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Microscopy Core

Please always reserve time on microscopes in iLabs and remove reservation if you need to cancel. Both microscopes in this core are biannually serviced and have been updated to the latest software that works for each unit. Microscopes areonly as good as the person using them, so please ask if you are having issues.

Having a reasonable understanding of how microscopes work will make it easy to assess if something isn’t right with your sample or the microscope.

Helpful links:

Microscope IconMicroscopy: (General knowledge and review)



Properties of Light IconProperties of Light: (light source)



Optical Filters IconOptical filters:


Fluorophore SelectionFluorophore selection: (This site will explain your excitation and emission requirements for imaging)



Nikon Eclipse Ti2-E Inverted Motorized Research Microscope System

Eclipse Ti2-E Inverted Motorized Research Microscope System – Nikon Eclipse Ti2-E Inverted Motorized Research Microscope with Perfect Focus System 4, CFI PLAN APO LAMBDA objectives (2X 0.1NA, WD 8.5MM; 4X 0.2NA, WD 20MM; 10X 0.45NA, WD 4MM; 20X 0.75NA, W.D. 1.0MM (DIC)), CFI SUPER PLAN FLUOR ELWD objective (40X 0.6NA, W.D. 2.8-3.6MM (DIC)) PLAN APO objective (60XA 1.4NA, WD 0.21MM OIL (DIC)), software controlled Lumencor AURAIII LED Light Engine (UV, cyan, green, red and near-IR LEDs), high-speed Finger Lakes Instrumentation 6 position filter wheel (DAPI -432/36nm; GFP - 515/30nm; TxRed - 595/31nm; Cy5 - 680/42nm; Cy7 - 809/81nm), Photometrics Prime 95B-25mm Back-illuminated sCMOS Camera (1608x1608 resolution at 30 FPS with 25mm field-of-view and ~95% peak quantum efficiency), Tokai Hit Stage-top Incubation System, Imaging Workstation (Windows10-based HP Z4 Advanced Biosystems Workstation with 31.5” and 27” UHD monitors for optimal display of control software and images), NIS-Elements AR Software (AI algorithms for optimal signal/noise imaging; 2D/3D deconvolution), a 36”x 48” Vibration Isolation Table.

Olympus BX41 Fluorescence Microscope w/Brightfield

CellSens software: (https://www.olympus-lifescience.com/en/software/cellsens/?gclid=EAIaIQobChMI-qLug-3h6wIVT77ACh0BvA3eEAAYASAAEgJc8_D_BwE) Basic version

Olympus BX41 Fluorescence Miscroscop w/Brightfield and DP73 Camera

Olympus Objective Key

The Nikon Eclipse TE2000 U with CFI60 Infinity Optical System w/Brightfield

Nikon Eclipse TE2000 with Micropublisher 5.0 RTV and CoolSNAP ES

Nikon Objectives with Magnification Index

This unit utilizes MetaMorph Software. Cameras: (https://www.photometrics.com/wp-content/uploads/2020/03/MicroPublisher-3.3-5.0-Datasheet.pdf)

Filter cubes for Nikon
Nikon Filter Cubs for Cyan and Yellow Fluorescent Proteins

The anatomy of an objective is important to getting the best image possible from all the hard work of preparing your sample.  The following applies to OIL objectives.

  • NEVER add oil to an objective UNLESS is says oil on the objective barrel.
  • Independent of the microscope being inverted or upright, the slide should be situated so the objective is looking through the coverslip and not the slide.

Index of a Nikon Plan Flour Objective

  • Cover glass thickness matters for resolution, this is found after the infinity symbol (6)
  • It is a good practice to make sure that the retraction stopper isn’t frozen in place by excess, old oil.  If it is stiff, you could break the coverslip.  (With lens paper over lens, gently press until you feel the objective give under your finger). (5)
  • After working with the OIL objective, please, using lens paper, gently clean the surface.  Remove the objective and return to its holder and place in left top drawer.  CLEAN your slide as well.
  • Immersion oil-Type NHV, designed for inverted scopes is a higher viscosity oil designed to remain in place between coverslip and objective.  Immersion oil-Type FF is a nearly, fluorescence free oil, meant to reduce background fluorescence. This core has both lens paper and glass cleaning wipes located in metal cabinet.

Index for Nikon Plan APO Objective

  • The higher the numerical (NA), the higher the resolving power. Using Nikon objectives from above:
    • 20X = NA (0.50)
    • 40X = NA (0.75)
    • 60X = NA (1.40)
  • The higher the NA, the shallower the depth of focus (DOF) DOF = The DOF is greatest on the lowest power objective (4X/10X). Each time you switch to a higher power (20X/40X/oil objectives [60X/100X]), the DOF is reduced. Therefore, a smaller part of the specimen is in focus at higher power. The amount of light transmitted to your eye is greatest at the low power WD = working distance of objective (for the image above, is 0.14mm) is the distance between the lens of the objective and the surface of your coverslip.

Nikon Microscope Users Guide