Most of these handouts are written by Doug Cromey with local users (SWEHSC, University of Arizona) in mind. Some of the material here will be useful to others from off-campus who may have similar equipment or interests. We cannot answer specific support questions from off-campus. 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.
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). Most of these documents were supported by the NIEHS-funded SWEHSC and Mr. Cromey would like to demonstrate to the funding agency 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.
- Basic Microscope Alignment
An introduction to aligning a light microscope for Koeller illumination. (Oct 2012, 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. (Oct 2012, 4 pages).
- Formaldehyde Fixatives
Background information on formaldehyde, optimal fixation suggestions and safety information. (Oct 2012, 3 pages)
- Light Microscope Vendors for Southern Arizona (updated February 2023)
Names and contact information for the local service and sales representatives for Leica, Nikon, Evident/Olympus, and Zeiss. In addition, local firms for microscope service and repair are featured.
- #1.5 Coverslips for Microscopy
The importance of this thin sliver of glass and sources for the new #1.5H high performance coverslips required for superresolution and better performance on high-end light microscopes. (updated August 2020)
- 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. (updated Jan 2018)
- Longer materials on Digital Image Ethics written by Doug Cromey include a 2010 Science and Engineering Ethics review article (Avoiding Twisted Pixels) and a 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 several useful illustrations for explaining key concepts. Mr. Cromey was a contributing author on the ORI sponsored website Online Learning tool for Research Integrity & Image Processing which includes illustrated tutorials and a case study.
- Potentially the most dangerous dialog box in Adobe Photoshop
Tips and warnings about the Image Size dialog box in Photoshop. (updated Jan 2018)
- Using the Histogram Tool
Understanding this often overlooked tool that is found in most image analysis/editing programs. (updated Jan 2018)
- Highlighting Letters and Arrows with Adobe Photoshop
Adding a thin highlight of contrasting color around lettering and arrows can make it easier to see these in publication figures. (added Jan 2018)
- Using guides in Photoshop to line up figure elements
Guides are easy to use alignment tools that can be placed in images (or groupings of images, like a publication figure) to help with layout and alignment. (added Jan 2018)
- Zeiss Elyra S.1 - Sample Preparation Guidelines for Superresolution Structured Illumination (SR-SIM) - Key details to get the highest image quality from SR-SIM. (updated March 2023)
- Zeiss Elyra S.1 - Tips covering image acquisition, processing data, and file management. (added June 2018)
- Zeiss ZEN lite software - Installing the free Zeiss ZEN software on a Windows PC - tips for installing this large software program, and how to avoid installing unnecessary drivers. (updated Sept 2018)
- Zeiss ZEN lite software - Using Zeiss ZEN software to export from CZI files to TIF - File export from ZEN is not as easy as it could be. (updated Sept 2018)
- Zeiss ZEN lite software - Zeiss ZEN – performing a maximum intensity projection of a Z-stack - Walks through the steps for creating a projection using either Zen Blue or Zen Black. (updated Sept 2018)
- Leica DMI6000 - User manual - Working with the software and microscope to capture color and fluorescence images, troubleshoot issues and tile-scanning large areas. (added Dec 2017, updated for LAS X 3.7 - February 2022, Google Drive link)
- Leica LAS-X lite software - Exporting large image data from the Leica *.LIF format using FIJI - Some larger tile scans create 24bit color merged images of a size that is greater than LAS-X can export. Step-by-step instructions for opening LIF files in FIJI/ImageJ and how to export the full resolution, merged color images. (added Dec 2017)
- Leica SP5 - 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. (updated July 2018) This microscope has been retired
Reviewed & updated 03/01/2023. Creation of this web page was originally supported as part of the Southwest Environmental Health Sciences Center at the University of Arizona, NIEHS P30 ES006694.