Nikon microscope 3 (LED/Screening)

Location: Maurice Shock Building, room 388.
Dr Kees Straatman (krs5/7085/2263)

A free NIS-Elements viewer can be downloaded from here.
A protocol to image large areas on a slide can be found here

Use for: screening, slide/tissue scanning, bright field/DIC imaging, fluorescence imaging, fixed and live cell imaging, multi position imaging, imaging of samples on slides, dishes and multi well plates, time series, Z-series.

The system can handle slides, 35 mm dishes and multi well plates. A holder for 4 slides is available.

Nikon Screen

With funding from the University Equipment Fund this system has been upgraded with Nikons' high content screening module JOBS and a 20x objective in August 2013. The JOBS software is a module of NIS-Elements which allows us to use this microscope as a screening station, using slides, dishes or multi well plates. Recently a further upgrade of JOBS has been installed which allows for automatic tissue scanning on slides.

Tissue scan

Figure 2; Tissue/slide scanning. A large stitched image containing 24 x 18 images. To show the individual images the borders are made visible but normally this is corrected in the software.

The Nikon3 microscope is a fully motorized system build on a Nikon eclipse Ti microscope. This microscope a LED light source for the wavelengths 365nm, 490nm, 565nm and 635nm for normal epifluorescence microscopy. For fast live cell imaging a dual filter block for excitation with 490 nm and 565 nm has been installed on this system. The system is has an environmental chamber with CO2 and temperature control as well as the Nikon Perfect Focus System (PFS) to keep the samples in focus during long live time imaging experiments.


For fluorescence image acquisition an Andor iXonEM+ EMCCD DU 885 camera is attached to the microscope. This is a 14 bit camera which can operate in both EM-CCD and CCD mode, has a pixel size of 8 x 8 µm and an image size of 1004 x 1002 pixels. Camera Specs.

A Nikon DS-Fi2 colour camera with DS-U3 controller has been installed on Nikon microscope 3 in autumn 2016. This upgrade allows for faster imaging of immunohistochemistry samples. Nikon 3 is now equipped with 2 cameras and the user has to chose which camera to use (Andor EM-CCD or Nikon DS-Fi2) when opening the NIS-Elements software. This purchase was funded by income generated by the ImageJ workshops organized by AIF.

LED light source:
- 365 nm
- 490 nm
- 565 nm
- 635 nm

Objectives on the microscope:



1 Plan Fluor 40x 0.75 No 0.72 Ph2 DLL
2 Plan Fluor 40x 1.3 Yes 0.2 DIC N2
3 Plan Apo TIRF 100X 1.49 Yes 0.12 DIC N2
4 Plan Fluor 10x 0.3 No 16 DIC N1
5 Plan Fluor 4x 0.13 No 16.4 No
6 S plan Fluor 20x 0.45 No 8.2-6.9 DIC N1

The 100x objective has cover glass correction (0.13-0.20) and temperature correction 23-37°C.


On the system:
DAPI - Ex: 340-380nm; Dichroic: DM400; Em: 435-485nm.
FITC - Ex: z488/10x; Dichroic: z488rdc; Em: HQ525/50m.
mCherry/Texas Red - Ex: ET560/40x; Dichroic: T585lp; Em: ET630/75m.
Cy5 - Ex:HQ620/60x; Dichroic: Q660LP; Em:HQ700/75m.

Spare filters:
488nm TIRF - Ex: zet488/10x; Dichroic: HHQ500lp/zt488rdc-xr; Em: ET525/50m.
561nm TIRF - Ex: z561/10x; Dichroic: HHQ575lp/ZT561rdc; Em: ET600/50m.
488nm + 561nm - Ex: z488/561x; Dichroic: zt488/561rpc; Em: zet488/561m.

Share this page: