Skip to main content
SpringerLink
Log in

Soft X-Ray Tomography Imaging for Biological Samples

  • Chapter
  • First Online:
Computational Methods for Three-Dimensional Microscopy Reconstruction

Part of the book series: Applied and Numerical Harmonic Analysis ((ANHA))

Abstract

Soft X-ray tomographic (TomoX) microscopy is becoming a valuable technique for the analysis of the organization of cellular structures, filling a resolution gap between electron and confocal microscopy. TomoX is based on the possibility of imaging three-dimensional fully hydrated cells under cryo-conditions without any chemical pretreatment using soft X-rays. Unfortunately, from an image formation point of view, TomoX projections suffer from inaccuracies due to the limited depth of field (DOF) of the objective lens. Thus, modeling the image formation process is decisive to understanding how TomoX projections are formed and to mitigating the effect of these DOF inaccuracies. A review of the state of the art regarding image modeling is presented in this chapter.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Agulleiro J, Fernandez J (2011) Fast tomographic reconstruction on multicore computers. Bioinformatics 27(4):582–583. doi: 10.1093/bioinformatics/btq692, http://bioinformatics.oxfordjournals.org/content/27/4/582.short

    Google Scholar 

  2. Agulleiro JI, Fernández JJ (2012) Evaluation of a multicore-optimized implementation for tomographic reconstruction. PloS One 7(11):e48261. doi: 10.1371/journal.pone.0048261, http://dx.plos.org/10.1371/journal.pone.0048261

  3. Agulleiro JI, Garzón EM, García I, Fernández JJ (2010) Vectorization with SIMD extensions speeds up reconstruction in electron tomography. J Struct Biol 170(3):570–575. doi: 10.1016/j.jsb.2010.01.008, http://www.ncbi.nlm.nih.gov/pubmed/20085820

    Google Scholar 

  4. Attwood D (2007) Soft x-rays and extreme ultraviolet radiation: Principles and applications, 1st edn. Cambridge University Press, New York

    Google Scholar 

  5. Bertilson M, von Hofsten O, Vogt U, Holmberg A, Christakou AE, Hertz HM (2011) Laboratory soft-x-ray microscope for cryotomography of biological specimens. Opt Lett 36(14):2728–2730. doi: 10.1364/OL.36.002728, http://www.ncbi.nlm.nih.gov/pubmed/21765523, http://ol.osa.org/abstract.cfm?URI=ol-36-14-2728

    Google Scholar 

  6. Born M, Wolf E (1999) Principles of optics: Electromagnetic theory of propagation, interference and diffraction of light, 7th edn. Cambridge University Press, Cambridge

    Book  Google Scholar 

  7. Carrascosa JL, Chichón FJ, Pereiro E, Rodríguez MJ, Fernández JJ, Esteban M, Heim S, Guttmann P, Schneider G (2009) Cryo-X-ray tomography of vaccinia virus membranes and inner compartments. J Struct Biol 168(2):234–9, doi: 10.1016/j.jsb.2009.07.009, http://www.ncbi.nlm.nih.gov/pubmed/19616103

  8. Chapman HN, Nugent K (2010) Coherent lensless X-ray imaging. Nat Photonics 4(12): 833–839. doi: 10.1038/nphoton.2010.240, http://www.nature.com/doifinder/10.1038/nphoton.2010.240

    Google Scholar 

  9. Chichón FJ, Rodríguez MJ, Pereiro E, Chiappi M, Perdiguero B, Guttmann P, Werner S, Rehbein S, Schneider G, Esteban M, Carrascosa JL (2012) Cryo X-ray nano-tomography of vaccinia virus infected cells. J Struct Biol 177(2):202–11. doi: 10.1016/j.jsb.2011.12.001, http://www.ncbi.nlm.nih.gov/pubmed/22178221

    Google Scholar 

  10. Cowley J (1995) Diffraction physics, 3rd edn. Elsevier, Amsterdam

    Google Scholar 

  11. Erhardt A, Zinser G, Komitowski D, Bille J (1985) Reconstructing 3-D light-microscopic images by digital image processing. Appl Opt 24(2):194. http://www.ncbi.nlm.nih.gov/pubmed/18216925

    Google Scholar 

  12. Folland GB (1992) Fourier analysis and its applications. Wadsworth & Brooks/Cole Advanced Books & Software, Pacific Grove California

    MATH  Google Scholar 

  13. Frank J (2006) Three dimensional electron microscopy of macromolecular assemblies. Oxford University Press, New York

    Book  Google Scholar 

  14. Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A (1996) SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. J Struct Biol 116:190–199

    Article  Google Scholar 

  15. Goodman JW (1996) Introduction to Fourier optics. McGraw-Hill, New York

    Google Scholar 

  16. Gros ML, McDermott G, Larabell C (2005) X-ray tomography of whole cells. Curr Opin Struct Biol 15:593–600. http://www.sciencedirect.com/science/article/pii/S0959440X05001569

    Google Scholar 

  17. Gu W, Etkin L, Gros ML, Larabell C (2007) X-ray tomography of Schizosaccharomyces pombe. Differentiation 75:529–535. http://onlinelibrary.wiley.com/doi/10.1111/j.1432-0436.2007.00180.x/full

