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Microscopy and Image Processing Resources


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

Image processing and analysis software

Note that the Microscopy Facility has two workstations with full versions of Nikon Elements and Adobe Photoshop software.

  • 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 this package of plugins from the Open Microscopy Environment project to allow ImageJ to open most major proprietary image formats.
  • 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 resources

3D printing and DIY labware

There are a ton of websites with open-source 3D printing designs and lab hacks… here are some great places to get started: