3D chemical mapping: Application of scanning transmission (soft) X-ray microscopy (STXM) in combination with angle-scan tomography in bio-, geo-, and environmental sciences

Methods in Molecular Biology

Volumn 1117, Issue , 2014, Pages 757-781

  Obst, Martin ^a   Schmid, Gregor ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

3D reconstruction; Angle scan tomography; Chemical microscopy; Chemical nanotomography; Chemical tomography; Scanning transmission (soft) X ray microscopy (STXM); Spectromicroscopy

Indexed keywords

CARBON NANOTUBE; GLASS; SILICON NITRIDE;

ANGLE SCAN TOMOGRAPHY; ARTICLE; ENVIRONMENT; IMAGE ANALYSIS; IMAGE RECONSTRUCTION; MICROSCOPY; PRIORITY JOURNAL; SCANNING TRANSMISSION X RAY MICROSCOPY; THREE DIMENSIONAL IMAGING; TOMOGRAPHY;

ELECTRON PROBE MICROANALYSIS; IMAGING, THREE-DIMENSIONAL; INORGANIC CHEMICALS; MICROSCOPY, ELECTRON, SCANNING TRANSMISSION; MODELS, MOLECULAR; ORGANIC CHEMICALS; TOMOGRAPHY SCANNERS, X-RAY COMPUTED;

EID: 84934440727     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-776-1_34     Document Type: Article

References (74)

