Correlation of the same fields imaged in the TEM, confocal, LM, and microCT by image registration: From specimen preparation to displaying a final composite image

Methods in Cell Biology

Volumn 124, Issue , 2014, Pages 391-417

  Keene, Douglas R ^a   Tufa, Sara F ^a   Wong, Melissa H ^b   Smith, Nicholas R ^b   Sakai, Lynn Y ^a   Horton, William A ^a  

^a SHRINERS HOSPITAL FOR CHILDREN   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

CLEM; Correlated imaging; Correlative microscopy; Electron microscopy; Fiji; Fluorescence microscopy; GFP; Image overlay; Image registration; ImageJ; Laser scanning confocal microscopy; Localization; Method; Protocol; Technique; TurboReg

Indexed keywords

ANIMAL; CELL CULTURE; COMPUTER INTERFACE; CONFOCAL MICROSCOPY; FIDUCIAL MARKER; HISTOLOGY; HUMAN; MICRO-COMPUTED TOMOGRAPHY; MICROTOMY; PROCEDURES; STAINING; STANDARDS; THREE DIMENSIONAL IMAGING; TRANSMISSION ELECTRON MICROSCOPY;

ANIMALS; CELLS, CULTURED; FIDUCIAL MARKERS; HUMANS; IMAGING, THREE-DIMENSIONAL; MICROSCOPY, CONFOCAL; MICROSCOPY, ELECTRON, TRANSMISSION; MICROTOMY; STAINING AND LABELING; TISSUE EMBEDDING; USER-COMPUTER INTERFACE; X-RAY MICROTOMOGRAPHY;

EID: 84907817125     PISSN: 0091679X     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-801075-4.00018-5     Document Type: Chapter

References (43)

