Nikon E600 microscope

Roger Gaudry Building, Room N-620
Simple Microscope usage price
Instrument intrusted to the CI2B by the department of microbiology

 

Applications

  • Upright microscope
  • Widefield imaging
    • Brightfield
    • Phase contrast
    • Polarized light
    • Fluorescence
  • Color camera

Light sources

  • Halogen lamp for 100W for transmitted light

  • Lumencor SOLA V-nIR for fluorescence

Emission peak (nm)Nominal power (mW)Measured power (mW)
39540
43035
47515
51020
55020
58020
64020
73010

Lumencor_SOLA_Datasheet.pdf
Lumencor_SOLA_Filter_Set_Recommendations.pdf
Lumencor_SOLA_User Manual.pdf

Objectives

  1. 4x/0.13 Air

  2. 10x/0.3 Air Ph1

  3. 20x/0.5 Air DIC

  4. 40x/0.75 Air Ph2

  5. 60x/0.85 Air
  6. 100x/1.3 Oil Ph3
PositionNameBrandFull nameIDMagnificationNumerical ApertureImmersionTypeWorking distance (mm)Transmittance
(% [nm])		TechniqueCover glass thickness (mm)
14x/0.13
Air		Nikon4x/0.3 Air
Plan Fluor		MRH000404x0.13AirPlan Fluor17.1


BF, Fluo-
210x/0.3
Air		Nikon10x/0.3 Air
Plan Fluor Ph1 DLL		MRH1010010x0.3AirPlan Fluor16

>75% [400-800]
Max % @500nm

BF, Pol, PhC, Fluo0.17
3

20x/0.5

Nikon20x/0.5 Air
Plan Fluor DIC M		MRH1020020x0.5

Air

Plan Fluor2.1
BF, Fluo0.17
4

40x/0.75
Air

Nikon40x/0.75 Air
Plan Fluor Ph2 DLL

MRH10400

40x

0.75

Air

Plan Fluor0.72>80% [400-750]
Max % @500nm		BF, Pol, PhC, Fluo0.17
560x/0.85
Air		Nikon60x/0.85 Air
Plan Fluor DIC		MRH0060060x0.85AirPlan Fluor0.30
BF, FluoAdjustable 0.11-0.23
6

100x/1.3
Oil

Nikon100x/1.3 Oil
Plan Fluor Ph3 DLL		MRH11900100x1.3OilPlan Fluor0.2>75% [400-800]
Max % @500nm
BF, Pol, PhC, Fluo0.17

Filter cubes

  1. DAPI/Hoechst/AMCA

  2. FITC/EGFP

  3. TRITC/Rhodamine

  4. TexasRed

  5. Empty
  6. Empty
PositionNameBrandIDExcitation filterDichroic mirrorEmission FilterComments
1DAPI/Hoechst/AMCAChromaCube set 31000v2350/50x
[325-375]		400LP460/50m
[435-485]
2FITC/EGFPChromaCube set 41001

480/40x
[420-500]

505LP

535/50m
[510-560]
3TRITC/RhodamineChroma

Cube set 41002c

545/30x
[530-560]		570LP620/60m
[590-650]
4Texas RedChroma

Cube set 41004

560/55x
[532-588]

595LP645/75m
[607-682]
5Empty





6Empty





Detector

  • Nikon DS-Ri2

CameraNikon DS-Ri2

Sensor Type

CMOS

Sensor Category

Color

Nb Pixels

 16.25 M

Pixel Layout

4908 x 3264

Pixel size

7.3 um

Sensor size

36.0 mm x 23.9 mm

Sensor diameter

43.3 mm

Bit depth

14-bit
Speed at full resolution6 images/s

Max QE

77 %
Readout noise2.2 e⁻

Cooling

Passive

Dark Current

0.6 e⁻/pixel/sec

Full well capacity

60 000 e-

Dynamic Range

1:25000

Interface

USB 3.0

Mount

F-mount

Nikon_Camera_DS-Ri2_Manual.pdf

  1. If not already done, turn on the computer (#1) and log in to Windows using your UdeM credentials
  2. Remove the dust cover from the microscope
  3. Turn on the microscope power bar (#2) on the left of the microscope

  4. If transmitted light is required, turn on the halogen lamp on the right side of the microscope (#3)

  5. When using the instrument for the first time, it is necessary to import the microscope configuration before starting the software. See the First Use section below.

  6. Start-up NIS-Elements
  7. Start-up Lumencor SOLA Controller

When using the instrument for the first time, it is necessary to import the microscope configuration into the software. This procedure is usually carried out during the training session. However, it can also be used to reset the software if it does not display correctly, for example. Running this procedure will erase all your experiment protocols and reset the software to its original settings (ask for support if you are not sure).

  1. If open, close NIS-Elements and wait until it is completely closed (up to 30 seconds)
  2. On your Desktop open the Softwares folder
  3. Open NIS Settings Utility
  4. Click on the Import tab
  5. Click on Browse
  6. Navigate to your C:\Users\Public\Documents
  7. Select the file Nikon_E600_NIS Settings.bin
  8. Click Select
  9. Select all items
  10. Click Import
  11. Click OK
  12. Close the NIS Settings
  13. You can now reopen NIS-Elements

During this procedure, you will:

  • Set the microscope in a safe configuration

  • Load your sample

  • Find and adjust the focus

Once completed, your sample will be ready for acquisition.


  • If this has not been done yet, select the lowest-magnification objective, 4×.

The 4× objective is the safest to use due to its long working distance (17 mm). The sample will appear in sharp focus well before the objective gets close. It is recommended to always focus first using the safest objective. Since the objectives are parafocal, focusing with these objectives will make it easier to locate the sample when switching to higher-magnification objectives.

