Opening Your Microscope Images

Unless you are collecting basic "screen-shot" quality images (jpgs), you will not be able to open your images using the basic software included in Windows and Mac OS. You have a few options:

  • You just want to see your images, adjust the brightness, export them as JPGs for a presentation, etc.
    • If you acquired them on one of the Nikon scopes, you can download a free viewing-only version of the Nikon Elements software here.
    • If you acquired them on one of the Leica scopes, you can download a free viewing-only version of the Leica LAS software here (for Windows only). 
  • If you want to do image processing/analysis or the above options don't work for you, I recommend using ImageJ. The rest of this section explains how to use ImageJ to open images and later sections provide resources for learning how to use this powerful program for image processing and analysis.

ImageJ is a free, open-source image processing and analysis software and will work on nearly any operating system. You need to install the FIJI version of ImageJ, which comes 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 file. If you already have ImageJ installed, you can install the Bio-Formats Package of plugins from the Open Microscopy Environment project to allow ImageJ to open most major proprietary image formats. Before you start using ImageJ, take a quick look through this webpage to orient yourself to the ImageJ program.

  1. Most image files can be opened by simply dragging and dropping the file onto the ImageJ toolbar. Alternatively, go to Plugins > Bio-Formats > Bio-Formats Importer and select the file to open.
  2. The Bio-Formats Import Options menu will display. There are many useful options in this menu, but unless you know what they do, I recommend using these basic options:
    • View stack with: Hyperstack
    • The Autoscale box should be checked
    • No other boxes should be checked
  3. Some file formats may require additional steps...
    • Leica (.lif) Project files: After you hit OK in the previous menu, the Bio-Formats Series Options window will display. Select the images you want to open and click OK. If a Console window also opens and lists warnings, ignore them.
    • If you have a true-color image (NOT fluorescence) and it displays as three separate red, green, and blue images overlayed in a single window with a slider at the bottom, go to the Image menu, select Type, then RGB Color. Close the old image and work with the new one.
  4. Want to know more about how to work with your images in ImageJ? See the information, below, in Image Processing and Analysis.

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)

Microscopy data management resources

Online microscopy references and tutorials

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