Confocal & Specialized Microscopy Image Analysis and Presentation

We offer a Windows workstation for image analysis and processing, and a color laser printer for documentation.

We provide consultation and training on the use of software for image processing, analysis, and presentation.

Facility software includes:

  • Volocity Restoration (deconvolution), Visualization and Quantitation
  • NIS Elements
  • ImageJ and Fiji
  • Apple Quicktime Pro

For use in your own lab, we recommend the following free software for microscope images.

For images from all microscopes:

Fiji For Mac, Windows, Linux. Fiji is just ImageJ pre-packaged with Bio-Formats and other plugins. It also checks for updates automatically.

ImageJ plus Bio-Formats plugin
For Mac, Windows, or Linux.

  1. Download ImageJ and install it (preferably in your Desktop directory).
  2. Update ImageJ to the newest version (Help > Update ImageJ).
  3. Download the Bio-Formats plugin. Click on loci_tools.jar next to “daily build.” This plugin enables you to open ND2 and several other microscope image formats.
  4. Quit ImageJ if it is running. Put loci_tools.jar into the plugins folder inside the ImageJ folder. Then restart ImageJ.
  5. Update ImageJ and Bio-Formats every month for best performance.

For Nikon images (ND2): NIS Elements Viewer For Mac or Windows. The Windows version has more features.

For Zeiss images (ZVI, CZI, LSM): These are for Windows only.
ZEN Lite https://www.zeiss.com/microscopy/us/downloads/zen.html