    Google Scholar 

  18. Hanssen E, Knoechel C (2012) Soft X-ray microscopy analysis of cell volume and hemoglobin content in erythrocytes infected with asexual and sexual stages of Plasmodium falciparum. J Struct Biol 177:224–232. http://www.sciencedirect.com/science/article/pii/S1047847711002589

  19. Heymann JB, Cardone G, Winkler DC, Steven AC (2008) Computational resources for cryo-electron tomography in Bsoft. J Struct Biol 161(3):232–242. doi: 10.1016/j.jsb.2007.08.002

    Article  Google Scholar 

  20. Howells M, Jacobsen C, Warwick T, Bos A (2007) Principles and applications of zone plate x-ray microscopes. In: Science in microscopy, vol 1984, {P.W} hawk edn. Springer, New York, pp 835–926. http://www.springerlink.com/index/W76K0246K3HG7W26.pdf

  21. Jacobson RE, Ray SF, Attridge GG, Axford NR (2001) Manual of photography: photographic and digital imaging, 9th edn. Focal Press, London. http://dl.acm.org/citation.cfm?id=558275

  22. Kirz J, Jacobsen C, Howells M (1995) Soft X-ray microscopes and their biological applications. Quart Rev Biophys 28:33–130

    Article  Google Scholar 

  23. Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visualization of three-dimensional image data using IMOD. J Struct Biol 116:71–76

    Article  Google Scholar 

  24. Larabell C (2004) X-ray tomography generates 3-D reconstructions of the yeast, Saccharomyces cerevisiae, at 60-nm resolution. Molecular Biol Cell 15:957–962 doi: 10.1091/mbc.E03, http://www.molbiolcell.org/content/15/3/957.short

    Google Scholar 

  25. Legall H, Blobel G, Stiel H, Sandner W, Seim C, Takman P, Martz DH, Selin M, Vogt U, Hertz HM, Esser D, Sipma H, Luttmann J, Höfer M, Hoffmann HD, Yulin S, Feigl T, Rehbein S, Guttmann P, Schneider G, Wiesemann U, Wirtz M, Diete W (2012) Compact x-ray microscope for the water window based on a high brightness laser plasma source. Opt Expr 20(16): 18362–18369. http://www.ncbi.nlm.nih.gov/pubmed/23038387

    Google Scholar 

  26. Martínez-Corral M, Zapata-Rodríguez C (1998) Effective Fresnel-number concept for evaluating the relative focal shift in focused beams. JOSA A 15(2):449–455. http://www.opticsinfobase.org/abstract.cfm?id=1405

  27. McDermott G, Le Gros Ma, Larabell Ca (2012) Visualizing cell architecture and molecular location using soft x-ray tomography and correlated cryo-light microscopy. Ann Rev Phys Chem 63:225–239. doi: 10.1146/annurev-physchem-032511-143818, http://www.ncbi.nlm.nih.gov/pubmed/22242730

  28. Mendoza-Yero O, Minguez-Vega G, Navarro R, Lancis J, Climent V (2010) PSF analysis of nanometric Fresnel zone plates. In: Proceeding of the EOS topical meeting on diffractive optics, Koli, Finland

    Google Scholar 

  29. Mielenz KD (1999) On the diffraction limit for lensless imaging. J Res NIST 104(5):479–485

    Article  Google Scholar 

  30. Nelson J, Huang X, Steinbrener J, Shapiro D, Kirz J, Marchesini S, Neiman AM, Turner JJ, Jacobsen C (2010) High-resolution x-ray diffraction microscopy of specifically labeled yeast cells. Proc Natl Acad Sci USA 107(16):7235–7239. doi: 10.1073/pnas.0910874107

    Article  Google Scholar 

  31. Oton J, Sorzano COS, Pereiro E, Cuenca-Alba J, Navarro R, Carazo JM, Marabini R (2012) Image formation in cellular X-ray microscopy. J Struct Biol 178(1):29–37. doi: 10.1016/j.jsb.2012.01.006, http://dx.doi.org/10.1016/j.jsb.2012.01.006

    Google Scholar 

  32. Parkinson D, McDermott G (2008) Quantitative 3-D imaging of eukaryotic cells using soft X-ray tomography. J Struct Biol 162:380–386. http://journals.cambridge.org/production/action/cjoGetFulltext?fulltextid=1945896

    Google Scholar 

  33. Rehbein S, Heim S, Guttmann P, Werner S (2009) Ultrahigh-resolution soft-X-ray microscopy with zone plates in high orders of diffraction. Phys Rev Lett 110801:1–4. doi: 10.1103/PhysRevLett.103.110801, http://link.aps.org/doi/10.1103/PhysRevLett.103.110801

    Google Scholar 

  34. Sakdinawat A, Attwood D (2010) Nanoscale X-ray imaging. Nat Photonics 4(12):840–848. doi: 10.1038/nphoton.2010.267, http://www.nature.com/doifinder/10.1038/nphoton.2010.267

    Google Scholar 

  35. Scheres SHW, Núñez Ramírez R, Sorzano COS, Carazo JM, Marabini R (2008) Image processing for electron microscopy single-particle analysis using XMIPP. Nat Protoc 3(6): 977–990. doi: 10.1038/nprot.2008.62, http://dx.doi.org/10.1038/nprot.2008.62

  36. Schneider G (1998) Cryo X-ray microscopy with high spatial resolution in amplitude and phase contrast. Ultramicroscopy 75(2):85–104. http://www.ncbi.nlm.nih.gov/pubmed/9836467

    Google Scholar 

  37. Sorzano COS, Marabini R, Velázquez-Muriel J, Bilbao-Castro JR, Scheres SHW, Carazo JM, Pascual-Montano A (2004) XMIPP: A new generation of an open-source image processing package for electron microscopy. J Struct Biol 148(2):194–204. doi: 10.1016/j.jsb.2004.06.006, http://www.ncbi.nlm.nih.gov/pubmed/15477099

    Google Scholar 

  38. Sypek M, Makowski M, Kolodziejczyk A, Navarro R (2010) Calculations of PSF functions for X-ray zone plates with high number of zones. In: Proceeding of the EOS topical meeting on diffractive optics, Koli, Finland

    Google Scholar 

  39. Thieme J, Schneider G, Knochel C (2003) X-ray tomography of a microhabitat of bacteria and other soil colloids with sub-100 nm resolution. Micron 34:339–344

    Article  Google Scholar 

  40. Uchida M, McDermott G, Wetzler M, Le Gros Ma, Myllys M, Knoechel C, Barron AE, Larabell Ca (2009) Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans. Proc Natl Acad Sci USA 106(46):19375–19380. doi: 10.1073/pnas.0906145106

    Article  Google Scholar 

  41. Wan Y, Chiu W, Zhou Z (2004) Full contrast transfer function correction in 3D cryo-EM reconstruction. In: Proceeding of communications, circuits and systems, vol 2

    Google Scholar 

  42. Weiss D, Schneider G, Niemann B, Guttmann P, Rudolph D, Schmahl G (2000) Computed tomography of cryogenic biological specimens based on x-ray microscopic images. Ultramicroscopy 84(3–4):185–197. http://www.ncbi.nlm.nih.gov/pubmed/10945329, http://www.sciencedirect.com/science/article/pii/S0304399100000346

    Google Scholar 

  43. Wolter H (1952) Spiegelsysteme streifenden Einfalls als abbildende optiken für Röntgenstrahlen. Annalen der Physik 445:94–114. doi: 10.1002/andp.19524450108

    Article  Google Scholar 

Download references

Acknowledgements

The authors would like to acknowledge the financial support from the Spanish Ministry of Economy and Competitiveness (MEC) through grants AIC-A-2011-0638 and BIO2010-16566; the Comunidad de Madrid through grant CAM(S2010/BMD-2305); and the European Community’s Seventh Framework Programme (FP7/2007–2013) under BioStruct-X (CAP-INFRAS/1376) and NSF grant DMS-1114901. C.O.S. Sorzano is a recipient of a Ramón y Cajal fellowship financed by the European Social Fund and MEC. Joaquín Otón is supported by a Juan de la Cierva fellowship from MEC with reference JCI-2010-07594.

Author information

Authors and Affiliations

  1. Biocomputing Unit, National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad Autónoma, 28049, Cantoblanco, Madrid, Spain

    J. Otón, F. J. Chichón & J. M. Carazo

  2. Biocomputing Unit, National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad AutÃşnoma, 28049, Cantoblanco, Madrid, Spain

    C. O. S. Sorzano & J. L. Carrascosa

  3. Bioengineering Laboratory, Universidad CEU San Pablo, Campus Urb. Montepríncipe s/n, 28668, Boadilla del Monte, Madrid, Spain

    C. O. S. Sorzano

  4. Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Cantoblanco, Madrid, Spain

    J. L. Carrascosa

  5. Escuela Politécnica Superior, Universidad Autónoma de Madrid, Campus Universidad Autónoma, 28049, Cantoblanco, Madrid, Spain

    R. Marabini

Authors
  1. J. Otón
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. O. S. Sorzano
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. F. J. Chichón
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J. L. Carrascosa
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. M. Carazo
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. R. Marabini
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to J. Otón .

Editor information

Editors and Affiliations

  1. Department of Computer Science, The Graduate Center City University of New York, New York, New York, USA

    Gabor T. Herman

  2. Department of Biology, Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA

    Joachim Frank

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this chapter

Cite this chapter

Otón, J., Sorzano, C.O.S., Chichón, F.J., Carrascosa, J.L., Carazo, J.M., Marabini, R. (2014). Soft X-Ray Tomography Imaging for Biological Samples. In: Herman, G., Frank, J. (eds) Computational Methods for Three-Dimensional Microscopy Reconstruction. Applied and Numerical Harmonic Analysis. Birkhäuser, New York, NY. https://doi.org/10.1007/978-1-4614-9521-5_8

Download citation

Publish with us

Policies and ethics

Search

Navigation