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Content: moving filesuseful referenceshistology resourcesother microscopy facilities

Moving files


You can transfer your files using SFTP or SCP. The facility has a file server at (, port 22) that you can use. Facility staff can supply the username and password. You can upload your files to the server from any of our computers and then download them to your own computer. Please do not upload any confidential files to the file server because they will be accessible to all facility users.

Note: There are shortcuts to SSH/SFTP on the desktop of our computers. Once on the server, you can create your own directories to store your files. Any SFTP/SCP command line or GUI clients will work, e.g., WinSCP and Fugu as listed on Tools for Safe and Secure Computing on UW IT Connect website.

tips for Fugu users: Transferring a folder needs to be done with SCP. Fugu will prompt you for that. SCP requires that you enter the password for every transfer and you can make it easier if you have all your files in a single folder before initiating the transfer.

Files can also be uploaded to your UW Central Storage Space e.g., Homer, Catalyst SharedSpaces, or U Drive. You can also setup your own SSH server to provide the file service. UNIX users, including Mac OSX can use sshd. You do need to know the ip address or node name in order to access your computer remotely. Please make sure your file server is properly configured and maintained for security reasons.

Removable media

Any USB or eSATA removable devices can be used and CD/DVD writers are also available. The TEM and SEM currently does not have any removable media option.

Options for PAB A033

For the Leica SP5, there is a private gigabit connection to our file server (, port 22) via a shortcut on the desktop labelled "ifuser@if (gigabit)". In addition, USB or eSATA removable devices, or recordable CD/DVD can be used. The fastest connection is via eSATA and please use the blue cable provided.

Examples of transfer speed of a 3 GB file on varous devices and network connections
Removable device/connection Transfer speed (MB/s)
1harddrive used: Western Digital RE4-GP and Hitachi 7K2000
2thumbdrive used: Patriot XPorter and OCZ Rally2
Please noted that device quality varies, your file transfer speed will be different.
1000 Mb/s network 22.6
100 Mb/s network 9.4
removable harddrive1, eSATA connection 91.1 to 167.1
removable harddrive, USB connection 24.5 to 27.3
USB thumb drive2 8.8 to 9.2

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Useful references

Titles with * can be made available for very short term loan from the Imaging Facility.

  • The Microscopy Society of America's Policy on Digital Imaging
  • General guidelines about image manipulation from either The NIH Catalyst or 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
  • spectra of various dyes, filters, and mirrors
  • The image processing handbook, John C. Russ, 4th ed, Boca Raton, Fla., CRC Press, 2002* (check UW lib holding of current edition or read online at CRCnetBASE)
  • Handbook of biological confocal microscopy, edited by James B. Pawley, 3rd ed, New York, Springer, 2006* (check UW lib holding of current edition)
  • 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*
  • 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)

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Histology resources

  • slides of various animal and plant sections are in KIN 28
  • empty slide boxes and trays available for short term loans are in PAA A059
  • microtome knife shapener and strop are in HCK 246

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Other microscopy facilities

Date last changed Oct 5th, 2016 @ 15:27:49 PDT