Nikon Eclipse Ni-E

Nikon Eclipse Ni-E

Installed May 2012. The Nikon NiE is a very nice general purpose research microscope. It is equipped for brightfield, DIC, phase and epifluorescence imaging. The microscope has 4X to 100X objectives so a wide range of samples can be accommodated. Epifluorescence imaging on this scope works best with thin, flat specimens.


  • Sign-in to iLab. Use kiosk in LMIC or your own phone or computer.
  • Sign in to LMIC software to transfer images (IU username).
  • Turn on Power Supply. Grey button at top of white APS box on shelf under scope.
  • Turn on computer on shelf under scope.
  • Start NIS Elements software.


  • Make sure images are saved.
  • Exit NIS Elements software.
  • Transfer images - LMIC Sign out form. Select Data Directory, add title, sign out. Wait until finished.
  • Shut down computer.
  • Clean objectives using Lens paper if oil or water were used.
  • Turn off power supply (Grey button again).
  • Cover scope.
  • Sign out of iLab.


  • The Nikon NiE is an upright, semi-automated microscope platform.
  • Hamamatsu Orca-Flash 2.8 sCMOS high resolution camera.
  • Lumencor SpectraX light source for fluorescence imaging of UV/DAPI, CFP, Green, YFP, Red, and Far-red (CY-5) fluorophores. Filters.
  • Motorized focus control for Z-stack images.
  • Controlled by Nikon Elements software.

Technical Notes

NIS Elements user-manual

NIS Element Viewer is a free but limited version of the imaging software that will work for viewing, exporting and some processing of your .nd2 files. Works on PC and MAC. Full version of NIS Elements is installed in the Imaris Workstation. 

Opening .nd2 files in FIJI is one of the option to see and analyse your data.