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Zeiss Axio-Observer Z1 inverted microscope

Roger Gaudry Building, Room R-421

Access upon request to the platform manager. Consult the and of the .

Serial Camera 1 22 12 5537 r3.1 426509-9901-000

Identifiant système 1024979772.

  1. Turn on the computer (#1)
  2. Turn on the microscope power bar (#2)

  3. If incubation is required, turn on the Okolab incubation module (#3A) and the Lauda water-bath (#3B) and open the CO2 (#3C) and N2 (#3D) tanks

    Make sure the humidifier and the water bath are clean and properly filled with distilled water.

  4. Log in Windows using your UdM credentials
  5. Start-up NIS-Elements

The first time you use the instrument, you need to import the microscope settings into the software. To do this follow the instructions Software setup.

  1. Save your data
  2. Close NIS-Elements
  3. Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
  4. Turn off the computer
  5. If oil objectives were used, clean it with lens cleaner and lens paper (not Kimwipes)
  6. If incubation was used, turn off the Okolab incubation module (#3A) and Lauda water-bath (#3B) and close the CO2 (#3C) and N2 (#3D) tanks
  7. Turn off the microscope power bar (#2)
  8. Cover the microscope

Important Reminders

  • Take back your samples including ones in the microscope
  • Leave the microscope and the working area clean
  • 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.

The first time you use the instrument, you need to import the microscope settings into the software. You will usually do this during the training session.
This procedure can also be performed if something is not working properly and if you want to reset the software to its original settings.

This process will delete all experiment protocols and reset the software to the original settings for this specific microscope.

  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 Desktop
  7. Select the file Nikon-Ti2 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


The following schematics depict the light path for transmitted (bright-field and Phase Contrast) and reflected (fluorescence) lights.

Nikon Ti2 Lightpath (pdf)

  • Nothing
  • Added to wiki

Stand

  • Nikon Ti2-E inverted  Serial 540156 System 170110-Sys-006287

Light sources

  • Transmitted LED light
    • ND32 filter
    • IR filter
    • Manual Polarizer
  • Lumencor SpectraX 6-NII-SE Serial 9409

Condenser

  • Motorized condenser Ti2-C-TC-E Serial 519097

  • Lens LWD NA 0.52

  • Filter turret 7 motorized positions

    1. Empty

    2. Empty

    3. Ph1

    4. Ph3

    5. Shutter

    6. Empty

    7. DIC N1

Objectives

  • 20x/0.5 Air Ph1 WD 2.1
  • 60x/1.4 Oil DIC WD 0.13
  • 100x/1.45 Oil Ph3 WD 0.13
  • 100x/1.45 Oil DIC WD 0.13
  • 4x/0.2 Air WD 20
  • 20x/0.75 Air DIC WD 1.0

Stage

  • Motorized stage Ti2 SHU compatible Serial 127808
  • Remote control joystick Ti2-S-JS Serial 127976
  • Inserts
    • Multi-well plate Ti2-S-HW with tilt adjustment (no incubation)
    • Combo slide 3cm dish  Ti2-S-HU with tilt adjustment (no incubation)
    • Okolab H101-CellASIC Frame with perfusion ports
      • 1 x 35mm petri dish 1x35-M + cover
      • 2 Chamber Slide 2xGS-M+ cover
      • 1 Multi-well for oil objectives MW-OIL
      • 6-well plate 6MW+ cover
      • 1 CellASIC + cover

Filters

  1. DAPI Cube Ex 383-408 DAPI-U DM 425 BA 435-485
  2. GFP Cube Semrock 96372 M349727 17
  3. Cy5 Cube Semrock 96376 M351081 8
  4. 77074160 Custom Quad C182279 Polychroic and quad bandpass emitter for use with the following single bandpass filters: ET395/25x, ET470/24x, ET550/15x, ET640/30x
  5. DIC Analyser Ti2-C-DICACL
  6. C197767 7707\4656 CFP\YFP\mCherry XT

Detector

  • Hamamatsu ORCA Flash V2 C11440-22CU CMOS Monochrome Camera 2048 x 2048 pixels, 16-bit, 30fps at full frame Serial 101081

Workstation

  • HP Z440 Workstation
  • Intel Xeon E5-1620 v4 @ 3.5GHz
  • RAM 32 GB DDR4 2400 MHz ECC (4 x 8 GB)
  • OS 500 GB SSD 550 MB/s
  • 4 TB HD Data Storage (2 x 2 TB spanned volume) 170 MB/s
  • Video Card nVidia GTX 1080 8GB DDR5 dedicated memory
  • Monitor HP Z24i display 24' 1920x1200
  • Software NIS-Elements AR v5.02

Incubation

  • Okolab BoldLine Temperature unit Serial 284-1058 H101 T Unit BL
  • Okolab BoldLine CO2/O2 Unit  0-10/1-18 Serial 088-1102
  • Okolab OkoTouch Serial 118-224
  • Lauda water-bath Model Eco RE415 S LCK 4910 Serial LCK-4910-16-0006 Okolab 1322-1006 2017-05-30

Consumables

  • CO2 Tank
  • N2 Tank
  • Liquid Light Guide


Troubleshooting

This can happen when the liquid running through the chamber is not flowing properly.

