FIB-SEM tomography in biology

Methods in Molecular Biology

Volumn 1117, Issue , 2014, Pages 541-558

  Kizilyaprak, Caroline ^a   Bittermann, Anne Greet ^b   Daraspe, Jean ^a   Humbel, Bruno M ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b ETH ZURICH   (Switzerland)

Author keywords

Biofi lm; Cell substrate interface; Focused ion beam scanning electron microscope (FIB SEM); Resin embedding; Targeted preparation; Tomography

Indexed keywords

ANALYTIC METHOD; ARTICLE; BIOFILM; ELECTRON BEAM TOMOGRAPHY; FOCUSED ION BEAM SCANNING ELECTRON MICROSCOPE TOMOGRAPHY; MOLECULAR BIOLOGY; PRIORITY JOURNAL; SURFACE PROPERTY; THIN LAYER PLASTIFICATION;

ELECTRON MICROSCOPE TOMOGRAPHY; HISTOCYTOLOGICAL PREPARATION TECHNIQUES; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, ELECTRON, SCANNING; SOFTWARE;

EID: 84934438646     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-776-1_24     Document Type: Article

References (45)

1. Seliger RL, Fleming WP (1974) Focused ion beams in microfabrication. J Appl Phys 45:1416-1422
2. Ishitani T, Hirose H, Tsuboi H (1995) Focused-ion-beam digging of biological specimens. J Electron Microsc 44:110-114
3. Ishitani T, Yaguchi T (1996) Cross-sectional sample preparation by focused ion beam: a review of ion-sample interaction. Microsc Res Tech 35:320-333
4. Giannuzzi LA, Drown JL, Brown SR et al (1998) Applications of the FIB lift-out technique for TEM specimen preparation. Microsc Res Tech 41:285-290
5. Giannuzzi LA, Stevie FA (1999) A review of focused ion beam milling techniques for TEM specimen preparation. Micron 30:197-204
6. Overwijk MHF, van den Heuvel FC, Bulle-Lieuwma CWT (1993) Novel scheme for the preparation of transmission electron microscopy specimens with a focused ion beam. J Vac Sci Technol B 11:2021-2024
7. Nalla RK, Porter AE, Daraio C et al (2005) Ultrastructural examination of dentin using focused ion-beam cross-sectioning and transmission electron microscopy. Micron 36:672-680
8. Giannuzzi LA, Phifer D, Giannuzzi NJ et al (2007) Two-dimensional and 3-dimensional analysis of bone/dental implant interfaces with the use of focused ion beam and electron microscopy. J Oral Maxillofac Surg 65:737-747
9. Hayles M, Stokes DJ, Phifer D et al (2006) A technique for improved focused ion beam milling of cryo-prepared life science specimens. J Microsc (Oxford) 226:263-269
10. Marko M, Hsieh CE, Schalek R et al (2007) Focused-ion-beam thinning of frozen hydrated biological specimens for cryoelectron microscopy. Nat Methods 4:215-217
11. Marko M, Hsieh CE, Moberlychan W et al (2006) Focused ion beam milling of vitreous water: prospects for an alternative to cryo-ultramicrotomy of frozen-hydrated biological samples. J Microsc (Oxford) 222:42-47
12. Rigort A, Bäuerlein FJB, Villa E et al (2012) Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. Proc Natl Acad Sci U S A 109:4449-4454
13. Rubino S, Akhtar S, Melin P et al (2012) A site-specifi c focused-ion-beam lift-out method for cryo transmission electron microscopy. J Struct Biol 180:572-576
14. Drobne D, Milani M, Ballerini M et al (2004) Focused ion beam for microscopy and in situ sample preparation: application on a crustacean digestive system. J Biomed Opt 9:1238-1243
15. Drobne D, Milani M, Lešer V et al (2008) Imaging of intracellular spherical lamellar structures and tissue gross morphology by a focused ion beam/scanning electron microscope (FIB/SEM). Ultramicroscopy 108:663-670
16. Drobne D, Milani M, Zrimec A et al (2005) Electron and ion imaging of gland cells using the FIB/SEM system. J Microsc (Oxford) 219:29-35
17. Drobne D, Milani M, Zrimec A et al (2005) Focused ion beam/scanning electron microscopy studies of Porcellio scaber (Isopoda, Crustacea) digestive gland epithelium cells. Scanning 27:30-34
18. Greve F, Frerker S, Bittermann AG et al (2007) Molecular design and characterization of the neuro-microelectrode array interface. Biomaterials 28:5246-5258
19. Inkson BJ, Mulvihill M, Möbus G (2001) 3D determination of grain shape in a FeAl-based nanocomposite by 3D FIB tomography. Scr Mater 45:753-58
20. Holzer L, Indutnyi F, Gasser PH et al (2004) Three-dimensional analysis of porous BaTiO3 ceramics using FIB nanotomography. J Microsc 216:84-95
21. Heymann JAW, Hayles M, Gestmann I et al (2006) Site-specifi c 3D imaging of cells and tissues with a dual beam microscope. J Struct Biol 155:63-73
22. Knott G, Marchman H, Wall D et al (2008) Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling. J Neurosci 28:2959-2964
23. De Winter DAM, Schneijdenberg CTWM, Lebbink MN et al (2009) Tomography of insulating biological and geological materials using focused ion beam (FIB) sectioning and low kV BSE imaging. J Microsc (Oxford) 233:372-383
24. Hekking LHP, Lebbink MN, De Winter DAM et al (2009) Focused ion beam-scanning electron microscope: exploring large volumes of atherosclerotic tissue. J Microsc (Oxford) 235:336-347
25. Heymann JAW, Shi D, Kim S et al (2009) 3D Imaging of mammalian cells with ion-abrasion scanning electron microscopy. J Struct Biol 166:1-7
26. Schroeder-Reiter E, Pérez-Willard F, Zeile U et al (2009) The osmium tetroxide-potassium ferrocyanide (OsFeCN) staining technique for electron microscopy: a critical evaluation using ciliates, algae, mosses, and higher plants. J Struct Biol 165:97-106
27. Lamers E, Walboomers XF, Domanski M et al (2011) Cryo DualBeam focused ion beam-scanning electron microscopy to evaluate the interface between cells and nanopatterned scaffolds. Tissue Eng Part C Methods 17:1-7
28. Denk W, Horstmann H (2004) Serial blockface scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol 2:1900-1909
29. Kosinski M, McDonald K, Schwartz J et al (2005) C. elegans sperm bud vesicles to deliver a meiotic maturation signal to distant oocytes. Development 132:3357-3369
30. Pellettieri J, Fitzgerald P, Watanabe S et al (2010) Cell death and tissue remodeling in planarian regeneration. Dev Biol 338:76-85
31. Rouquette J, Genoud C, Vazquez-Nin GH et al (2009) Revealing the high-resolution three-dimensional network of chromatin and interchromatin space: a novel electronmicroscopic approach to reconstructing nuclear architecture. Chromosome Res 17:801-810
32. Loussert C, Forestier C-L, Humbel BM (2012) Correlative light and electron microscopy in parasite research. Methods Cell Biol 111:59-73
33. Lucas MS, Günthert M, Gasser P et al (2012) Bridging microscopes: 3D correlative light and scanning electron microscopy of complex biological structures. Methods Cell Biol 111:325-356
34. Bittermann AG, Schaer D, Mitsi M et al. (2012) Thin layer plastifi cation vs. block embedding: two alternative preparation strategies for 3D-imaging of cultured cells and biofi lms by FIB/SEM. In: Society EM (ed) European Microscopy Conference 2012. Wiley, Manchester
35. Schnepf E, Hausmann K, Herth W (1982) The osmium tetroxide-potassium ferrocyanide (OsFeCN) staining technique for electron microscopy: a critical evaluation using ciliates, algae, mosses, and higher plants. Histochemistry 76:261-271
36. Stäubli W (1963) A new embedding technique for electron microscopy, combining a water-soluble epoxy resin (Durcupan) with water-insoluble Araldite. J Cell Biol 16:197-201
37. Spurr AR (1969) A low-viscosity epoxy resin embedding medium for electron microscopy. J Ultrastruct Res 26:31-43
38. Craig EL, Frajola WJ, Greider MH (1962) An embedding technique for electron microscopy using EPON 812. J Cell Biol 12:190-194
39. Luft JH (1961) Improvements in epoxy resin embedding methods. J Biophys Biochem Cytol 9:409-414
40. Humbel BM, Schwarz H (1989) Freezesubstitution for immunochemistry. In: Verkleij AJ, Leunissen JLM (eds) Immuno-gold labeling in cell biology. CRC, Boca Raton, pp 115-134
41. Steinbrecht RA, Müller M (1987) Freezesubstitution and freeze-drying. In: Steinbrecht RA, Zierold K (eds) Cryotechniques in biological electron microscopy. Springer, Berlin, pp 149-172
42. Müller M, Moor H (1984) Cryofi xation of thick specimens by high pressure freezing. In: Revel JP, Barnard T, Haggis GH (eds) Science of biological specimen preparation 1983. SEM Inc., AMF O'Hare, IL, pp 131-138
43. Kremer JR, Mastronarde DN, McIntosh JR (1996) Computer visualization of threedimensional image data using IMOD. J Struct Biol 116:71-76
44. Collins TJ (2007) ImageJ for microscopy. Biotechniques 43:S25-S30
45. Schindelin J, Arganda-Carreras I, Frise E et al (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9: 676-682