1. Kirz J, Rarback H (1985) Soft-X-ray microscopes. Rev Sci Instrum 56:1-13
2. Kilcoyne ALD, Tyliszczak T, Steele WF et al (2003) Interferometer- controlled scanning transmission X-ray microscopes at the Advanced Light Source. J Synchrotron Radiat 10:125-136
3. Wiesemann U, Thieme J, Guttmann P et al (2003) First results of the new scanning transmission X-ray microscope at BESSY-II. J Phys IV 104:95-98
4. Kaznatcheev KV, Karunakaran C, Lanke UD et al (2007) Soft X-ray spectromicroscopy beamline at the CLS: commissioning results. Nucl Instrum Methods A Phys Res Sect A 582:96-99
5. Kaulich B, Bacescu D, Susini J et al (2006) TwinMic -A European twin X-ray microscopy station commissioned at ELETTRA. In: Aoki S, Kagoshima Y, Suzuki Y (eds) IPAP Conference Series 7. Himeji, Japan, pp 22-25
6. Xue CF, Wang Y, Guo Z et al (2010) Highperformance soft x-ray spectromicroscopy beamline at SSRF. Rev Sci Instrum 81:103502. doi: 10.1063/1.3491837
7. Raabe J, Tzvetkov G, Flechsig U et al (2008) PolLux: a new facility for soft X-ray spectromicroscopy at the Swiss Light Source. Rev Sci Instrum 79:113704. doi: 10.1063/1.3021472
8. Hitchcock AP (2012) Soft X-ray imaging and spectromicroscopy. In: van Tendeloo G, van Dyck D, Pennycook SJ (eds) Handbook of nanoscopy. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, pp 745-791
9. Willmott P (2011) Synchrotron physics. In: Willmott P (ed) An Introduction to synchrotron radiation. John Wiley & Sons Ltd, Chichester, pp 39-86
10. Bluhm H, Andersson K, Araki T et al (2006) Soft x-ray microscopy and spectroscopy at the molecular environmental science beamline at the advanced light source. J Electron Spectrosc 150:86-104
11. Lawrence JR, Hitchcock AP (2011) Synchrotron-based X-Ray and FTIR absorption spectromicroscopies of organic contaminants in the environment. In: Xing B, Senesi N, Huang PM (eds) Biophysico-chemical processes of anthropogenic organic compounds in environmental systems. Wiley, Hoboken, pp 341-368
12. Behrens S, Kappler A, Obst M (2012) Linking environmental processes to the in situ functioning of microorganisms by high-resolution secondary ion mass spectrometry (NanoSIMS) and scanning transmission X-ray microscopy (STXM). Environ Microbiol 14:2851-2869
13. Jacobsen C, Wirick S, Flynn G et al (2000) Soft X-ray spectroscopy from image sequences with sub-100 nm spatial resolution. J Microsc (Oxford) 197:173-184
14. Henke BL, Gullikson EM, Davis JC (1993) X-Ray interactions -photoabsorption, scattering, transmission, and refl ection at E = 50-30,000 Ev, Z = 1-92. Atom Data Nucl Data Tables 54:181-342
15. Thompson AC, Attwood D, Gullikson E et al (2009) X-ray properties of the elements. In: Thompson AC (ed) X-ray data booklet, 3rd edn. Lawrence Berkeley National Laboratory, Berkeley, pp 1-53
16. Willmott P (2011) Spectroscopic techniques. In: Willmott P (ed) An introduction to synchrotron radiation. John Wiley & Sons Ltd, Chichester, pp 223-302
17. Lawrence JR, Swerhone GDW, Leppard GG et al (2003) Scanning transmission X-ray, laser scanning, and transmission electron microscopy mapping of the exopolymeric matrix of microbial biofi lms. Appl Environ Microbiol 69:5543-5554
18. Dynes JJ, Tyliszczak T, Araki T et al (2006) Speciation and quantitative mapping of metal species in microbial biofi lms using scanning transmission X-ray microscopy. Environ Sci Technol 40:1556-1565
19. Hitchcock AP, Dynes JJ, Lawrence JR et al (2009) Soft X-ray spectromicroscopy of nickel sorption in a natural river biofi lm. Geobiology 7:432-453
20. Lawrence JR, Dynes JJ, Korber DR et al (2012) Monitoring the fate of copper nanoparticles in river biofi lms using scanning transmission X-ray microscopy (STXM). Chem Geol 329:18-25
21. Hunter RC, Hitchcock AP, Dynes JJ et al (2008) Mapping the speciation of iron in Pseudomonas aeruginosa biofi lms using scanning transmission X-ray microscopy. Environ Sci Technol 42:8766-8772
22. Miot J, Benzerara K, Morin G et al (2009) Iron biomineralization by anaerobic neutrophilic iron-oxidizing bacteria. Geochim Cosmochim Acta 73:696-711
