.1107/S1600577514013964