Nikon Eclipse confocal microscope

3D visualisation of a dinoflagellate made with confocal microscopy

The microscope works in two basic modes - epifluorescence and reflection. In epifluorescent mode, the laser excites fluorescence within the sample - this is either natural fluorescence (autofluorescence) or a fluorescent dye that has been attached to a specific site on the sample using an antibody label. We can also use non-specific fluorescent dyes. Using different dye and laser combinations, we can simultaneously label different parts of the sample to differentiate specific features in 3D.

In reflection mode, the laser is simply reflected off surfaces within the sample. The microscope can also combine epifluorescent and reflection mode images.

In both modes the returning light rays are fed through a pinhole that excludes out of focus information. This means that only the focused image plane is viewed.

Sequential image planes can be scanned and built up into a stack of images. These can be manipulated to provide extended focus images and 3D images. Alternatively, the image stack can be rotated to provide views from tilted viewpoints or at right angles to the plane of section.

Key instrument features

  • A variety of lenses are available for applications across a wide range of specimen types, including low-power objectives, lenses selected for reflection mode imaging, materials science applications and multi-immersion lenses for examining wet specimens.
  • Epifluorescence imaging is provided using LED light sources with filters for DAPI, FITC and TRITC.
  • Enhanced contrast is provided by phase contrast and differential interference contrast (DIC), a technique similar to Nomarsky phase interference.
  • Transmitted light images can be captured through the integrated Nikon DS-Fi1 digital colour camera system.
  • Confocal microscope software enables 3D montaging, allowing the examination of large areas at high resolution in 3D.
Nikon Eclipse A1-Si confocal microscope

The Nikon Eclipse upright microscope with A1-Si confocal microscope

Museum lead

Dr Alex Ball

Key facts

  • Technique: confocal microscopy
  • Image output: up to 4k x 4k pixels TIFF images with up to four fluorescence channels and one transmitted light channel simultaneously
  • Specifications: four lasers at 405nm, 488nm, 561nm and 640nm, four PMT detectors, a 32-channel spectral detector with 2.5nm, 6nm or 10nm diffraction grating, and a transmitted light detector