23. Miot J, Maclellan K, Benzerara K et al (2011) Preservation of protein globules and peptidoglycan in the mineralized cell wall of nitratereducing, iron(II)-oxidizing bacteria: a cryo-electron microscopy study. Geobiology 9:459-470
24. Pantke C, Obst M, Benzerara K et al (2012) Green rust formation during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1. Environ Sci Technol 46:1439-1446
25. Hitchcock AP, Obst M, Wang J et al (2012) Advances in the detection of As in environmental samples using low energy X-ray fluorescence in a scanning transmission X-ray microscope: arsenic immobilization by an Fe(II)-oxidizing freshwater bacteria. Environ Sci Technol 46:2821-2829
26. Miot J, Benzerara K, Obst M et al (2009) Extracellular iron biomineralization by photoautotrophic iron-oxidizing bacteria. Appl Environ Microbiol 75:5586-5591
27. Chan CS, De Stasio G, Welch SA et al (2004) Microbial polysaccharides template assembly of nanocrystal fibers. Science 303:1656-1658
28. Chan CS, Fakra SC, Edwards DC (2009) Iron oxyhydroxide mineralization on microbial extracellular polysaccharides. Geochim Cosmochim Acta 73:3807-3818
29. Chan CS, Fakra SC, Emerson D et al (2011) Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation. ISME J 5:717-727
30. Coker VS, Byrne JM, Telling ND et al (2012) Characterisation of the dissimilatory reduction of Fe(III)-oxyhydroxide at the microbemineral interface: the application of STXMXMCD. Geobiology 10:347-354
31. Lam KP, Hitchcock AP, Obst M et al (2010) Characterizing magnetism of individual magnetosomes by X-ray magnetic circular dichroism in a scanning transmission X-ray microscope. Chem Geol 270:110-116
32. Pecher K, McCubbery D, Kneedler E et al (2003) Quantitative charge state analysis of manganese biominerals in aqueous suspension using scanning transmission X-ray microscopy (STXM). Geochim Cosmochim Acta 67: 1089-1098
33. Toner B, Fakra S, Villalobos M et al (2005) Spatially resolved characterization of biogenic manganese oxide production within a bacterial biofi lm. Appl Environ Microbiol 71:1300-1310
34. Benzerara K, Yoon TH, Tyliszczak T et al (2004) Scanning transmission X-ray microscopy study of microbial calcifi cation. Geobiology 2:249-259
35. Obst M, Dynes JJ, Lawrence JR et al (2009) Precipitation of amorphous CaCO(3) (aragonite-like) by cyanobacteria: a STXM study of the infl uence of EPS on the nucleation process. Geochim Cosmochim Acta 73: 4180-4198
36. Norlund KLI, Southam G, Tyliszczak T et al (2009) Microbial architecture of environmental sulfur processes: a novel syntrophic sulfurmetabolizing consortia. Environ Sci Technol 43:8781-8786
37. Johansson GA, Tyliszczak T, Mitchell GE et al (2007) Three-dimensional chemical mapping by scanning transmission X-ray spectromicroscopy. J Synchrotron Radiat 14:395-402
38. Obst M, Wang J, Hitchcock AP (2009) Soft X-ray spectro-tomography study of cyanobacterial biomineral nucleation. Geobiology 7:577-591
39. Herman GT, Lent A, Rowland SW (1973) ART: mathematics and applications: a report on the mathematical foundations and on the applicability to real data of the algebraic reconstruction techniques. J Theor Biol 42:1-32
40. Gilbert P (1972) Iterative methods for the three-dimensional reconstruction of an object from projections. J Theor Biol 36:105-117
41. Maser J, Osanna A, Wang Y et al (2000) Soft X-ray microscopy with a cryo scanning transmission X-ray microscope: I. Instrumentation, imaging and spectroscopy. J Microsc (Oxford) 197:68-79
42. Wang Y, Jacobsen C, Maser J et al (2000) Soft X-ray microscopy with a cryo scanning transmission X-ray microscope: II Tomography. J Microsc (Oxford) 197:80-93
43. Johansson GA, Dynes JJ, Hitchcock AP et al (2006) Chemically sensitive 3D imaging at sub 100 nm spatial resolution using tomography in a scanning transmission x-ray microscope. Proc SPIE 6318. doi: 10.1117/12.681217
44. Hitchcock AP, Johansson GA, Mitchell GE et al (2008) 3-d chemical imaging using anglescan nanotomography in a soft X-ray scanning transmission X-ray microscope. Appl Phys A Mater Sci Process 92:447-452
45. Obst M, Hitchcock AP, Ayers T et al (2009) A novel wet cell for in situ 2D and 3D STXM studies. In: Dalzell M (ed) Canadian Light Source activity report 2008. Canadian Light Source, Inc., Saskatoon, pp 142-143
46. Wang J, Hitchcock AP, Karunakaran C et al (2011) 3D chemical and elemental imaging by STXM spectrotomography. In: McNulty I, Eyberger C, Lai B (eds) AIP Conference Proceedings 1365. Chicago, pp 215-218
47. Hilhorst J, van Schooneveld MM, Wang J et al (2012) Three-dimensional structure and defects in colloidal photonic crystals revealed by tomographic scanning transmission X-ray microscopy. Langmuir 28:3614-3620
48. Hitchcock AP, Araki T, Ikeura-Sekiguchi H et al (2003) 3d chemical mapping of toners by serial section scanning transmission X-ray microscopy. J Phys IV (France) 104:509-512
49. Neu TR, Manz B, Volke F et al (2010) Advanced imaging techniques for assessment of structure, composition and function in biofi lm systems. FEMS Ecol 72:1-21
50. Weiss D, Schneider G, Niemann B et al (2000) Computed tomography of cryogenic biological specimens based on X-ray microscopic images. Ultramicroscopy 84:185-197
51. Gu WW, Etkin LD, Le Gros MA et al (2007) X-ray tomography of Schizosaccharomyces pombe . Differentiation 75:529-535
52. Schrlau MG, Falls EM, Ziober BL et al (2008) Carbon nanopipettes for cell probes and intracellular injection. Nanotechnology 19:015101. doi: 10.1088/0957-4484/19/01/015101
53. Hitchcock AP (2013) aXis2000 Is an IDLbased analytical package. http://unicorn. mcmaster.ca/aXis2000.html
54. Exelis Visual Information Solutions I (2012) IDL. http://www.exelisvis. com/
55. Fiji (2013) www.fi ji.sc
56. Schindelin J, Arganda-Carreras I, Frise E et al (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9: 676-682
57. TomoJ (2013) http://u759.curie.fr/en
58. Sorzano CO, Messaoudi C, Eibauer M et al (2009) Marker-free image registration of electron tomography tilt-series. BMC Bioinformatics 10:124. doi: 10.1186/1471-2105-10-124
59. Messaoudii C, Boudier T, Sanchez Sorzano CO et al (2007) TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy. BMC Bioinformatics 8:288. doi: 10.1186/1471-2105-8-288
60. IMOD (2012) http://bio3d.colorado.edu/imod/
61. Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visualization of threedimensional image data using IMOD. J Struct Biol 116:71-76
62. IMODJ (2008) http://www.snv.jussieu.fr/~wboudier/softs/imodj.html
63. UCSF Chimera (2013) http://www.cgl.ucsf. edu/chimera/
64. Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera -A visualization system for exploratory research and analysis. J Comput Chem 25:1605-1612
65. ilastik (2012) http://www.ilastik.org/.
66. Sommer C, Straehle C, Kothe U et al (2011) Ilastik: interactive learning and segmentation toolkit. In: Proceedings. IEEE international symposium on biomedical imaging. Chicago, pp 230-233
67. SM-Beamline (2012) http://exshare.lightsource. ca/sm/Pages/SM-Home.aspx
68. Myneni SCB (2002) Soft X-ray spectroscopy and spectromicroscopy studies of organic molecules in the environment. In: Fenter PA, Rivers ML, Sturchio NC et al (eds) Applications of synchrotron radiation in low-temperature geochemistry and environmental sciences. Mineralogical Society of America, Chicago, pp 485-579
69. Koprinarov IN, Hitchcock AP, McCrory CT et al (2002) Quantitative mapping of structured polymeric systems using singular value decomposition analysis of soft X-ray images. J Phys Chem B 106:5358-5364
70. Dynes JJ, Lawrence JR, Korber DR et al (2006) Quantitative mapping of chlorhexidine in natural river biofi lms. Sci Total Environ 369:369-383
71. Jacobsen C, Feser M, Lerotic M et al (2003) Cluster analysis of soft X-ray spectromicroscopy data. J Phys IV 104:623-626
72. Crowther RA, Henderson R, Smith JM (1996) MRC image processing programs. J Struct Biol 116:9-16
73. Wang J, Button GA, West MM et al (2009) Quantitative evaluation of radiation damage to polyethylene terephthalate by soft X-rays and high-energy electrons. J Phys Chem B 113: 1869-1876
74. Yang J, Regier T, Dynes JJ et al (2011) Soft X-ray induced photoreduction of organic Cu(II) compounds probed by X-ray absorption near-edge (XANES) spectroscopy. Anal Chem 83:7856-7862