  • Place the test slide on the microscope stage, with the coverslip toward the objective.

Using a test slide will significantly reduce the time needed to set up the instrument.

  • If necessary, move the stage so that the sample is centered under the objective
  • Select the desired imaging mode (Brightfield or Fluorescence)
    • For brightfield use epi-filter #5, turn on the halogen lamp switch on the right of the microscope. You may adjust the intensity by turning the knob on the left of the microscope
    • For fluorescence use epi-filter #1 for DAPI, #2 for FITC, #3 for TRITC, #4 for TexasRed, open the fluorescence shutter located just below the epi-filter turret. You may turn ON and OFF and adjust the intensity of the fluorescence with the Lumencor SOLA Controller software
  • Ensure that the light is clearly visible through the eyepieces before continuing
  • Adjust the focus using the main focus knob while looking through the eyepieces until the image is perfectly sharp

First perform the initial focusing with the safest objective before selecting a higher-magnification objective.

After completing the initial focus:

  • Select the desired air objective (10×, 20×, 40×, or 60×).

The 60× objective is the best air objective because it has the highest numerical aperture (0.85).

  • Adjust the focus using the fine focus knob while looking through the eyepieces until the image is perfectly sharp.

Your sample is now ready for acquisition!


After completing the initial focus:

  • Rotate the objective turret to a position between the 60× and 100× objectives (this will give you room for the next step)

  • Place a drop of oil on your sample

  • Rotate the objective turret to position the 100× objective over the sample

  • Adjust the focus using the fine focus knob while looking through the eyepieces until the image is perfectly sharp

Your sample is now ready for acquisition!

  • Files can be saved temporarily (during acquisition) on the local C: drive (desktop)
  • At the end of each session, copy your data to your external drive and delete it from the local C: drive
  • You can store your files on the D: drive (Data Storage). If you do, please create a folder per laboratory using the principal investigator last name. Within, create one folder per user (Firstname_Lastname).
In any case, your files should be removed from the C: drive.
  • Save your data
  • Close NIS-Elements
  • Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
  • If used, clean oil objectives with lens cleaner and paper
  • Select the 4x objective and place the objectives in a safe position
  • Turn off the microscope power bar (#2)
  • Turn off the computer
  • Cover the instrument with the protective dust cover
  • Take back your samples including ones in the microscope
  • Leave the microscope and the working area clean
  • Adjust focus drive jitter
  • Bring new test slides
  • New installation of windows 11 23H2
  • BIOS updated to v2.61
  • Added Lumencor SOLA v-nIR
  • Added Fluorescent light collimator
  • Added 4x/0.13 Air
  • Added 20x/0.5 Air
  • Added 60x/0.85 Air
  • Updated E600 settings file
  • Replacement mercury lamp bulb HBO 1003W/2
  • 256 GB SSD added in workstation for OS
  • Windows 10 Installation
  • BIOS updated to v2.47
  • Camera Firmware updated to v2.11
  • NIS-Elements Basic Research v4.6 64-bits installed
  • Creation NIS Elements Settings
  • FITC and TxRed cubes excitation and emission filters slightly damaged. Dichroic OK
  • Nikon Preventive Maintenance
  • Adjustment and cleaning Stage Nosepiece, condenser, filter turret, focus drive, shutters
  • 100x slightly damaged but not the lens
  • Fluorescence cubes damaged: FITC, TexasRed
  • Focus drive has a jitter

Stand

Nikon Eclipse E600 upright Serial 725540

Light sources

Condenser

  • Manual Condenser Universal C-CU Serial 081901
  • Lens Dry NA 0.9
  • 7 positions manual condenser filter turret
  1. A Empty
  2. Ph1
  3. Ph2
  4. Ph3
  5. DICM
  6. DICH
  7. Empty

Objectives

  1. 4x/0.13 Air MRH00040
  2. 10x/0.3 Air MRH10100
  3. 20x/0.5 Air MRH10200
  4. 40x/0.75 Air MRH10400
  5. 60x/0.85 Air MRH00600
  6. 100x/1.3 Oil MRH11900

Stage

  • Manual Stage

Filters

Manual 6 positions epi-filter turret

  1. DAPI/Hoechst/AMCA 31000v2
  2. FITC/EGFP 41001
  3. TRITC/Rhodamine 41002c
  4. TexasRed 41004
  5. Empty
  6. Empty

Detector

  • Nikon DS-Ri2 Serial 701234

Workstation

  • HP Z440 Workstation Serial
  • I155434-CIB
  • Intel Xeon E5-1630 v3 @ 3.7 GHz
  • RAM 32 GB DDR4 2133 MHz (4 x 8 GB)
  • OS 1 TB SSD 550 MB/s
  • 2 TB HD Data Storage 150 MB/s
  • Video Card NVIDIA Quadro K620 2 GB DDR3 863 GFLOPS
  • Monitor HP Z24i display 24' 1920 x 1200
  • Software NIS-Elements  BR v4.60 SN=1121159628-524292 HASP=2514B2EA

Anti-vibration table

  • None

Consumables

Manuals

Troubleshooting

This happens when NIS-Elements does not find the camera. It is usually because the camera is not powered on.

  • Turn off NIS-Elements
  • Turn on the camera (both the microscope power bar and the camera need to be ON
    (the camera is usually ON, the switch is on the top of the camera)
  • Check the camera is correctly connected to the computer via a USB cable
  • Turn on NIS-Elements

FAQ

No. This is an upright microscope designed to observe specimen mounted between a slide and a 0.17 mm thick coverslip.