Microscope Objective and Filter Specification Sheets

These sheets also list pixels sizes, which are necessary for creating scale bars and performing spatial measurements.

Spectra and properties of fluorescent molecules and proteins

Image processing and analysis


Ethics (yes, it's something you must think about when you do any kind of image processing/analysis)


Note that the Microscopy Facility has a stand-alone workstation with a full version of Nikon Elements and Adobe Photoshop.

  • ImageJ/FIJI: Free, open-source image processing and analysis software
    • We recommend installing FIJI, which is a version of ImageJ that is pre-configured with lots of useful plugins. To install FIJI, click on the correct link for your operating system and save the file anywhere convenient (except in your Program Files folder). Uncompress the downloaded file and you're ready to go! Just double-click on the fiji.app file.
    • If you already have ImageJ installed, you can download the Bio-Formats Package of plugins from the Open Microscopy Environment project to allow ImageJ to open most major proprietary image formats.
    • Get started using ImageJ/FIJI: check-out our basic guide.
  • NIS-Elements Viewer: free, basic version of Nikon Elements
  • GIMP: Free, open-source photo editing program (similar to Photoshop)
  • Inkscape: Free, open-source illustration program (similar to Illustrator)
  • Nyquist Calculator: online calculator to estimate the optical slice thickness and optimal step size for your instrument; will also calculate the point spread function (PSF) for your microscope.

Microscopy data management resources

Online microscopy references and tutorials

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