Image Processing

The Microscopy and Imaging Facility has a number of computers available to assist you with your image processing needs. Computers in the facility include the following software:

  • Nikon Elements: Offline software for Nikon microscope images. Applications include 3D reconstruction, deconvolution, cell counting, intensity analysis, JOBS, spectral unmixing, STORM analysis.
  • ZEN: Offline software for Zeiss microscope images. Applications include 3D reconstruction, FRAP, image processing, and analysis.
  • Imaris: Advanced 3D and 4D rendering and measurements, particle tracking, cell counting
  • Metamorph Imaging Software: Typical applications include: particle counting and measurement from TEM, fluorescence overlays, projections and movies.
  • FlowJo v.10: Flow cytometry analysis
  • FCS Express v.6: Flow cytometry analysis
  • FCS Express 5 Plus: Flow cytometry and microscopy image analysis
  • Modfit LT v3.0: Cell cycle analysis software and report generation
  • IDEAS: Amnis ImageStream data analysis
  • Adobe CS Suite: Includes Photoshop, Illustrator, ImageReady and InDesign. Tutorials are available for image optimization in preparation for image processing or publication.

Computer Access

To gain access to the software computers, you must contact Anna Webb or Richard Salinas.


The image processing computers are located in NMS 2.114, MBB 1.426T, and HDB 3.222K.


There are no fees for the use of these computers and software for facility users.