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Useful references

Titles with * can be made available for very short term loan from the Imaging Facility. Titles followed by confocal are part of the confocal reading materials.

  • The Microscopy Society of America's Policy on Digital Imaging
  • General guidelines about image manipulation from JCB
  • Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images, Douglas W. Cromey, 2010, Science and Engineering Ethics, 16(4): 639-667, from Springer
  • Olympus Microscopy Resource Center: a good online resources on key concepts in microscopy, including confocal
  • Leica Science Lab carries short articles on microscopy and histology. The Confocal Microscopy section has SP5 relevent information and a few are listed below. confocal
  • 8-bit or 12-bit? confocal
  • sampling rate and z step size confocal
  • a more detail tutorial on confocal imaging from University Of Helsinki confocal
  • an online training course for confocal microscopy on MyScope from Microscopy Australia
  • Handbook of biological confocal microscopy, edited by James B. Pawley, 3rd ed, New York, Springer, 2006* (check UW lib holding of this edition) confocal
    • Chapter 4: Points, Pixels, and Gray Levels: Digitizing Image Data is on academia. It explains the fundamental concepts of acquiring digital images.
  • Fluorophore selection from ThermoFisher: a dashboard showing the performance of a fluorophore to help you make an informed selection.
  • FPbase: spectrum viewer for fluorophores and more.
  • The image processing handbook, John C. Russ, 2nd ed, Boca Raton, Fla., CRC Press, 1995* (check UW lib holding of this older edition, or read the current edition online from ENGnetBas)
  • Practical methods in electron microscopy, edited by Audrey M. Glauert, Amsterdam, North-Holland Pub. Co., 1972- (check UW lib holdings)
    • v. 1, pt. 1. Specimen preparation in materials science, P.J. Goodhew; pt. 2. Electron diffraction and optical diffraction techniques, B.E.P. Beeston, R.W. Horne, and R. Markham
    • v. 2. Principles and practice of electron microscope operation
    • v. 3, pt. 1. Fixation, dehydration, and embedding of biological specimens, A.M. Glauert*; pt. 2. Ultramicrotomy, N. Reid*
    • v. 4. Design of the electron microscope laboratory, R.H. Alderson
    • v.5, pt. 1. Staining methods for sectioned material, P.R. Lewis*; pt. 2. X-ray microanalysis in the electron microscope, J.A. Chandler
    • v. 6. pt. 1. Autoradiography and immunocytochemistry, M. A. Williams; pt. 2. Quantitative methods in biology, M.A. Williams
    • v. 7. Image analysis, enhancement, and interpretation, D.L. Misell*
    • v. 8. Replica, shadowing, and freeze-etching techniques, J.H.M. Willison
    • v. 9. Dynamic experiments in the electron microscope, E.P. Butler, K.F. Hale
    • v. 10. Low temperature methods in biological electron microscopy, A. W. Robards, U. B. Sleytr
    • V. 11. Thin Foil Preparation for Electron Microscopy, P.J. GOODHEW
    • v. 12. Electron Diffraction: An Introduction for Biologists, D.L. MISELL and E.B. BROWN
    • v. 13. Sectioning and Cryosectioning for Electron Microscopy, Norma Reid and Julian E. Beesley
    • v. 14. Cytochemical staining methods for electron microscopy, P.R. Lewis, D.P. Knight
    • v. 15. Vacuum Methods in Electron Microscopy, Wilbur C. Bigelow
    • v. 16. X-ray Microanalysis for Biologists, Alice Warley
    • v. 17. Biological specimen preparation for transmission electron microscopy, Audrey M. Glauert, Peter R. Lewis
    • v. 18. Negative Staining Methods for Electron Microscopy, R.W. Home, E.A. Munn
  • Electron Microscopy, J.J. Bozzola, L.D. Russell, Jones & Bartlett, Boston, 1992* (check UW lib holdings on a more recent edition)
  • The Operation of Transmission and Scanning Electron Microscopes, D. Chescoe and P. J. Goodhew, 1990*
  • Scanning electron microscopy: a student's handbook, Michael T. Postek et al., Ladd Research Industries, Inc., 1980* (check UW lib holdings)
  • Artifacts in Biological Electron Microscopy, edited by Richard F. E. Crang and Karen L. Klomparens, Plenum Press, 1988* (check UW lib holdings)
  • basic concepts of focus and stigmation in TEM on MyScope by Microscopy Australia

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Useful resources

Biology has a few STF-funded hardware and software resources that are particulary suitable for image analyses.

  • STF 2020-35: Imaris 9.5 for Cell Biologists, floating licenses
  • STF 2020-34: 24" and 32" display graphics tablets
  • STF 2017-101: high performance computers with dual Xeon processors, 128 or 256 GB of RAM, and NVIDIA Quadro P2000 and GeForce GTX 1080 GPU.

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Other microscopy facilities

Date last changed Sep 1st, 2021 @ 20:35:17 PDT