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Printable materials


Our handouts are written with local users from the SWEHSC (or the AZ Health Sciences Center) in mind. Some of the material here will be useful to others from outside the University of Arizona who may have similar equipment. We cannot answer specific support questions from outside the SWEHSC. Please be aware that your instrument may have slightly different software or hardware than ours and that the rules for what users are allowed to do on any specific piece of equipment vary widely.


Fair use

Individuals are welcome to print copies of these handouts for their personal use. Any other use of these materials (classroom materials, core facility distribution, etc) requires permission (contact information for Mr. Cromey is available on the left of this page). We are a grant-funded center and we would like to demonstrate to our funding agency (using website logs and emailed requests for specific use as class materials, etc) that the materials available here are of value to the greater scientific community.

You are welcome to link to these materials from other sites on the WWW, however, we specifically request that you do not host these files on your own servers. We update these files periodically, so the most current version will only be available on this web server.



(NOTE: This is an accordion menu. Click on any of the grey boxes to see additional information.)


  • Basic Microscope Alignment
    An introduction to aligning a light microscope for Koeller illumination. (2 pages)
  • Light Microscopy Tips
    A collection of tips, including information about: Recommended coverslip thickness, Coverslip mounting media, Don’t mix immersion oils from different vendors, Mixing and matching microscope objectives, and Cleaning Microscope Objectives. (4 pages).
  • Formaldehyde Fixatives
    Background information on formaldehyde, optimal fixation suggestions and safety information. (3 pages)
  • Light Microscope Vendors for Southern Arizona - updated October 2012
    Names and contact information for the local service and sales representatives for Leica, Nikon, Olympus, and Zeiss. In addition, local firms for microscope service and repair are featured. (1 page)

Digital Imaging

  • Digital Imaging Ethics
    An overview of the issues related to digital image ethics. Includes a list of twelve guidelines for editing digital images in an ethical and scientific manner. (6 pages)
  • Longer materials on Digital Image Ethics written by Doug Cromey include a 2010 Science and Engineering Ethics review (Avoiding Twisted Pixels) and an upcoming chapter in Cell Imaging Techniques: Methods and Protocols (2012) entitled Digital Images are Data.  The SEE article was written for ethicists, and includes a glossary.  The book chapter was intended for people who already have some experience with microscopy/digital imaging.  Both have serveral useful illustrations for explaining key concepts.
  • Potentially the most dangerous dialog box in Adobe Photoshop™
    Tips and warnings about the Image Size dialog box in Photoshop™. (1 page)
  • Using the Histogram Tool
    Understanding this often overlooked tool that is found in most image analysis/editing programs. (1 page).

Instrument-specific handouts

  • Improving Image Quality on the UACC Leica SP5 confocal
    An overview of the tools and choices that need to be made to optimize image quality on this instrument. Includes a table with information about objectives and suggested images sizes to satisfy Nyquist sampling. (11 pages).