The majority of our PDF tips & tutorials are hosted on the University of Arizona Microscopy Alliance website. We also have some tutorial videos on our Imaging Cores - Optical YouTube channel. Here's a list of what's available (dates are when the document was last updated):
General resources
- Basic Microscope Alignment (PDF, March 2026)
- Light Microscopy Tips (PDF, March 2026)
- Formaldehyde Fixatives (PDF, March 2026)
- Light Microscope Vendors for Southern Arizona (PDF, updated regularly)
- #1.5 Coverslips for Microscopy (PDF, October 2025)
Digital Imaging
- Digital Imaging Ethics (PDF, Jan 2018)
- (This PDF is a quick summary, for more detail see either Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images (Cromey, 2010) or Digital Images Are Data: And Should Be Treated as Such (Cromey, 2012).
- Potentially the most dangerous dialog box in Adobe Photoshop (PDF, Sept 2025)
- Using the Histogram Tool (PDF, Mar 2026)
- Highlighting Letters and Arrows with Adobe Photoshop (PDF, Sept 2025)
- Using guides in Photoshop to line up figure elements (PDF, Jan 2018)
Instrument or Software specific handouts
- Zeiss Elyra S.1 - Sample Preparation Guidelines for Superresolution Structured Illumination (SR-SIM) (PDF, Mar 2023)
- Zeiss Elyra S.1 - Tips covering image acquisition, processing data, and file management (PDF, June 2018)
- Zeiss ZEN software - Installing the free Zeiss ZEN software on a Windows PC (PDF, April 2026)
- Zeiss ZEN software - Using Zeiss ZEN software to export from CZI files to TIF (PDF, Sept 2023)
- Zeiss ZEN software - Zeiss ZEN – performing a maximum intensity projection of a Z-stack (PDF, Sept 2023)
- Leica DMI6000 - User manual (PDF, Feb 2022)
- Leica DMI6000 - Exporting large image data from the Leica *.LIF format using FIJI (PDF, Dec 2017)
YouTube videos
- Sample preparation for Microscopy (YouTube playlist, July 2024)
- ZEN Blue - bulk export of CZI files to TIF files (YouTube, Oct 2024)
- iLab Basics for users of the ORP Imaging Cores - Optical (YouTube, May 2022)
- OMERO image data management (brief introduction to the kinds of things that OMERO can do, YouTube, April 2024)
- A more detailed YouTube playlist, OMERO 101 for users, groups and data management is available for labs planning to use the UA installation of OMERO. (YouTube playlist, Mar 2025)