1. Aebi U., Pollard T.D. A glow discharge unit to render electron microscope grids and other surfaces hydrophilic. Journal of Electron Microscopy Technique 1987, 7:29-33.
2. Albrecht M. Color blindness. Nature Methods 2010, 7:775.
3. Bell K., Mitchell S., Paultre D., Posch M., Oparka K. Correlative imaging of fluorescent proteins in resin-Embedded plant material. Plant Physiology 2013, 161:1595-1603.
4. Bizzarri R., Serresi M., Luin S., Beltram F. Green fluorescent protein based pH indicators for in vivo use: A review. Analytical and Bioanalytical Chemistry 2009, 393:1107-1122.
5. Brown T.A., Fetter R.D., Tkachuk A.N., Clayton D.A. Approaches toward super-resolution fluorescence imaging of mitochondrial proteins using PALM. Methods 2010, 51:458-463.
6. Campbell T.N., Choy F.Y.M. The effect of pH on green fluorescent protein: A brief review. Molecular Biology Today 2001, 2:1-4.
7. Carlson D.B., Evans J.E. Low-cost cryo-light microscopy stage fabrication for correlated light/electron microscopy. Journal of Visualized Experiments 2011, 52:2909.
8. Ellisman M.H., Deerinck T.J., Shu X., Sosinsky G.E. Picking faces out of a crowd: Genetic labels for identification of proteins in correlated light and electron microscopy imaging. Methods in cell biology 2012, Vol. 111:75-93. Academic Press. T. Müller-Reichert, P. Verkade (Eds.).
9. Fabig G., Kretschmar S., Weiche S., Eberle D., Ader M., Kurth T. Labeling of ultrathin resin sections for correlative light and electron microscopy. Methods in cell biology 2012, Vol. 111:75-93. Academic Press. T. Müller-Reichert, P. Verkade (Eds.).
10. Handschuh S., Baeumler N., Schwaha T., Ruthensteiner B. A correlative approach for combining microCT, light and transmission electron microscopy in a single 3D scenario. Frontiers in Zoology 2013, 10-44.
11. Haupts U., Maiti S., Schwille P., Webb W.W. Dynamics of fluorescence fluctuations in green fluorescent protein observed by fluorescence correlation spectroscopy. Proceedings of the National Academy of Sciences of The United States of America 1998, 95:13573-13578.
12. Hayat M.A. Principles and techniques of electron microscopy. Biological applications 1970, Vol. 1. Van Nostrand Reinhold Company, New York, NY.
13. Henke B.L., Gullikson E.M., Davis J.C. X-ray interactions: Photoabsorption, scattering, transmission, and reflection at E=50-30000 eV, Z=1-92. Atomic Data Nuclear Data Tables 1993, 54:181-342.
14. Jeffery N.S., Stephenson R.S., Gallagher J.A., Jarvis J.C., Cox P.G. Micro-computed tomography with iodine staining resolves the arrangement of muscle fibers. Journal of Biomechanics 2010, 44:189-192.
15. Johnson J.T., Hansen M.S., Wu I., Healy L.J., Johnson C.R. Virtual histology of transgenic mouse embryos for high-throughput phenotyping. PLoS Genetics 2006, 2:471-477.
16. Keene D.R., Tufa S.F., Lunstrum G.P., Holden P., Horton W.A. Confocal/TEM overlay microscopy: A simple method for correlating confocal and electron microscopy of cells expressing GFP/YFP fusion proteins. Microscopy and Microanalysis 2008, 14:342-348.
17. Kopek B.G., Shtengel G., Grimm J.B., Clayton D.A., Hess H.F. Correlative photoactivated localization and scanning electron microscopy. PLoS One 2013, 8:e77209.
18. Kopek B.G., Shtengel G., Xu C.S., Clayton D.A., Hess H.F. Correlative 3D superresolution fluorescence and electron microscopy reveal the relationship of mitochondrial nucleoids to membranes. Proceedings of the National Academy of Sciences 2012, 109:6136-6141.
19. Kukulski W., Schorb M., Welsch S., Picco A., Kaksonen M., Briggs J.A. Precise, correlated fluorescence microscopy and electron tomography of lowicryl sections using fluorescent fiducial markers. Methods in cell biology 2012, Vol. 111:75-93. Academic Press. T. Müller-Reichert, P. Verkade (Eds.).
20. Lee D.W., Jensen C.M. Dry-ice bath based on ethylene glycol mixtures. Journal of Chemical Education 2000, 77:629.
21. McDonald K.L. A review of high-pressure freezing preparation techniques for correlative light and electron microscopy of the same cells and tissues. Journal of Microscopy 2009, 235:273-281.
22. McDonald K.L., Sharp D.J., Rickoll W. Postembedding immunolabeling of thin sections of Drosophila tissues for transmission electron microscopy. Drosophila protocols, Cold Spring Harbor Protocols 2012, 7:810-812. CSHL Press, Cold Spring Harbor, NY. Sullivan (Ed.).
23. Metscher B.D. Micro-CT for comparative morphology: Simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues. BMC Physiology 2009, 9:11.
24. Micheva K.D., Busse B., Weiler N.C., O'Rourke N., Smith S.J. Single-synapse analysis of a diverse synapse population: Proteomic imaging methods and markers. Neuron 2010, 68:639-653.
25. Neues F., Epple M. X-ray microcomputer tomography for the study of biomineralized endo- and exoskeletons of animals. Chemical Reviews 2008, 108:4734-4741.
26. Newman G.R., Hobot J.A. Modern acrylics for post-embedding immunostaining techniques. The Journal of Histochemistry and Cytochemistry 1987, 35:971-981.
27. Oest M.E., Jones J.C., Hatfield C., Prater M.R. Micro-CT evaluation of murine fetal skeletal development yields greater morphometric precision over traditional clear-staining methods. Birth Defects Research. Part B, Developmental and Reproductive Toxicology 2008, 83:582-589.
28. Reddick L.E., Alto N.M. Correlative light and electron microscopy (CLEM) as a tool to visualize microinjected molecules and their eukaryotic sub-cellular targets. Journal of Visualized Experiments 2012, 63:e3650.
29. Schellenberger P., Kaufmann R., Siebert C.A., Hagen C., Wodrich H., Grünewald K. High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers. Ultramicroscopy 2014, 143:41-51.
30. Schwartz C.L., Sarbash V.I., Ataullakhanov F.I., McIntosh J.R., Nicastro D. Cryo-fluorescence microscopy facilitates correlations between light and cryo-electron microscopy and reduces the rate of photobleaching. Journal of Microscopy 2007, 227:98-109.
31. Sengle G., Tufa S.F., Sakai L.Y., Zulliger M.A., Keene D.R. A correlative method for imaging identical regions of samples by micro-CT, light microscopy, and electron microscopy: Imaging adipose tissue in a model system. The Journal of Histochemistry and Cytochemistry 2013, 61:263-271.
32. Shu X., Lev-Ram V., Deerinck T.J., Qi Y., Ramko E.B., Davidson M.W., et al. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biology 2011, 4:e1001041.
33. Sims P.A., Hardin J.D. Visualizing green (GFP) and red (DsRed) fluorescent proteins in thin sections with laser scanning confocal and transmission electron microscopy. Microscopy and Microanalysis 2005, 11(Suppl. 2):6-7.
34. Sims P.A., Hardin J.D. Fluorescence-integrated transmission electron microscopy images: Integrating fluorescence microscopy with transmission electron microscopy. Methods in Molecular Biology 2007, 369:291-308.
35. Smith E.A., Cinquin B.P., Do M., McDermott G., Le Gros M.A., Larabell C.A. Correlative cryogenic tomography of cells using light and soft x-rays. Ultramicroscopy 2014, 143:33-40.
36. Spiegelhalter C., Tosch V., Hentsch D., Koch M., Kessler P., Schwab Y., et al. From dynamic live cell imaging to 3D ultrastructure: Novel integrated methods for high pressure freezing and correlative light-Electron microscopy. PLoS One 2010, 5:e9014.
37. Thévenaz P., Ruttimann U.E., Unser M. A pyramid approach to subpixel registration based on intensity. IEEE Transactions on Image Processing 1998, 7:27-41.
38. Tokuyasu K.T. A technique for ultracryotomy of cell suspensions and tissues. The Journal of Cell Biology 1973, 57:551-565.
39. van Driel L.F., Valentijn J.A., Valentijn K.M., Koning R.I., Koster A.J. Tools for correlative cryo-fluorescence microscopy and cryo-electron tomography applied to whole mitochondria in human endothelial cells. European Journal of Cell Biology 2009, 11:669-684.
40. Verkade P. Moving EM: The rapid transfer system as a new tool for correlative light and electron microscopy and high throughput for high-pressure freezing. Journal of Microscopy 2008, 230:317-328.
41. Watanabe S., Punge A., Hollopeter G., Willig K.I., Hobson R.J., Davis M.W., et al. Protein localization in electron micrographs using fluorescence nanoscopy. Nature Methods 2011, 8:80-84.
42. Yuan Y., Li M., Hong N., Hong Y. Correlative light and electron microscopic analyses of mitochondrial distribution in blastomeres of early fish embryos. The FASEB Journal 2014, 28(2):577-585.
43. Metscher, B. D. Micro-CT for developmental biology: A versatile tool for high-contrast 3D imaging at histological resolutions. Developmental Dynamics 2009b, 238, 632-640.