  • Pause your experiment
  • Turn off the Okolab environment controller 3A and 3B
  • Disconnect the blue end of the connection pipe (at the junction with the spring shape objective warmer)
  • Place the open end into a dish to collect liquid
  • Turn the Lauda water bath back ON (3B)
  • The liquid should flow quite rapidly, if not proceed as follow
    • Turn OFF the Lauda water bath (3B)
    • Take the 20 mL syringe located inside the drawer labelled Tubing
    • Connect it to the open end of the blue pipe
    • Use the syringe to blow pressurized air into the pipes to clear it out
    • Remove the syringe (and store it back into the Tubing drawer)
    • Test if the liquid is now flowing properly by turning the Lauda water bath back ON (3B)
      • If not repeat the procedure
      • If so, turn OFF the Lauda water-bath (3B)
      • Reconnect the blue and green pipes together
      • Turn the Okolab environment controller 3A and 3B back ON

Be careful not to touch your sample when performing these actions as it may displace your current acqusition

How the Okolab chamber works

  1. The liquid from the water bath enters the lead first via the red pipe

  2. Then it goes through the lead circuitry to keep it warm
  3. It exists via the unlabeled tube and enters the incubation chamber main body
  4. It goes through the circuitry of the main body and exits via the green labelled tube

One must maintain a decent amount of liquid in the Lauda water bath to avoid bubble formation in the circuitry

Because the circuitry inside the top lead and the incubation chamber main body is thin it can get clogged. The procedure above can solve this issue.


This happens when the mixed-gas humidifier is overfilled. Bubbles created by the gas going through the humidifier can bring liquid into the gas feed line.

  • Turn off the Okolab module and the water bath
  • Remove your sample and store it properly
  • Dry the incubation chamber with a clean tissue
  • Carefully remove the cap of the humidifier glass bottle

Pay extra care when manipulating the humidifier bottle as it is made of glass and is very fragile

  • Remove distilled water from the humidifier

Humidifier shouldn't be more than 2/3rd filled

  • Close the humidifier by replacing the cap
  • Turn on the Okolab module and the water bath

This can happen during long experiments. The high humidity of the gas mixture condensates in the pipe between the humidifier and the incubation chamber.

  • Pause your experiment
  • Disconnect both ends of the yellow tube from the humidifier
  • Drain the tube from any liquid
  • Reconnect the yellow tube to the humidifier
  • You can use a syringe or gas pressure to blow out any liquid from the incubation chamber cover

Be careful not to touch your sample when performing this action

  • Wipe any liquid with a tissue
  • Reconnect the yellow tube to the incubation chamber 


FAQ

  • Yes. This is an inverted microscope designed to look at specimen in a dish or a multi-well plate
  • The objectives are optimized to image through thin glass bottom multi-well plates
  • You may also image specimen mounted between a slide and a 0.17mm thick coverslip
  • For long timelapse, be aware of photo-toxicity

You may use a trick to warmup the incubation chamber faster. Using this method. you should reach a stable temperature within 30 minutes.

Do NOT proceed with your sample but with a blank control (dish with distilled water for example)

  • Place your blank control in the incubation chamber
  • Immerge the tip of the sample temperature probe in the blank
  • Set the Okolab temperature Control Mode to Chamber (Settings>Temperature>Control Mode>Chamber>Save)
  • Set the Okolab temperature to 50°C (Home>Temperature>50°C>Set)
  • Check the temperature of the sample (Menu Magnifier>Sample Temperature). It should take between 10 to 15 minutes for the blank to reach 30°C. 

The Lauda water bath is faster to warm up water than to cool it down. Make sure to anticipate and not pass beyond the desired temperature.
If your desired temperature is 37°C, you can stop the procedure when the blank has reached 30°C.

When the blank has reach the desired temperature

  • Set the Okolab temperature back to 37°C (Home>Temperature>37°C>Set)
  • Set the Okolab temperature Control Mode to Sample (Settings>Temperature>Control Mode>Sample>Save)
  • Wait 10 to 20 minutes until the temperature stabilizes
  • Then you can safely replace the blank with your sample


Core Facilities CIB               Structural Biology    |    Cytometry    |    Microscopy    |    Histology

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