Nikon inverted microscope Room MSB 595B

To sign up for microscope in advance

Microscopes uses Nikon Elements software. [User's Guide v. 4.0 PDF]


This microscope is good for routine snapshots of Blue, Green, Red, Far-Red fluorescence.

1.) The Channels are not in perfect XY registration due to old filter blocks.
2.) Chromatic aberration, especially at low magnifications, may require refocusing between channels, especially blue.

Do not use for brightfield histology in color. Use the upright microscope in the same room.

Please always sign in logbook even if only using the computer.


When the software starts up, sometimes it does not connect to the Intenseilight for fluorescence illumination.

You may check this manually by looking in the Devices menu and selecting Manage devices...

This will show you whether the light source is attached.

If it is not connected, quit the software and restart. It should connect on the restart. If not, you may try clicking on Intensilight and then clicking on the Connect button.

Also, sometimes you don't have enough light going to the sample because of the ND filters built in to the unit.

Go to the Intensilight pad and make sure the ND setting is at 1 (brightest) or 2 (half as bright).


Nikon DS-Qi1 camera installed on 1 April 2015.

Recommend using at full 1280 x 1024 with binning 1 X 1. New spatial scale information here.

Other changes:

When you turn on the computer, it will log into a common account.

When you run NIS Elements, the first thing you should do (if you have used the system before) is load your favorite settings. There are two parts to this.
1. Load Optical Configurations. These are the camera and other microscope settings.
Calibration > Optical Configurations... > Import
2. Change the layout of the screen.

You may customize the look of the program screen. In the lower left there are tabs.
When you have the screen arranges the way you want, right click on the active tab and Save As with your name. You can also find more options inthe Layout Manager.

Saving/load your own settings.
When you have all your exposure times, channels, etc set, you may save them all.
Calibration > Optical Configurations... > Export

Recommend not using 100X except for 1 ms exposures due to shaking.

Save Files Efficiently
Using the ND Acquisition method for snapping pictures, especially multiple channel ones, will save you a lot of time!

DO NOT STORE FILES ON THE DESKTOP. Files on the Desktop may be deleted without warning.
You may put files in a Users Files directory or My Documents.

When you run Explorer there will be tabs for this web page so you can see this info or the Sign Up webpage.
Do Not Ever look at an off campus webpage.


Startup Instructions

  1. Sign logbook.
  2. Turn on fluorescent light source (if needed).
  3. Turn on computer (power switch in upper left of computer).
  4. Turn on all other microscope components with one switch (power switch on table to right of microscope main body).
  5. Run Nikon Elements software.
  6. Optional: Load your settings for the Optical Configurations and for the screen layout.
        If devices do not connect to Nikon software, troubleshoot here.

Do not turn on/off individual microscope control boxes!!

Aligning Light for Brightfield

If imaging by brightfield, phase contrast, or DIC/Nomarski, always set condenser for Kohler illumination.
1. Focus on sample
2. set condenser for BF
3. Close Field Diaphagm
4. Move condenser up and down using knob on right until center octagon is in focus
5. Center by turning two knobs on condenser.
6. Open field diaphragm to edge of visible field, not all the way.


Standard lenses on this microscope:


For best images use #1.5 coverslips. The lenses are designed specifically for #1.5 coverslips.


There are two 40X lenses. Which 40X lens should you use?

The 40X lens with the numbers printed in green is designed for tissue culture plastic.  It will work with coverslips, but has a ring on it that needs to be adjusted.  It is an air objective.  DO NOT put oil on it!

The 40X N.A. 1.3 lens with oil is designed for higher resolution.

Click here to see a comparison of these two lenses.

To get the best resolution, you need to adjust the collar.

As pictured, the adjustment is a little bit too far open for a #1.5 coverslip, but close enough. If you were imaging through a plastic tissue culture dish, the setting would likely be between 1 and 2. (The units are mm.)

You cannot easily see the collar underneath the stage. Therefore:
1. Focus on sample best possible.
2. Reach under stage to turn ring on objective a little.
3. Refocus, turn ring, and repeat until image has maximum crispness.

Also, this may also be done when in the fluorescence mode. It is important to make this adjustment or else your pictures will not be in proper focus.




<-- Back

comments, questions, suggestions for this web page: or