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Zeiss Axio-Imager Z2 upright microscope

J-A Bombardier Building, Room 3223
Advanced Microscope Tier 1 usage price

Instrument awarded to Dr. Pascal Chartrand by the Canadian Foundation for Innovation (CFI)

  • Applications
    • Transmitted light
    • Interference Contrast (DIC)
    • Fluorescence

  • Light sources

  • Objectives

  1. 10x/0.30 Air WD 5.30

  2. 20x/0.80 Air WD 0.61

  3. 40x/0.75 Air WD 0.71

  4. 63x/1.40 Oil WD 0.19

  5. 100x/1.30 Oil WD 0.20

  6. 100x/1.40 Oil WD 0.17

    Position

    Nom

    Marque

    Nom complet

    Identifiant

    Grossissement

    Ouverture numérique

    Immersion

    Type

    Distance de travail (mm)

    Transmittance

    (% [nm])

    Technique

    Épaisseur du couvre-objet (mm)

    1

    10x/0.30
    Air

    Zeiss

    10x/0.3 DIC I

    EC Plan-Neo Fluar

    M27

    420340-9901-000

    10x

    0.3

    Air

    Plan Neofluar

    5.2

    >90% [480-780]

    BF, DIC, Fluo

    0.17

    2

    20x/0.80
    Air

    Zeiss

    20x/0.8 DIC II

    Plan-Apochromat
    W0.8x1/36"

    440640-9903-000

    20x

    0.8

    Air

    Plan Apochromat

    0.55

    >90% [410-800]

    BF, DIC, Fluo

    0.17

    3


    40x/0.75
    Air


    Zeiss

    40x/0.75 DIC II
    EC Plan-Neofluar
    M27

    420360-9900-000

    40x

    0.75


    Air


    Plan Neofluar

    0.71

    >90% [410-780]

    BF, DIC, Fluo

    0.17

    4

    63x/1.40

    Huile

    Zeiss

    63x/1.4 DIC III

    Plan-Apochromat

    M27

    420782-9900-000

    63x

    1.4


    Huile


    Plan Apochromat

    0.19

    >80% [440-710]

    BF, DIC, Fluo

    0.17

    5

    100x/1.30
    Huile

    Zeiss

    100x/1.3 DIC III
    EC Plan-Neofluar
    M27

    420490-9900-000

    100x

    1.3


    Huile


    Plan Neofluar

    0.20

    >80% [400-820]

    BF, DIC, Fluo

    0.17

    6

    100x/1.40
    Huile

    Zeiss

    100x/1.4 DIC III
    Plan-Apochromat
    M27

    420792-9900-000

    100x

    1.4


    Huile


    Plan Apochromat

    0.17

    >80% [400-820]

    BF, DIC, Fluo

    0.17

    BF: Bright-field
    DIC: Interference contrast

  • Filter cubes
  1. DAPI
  2. GFP
  3. YFP
  4. DsRed/Cy3
  5. TxRed
  6. Cy3.0
  7. Cy3.5
  8. Cy5
  9. DIC analyzer
  10. Empty

    Position

    Nom

    Marque

    Identifiant

    Filtre d'excitation 

    Miroir dichroïque

    Filtre d'émission

    Commentaire



    1

    DAPI

    Filter Set 49

    Zeiss

    488049-9901-000

    365/50

    [340-390]

    395LP

    445/50

    [420-470]




    2

    GFP

    Filter Set 38

    Zeiss

    000000-1031-346

    470/40
    [450-490]

    495LP

    525/50

    [500-550]


    FT 495

    BP 525/50

    3

    YFP

    Filter Set 46

    Zeiss

    000000-1196-681

    500/20

    [490-510]

    515LP

    535/30

    [520-550]




    4

    DsRed

    Filter Set 43

    Zeiss

    000000-1114-101

    545/25

    [533-557]

    570LP

    605/70

    [570-640]

    FT 570

    BP 605/70


    5

    TxRed

    Filter Set 45

    Zeiss

    000000-1114-462

    560/40

    [540-580]

    585LP

    630/75

    [593-667]




    6

    Cy3.0

    Chroma

    SP102v1

    546/11
    [541-551]

    557LP

    567/15

    [560-574]




    7

    Cy3.5

    Chroma

    SP103v1

    581/10
    [576-586]

    593LP

    617/40

    [597-637]




    8

    Cy5 narrow

    Chroma

    49009

    640/30
    [625-655]

    660LP

    690/50

    [665-715]




    9

    Analyseur DIC

    Zeiss








    10

    Vide










Startup
  1. Remove the dust cover from the microscope
  2. Turn on the computer (#1)

  3. Turn on the X-Cite exacte lamp on the shelf to the left of the microscope (#2)

    The X-Cite exact lamp display will flash during heating (approximately 4 minutes) and will then be operational.

    The exact X-Cite lamp must be turned on for at least 30 minutes before being turned off and vice versa

  4. Turn on the power bar on the shelf above the computer (#3)

  5. Press the microscope start button located on the rear left of the microscope (#4)

  6. Use your UdM credentials to log in to Windows

    When using for the first time, it is necessary to import the microscope-specific parameters BEFORE starting the software. See the First Use section below.

  7. Start the Zen Blue software

First Use

When using for the first time, it is necessary to import the microscope-specific parameters into the software. This procedure is usually carried out during the training session. However, it is also possible to use it to reset the software if it is not displayed correctly, for example.

Please note, this procedure will delete all your experiment protocols and restore the software to its original settings.

  1. If open, close the Zen Blue software and wait for it to close completely (up to 30 seconds)
  2. On the Desktop open the Documentation folder
  3. Double-click Settings for Axio-Imager Z2
  4. A script will run and a black window will appear briefly
  5. You can then reopen the Zen Blue software
Loading samples

This procedure puts the microscope in a safe configuration and performs a focus calibration. At the end of this procedure the microscope will be ready for acquisition.

Focus Calibration Z

On the microscope touch screen:

  1. Press Home>Load Position to lower the stage to its lowest position
  2. Press Set Work Position to store this position
  3. If necessary, move the focus slightly up to remove the “Lower Z limit reached” message displayed on the touchscreen
  4. Press Home>Microscope>Turret>Objectives>10x to select the 10x objective
  5. If asked, tap Done to remove the oil lens cleaning warning
  6. Press Home>Microscope>XYZ>Position>Z-Position>Set zero>Auto to perform focus calibration
  7. Press OK to start the focus calibration procedure
  8. Wait a few seconds for the calibration to be completed

Once calibrated, the focus can be found at Z = 11 mm). The Z value can be found on the microscope touch screen Home>Z-Position

First focus

Important

Make sure to calibrate the focus before performing the first focus.

On the microscope touch screen:

  1. Press Home>Microscope>Turret>Objectives
  2. Press 10x to select the 10x lens

    The 10x objective is the safest because it has the longest working distance (5.3 mm). The sample will appear perfectly sharp long before the lens approaches it. It is recommended to always first focus with the safest lens. The objectives are para-focal, focusing with the safest objective will then allow you to easily find your sample with another objective.

  3. Press Home>Load Position to lower the stage to its lowest position
  4. Press Set Work Position to store this position
  5. If necessary, move the focus slightly up to remove the “Lower Z limit reached” message displayed on the touchscreen
  6. Place the test slide on the microscope stage with the coverslip toward the objective

    Important

    Always use the test slide to perform the first focus.

  7. If necessary, move the stage so that the sample is centered on the objective

On the computer:

  1. Open the Zen Blue software
  2. In the Locate tab, select BF or the desired fluorescence (GFP, DsRed, DAPI, etc…) to activate the configuration
  3. Adjust the focus with the main dial while looking through the eyepieces until the image is perfectly sharp

    Once calibrated, the focus can be found at Z = 11 mm). The Z value can be found on the microscope touch screen Home>Z-Position


  4. In the Locate tab, select Off to turn off the illumination
Seconday focus

Important

First focus with the safest lens before selecting another lens and continuing with secondary focus.

Focusing with air objectives

After performing the first focus, on the microscope touch screen:

  1. Press Home>Microscope>Turret>Objectives
  2. Press 20x or 40x to select the desired lens

    The 20x objective is the best Air objective because it has the greatest number of optical corrections (Plan Apochromat) and the largest numerical aperture (0.8). It offers a lateral resolution of 420nm at a wavelength of 550nm.


  3. Adjust the focus with the precision dial while looking through the eyepieces until the image is perfectly sharp
  4. Your sample is ready for acquisition!
Focusing with oil lenses

After performing the first focus, on the microscope touch screen:

  1. Press Home>Microscope>Turret>Objectives

  2. Press 63x Oil, 100x Oil (1.3) ou 100x Oil (1.4) to select the desired lens. The microscope will automatically lower the stage so that the sample is accessible.

    The 63x objective is the best oil objective because it has the most optical corrections (Plan Apochromat) and the largest numerical aperture (1.4). It offers a lateral resolution of 240nm at a wavelength of 550nm.

  3. Place a drop of oil on your sample
  4. Press Done. The microscope will automatically return the sample to its original position

In Zen Blue software:

  1. In the Locate tab, select BF or the desired fluorescence (GFP, DsRed, DAPI, etc…) to activate the configuration
  2. Adjust the focus with the precision dial while looking through the eyepieces until the image is perfectly sharp
  3. In the Locate tab, select Off to turn the illumination off
  4. Your sample is ready for acquisition!
Storage management
  • 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.

Shutdown
  1. Save your data
  2. Close the software Zen Blue
  3. Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
  4. If used, clean oil lenses with lens cleaner and paper

  5. Turn off the power bar on the shelf above the computer (#3)

  6. Turn off the X-Cite exacte lamp (#2)

    The X-Cite lamp must be on for at least 30 min before being turned off and vice-versa

  7. Turn off the computer
  8. Cover the microscope

Important Reminders

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

The following diagrams allow you to follow the light path in transmitted light (bright field, DIC) and in reflected light (fluorescence).

To do
  • Quality control for Illumination, Liquid light guide and filters quality.
  • Camera sensor clean up
2024-02-14 Added to wiki
  • User guide added to Wiki French and english version
2022-03-28
  • Objective 10-0.3 Plan NeoFluor #420340-9901-000 added
  • Parafocality adjustment using 100x-1.4 as reference
  • Condenser removed and cleaned (broken glass)
2021-10-20
  • Zen 2.6 updated hotfix 12
  • Microsoft Windows updated
2021-10-18
  • X-Cite Liquid light guide replaced (Transmittance was 75% remaining)
  • Fluorescence Light bulb replaced (was 2593 hours)
  • Power output at the sample using 20x objective GFP cube 488nm is 116mW
  • Objective parafocality adjusted
  • Objective Focus speed was changed 10x: 7; 20x: 6; 4-x: 5; 63x: 3; 100x-1.3: 3; 100x-1.4: 3.
  • Condenser lens cleaned (oil)
  • Data storage OK
2021-09-27
  • Added to wiki

Stand

  • Zeiss AxioImager Z2 upright Serial: 35230001000
    Part Number: 430000-9902
    System ID 1022265893

  • Camera adapter Model 60N-C, 1", 1x, Model: 426114

  • Motorized Neutral density filters for transmitted light

  • Manual Field diaphragm for transmitted light

  • Manual polarizer
  • Left imaging port with manual splitter camera adapter Model 60N-C, 1", 1x, Model: 426114
  • Trinocular with 100% ocular 40% occular/70% camera and 100% manual splitter
  • 3mm liquid light guide #805-0038
  • Zeiss 423302-0000 Collimator
  • Motorized Aperture diaphragm
  • Motorized Fluorescence field diaphragm

Light sources

  • Transmitted Halogen light 12V 100W HAL 100 #423000
    • TBD Filters
  • X-Cite exacte 200 W Model XCT10A Serial: XCT10A-0156

Condenser

  • Motorized condenser #424201-9902

  • Lens NA 0.9 WD TBD Part Number: TBD

  • Manual polarizer

  • Filter turret 6 positions manual

    1. H Empty

    2. D Darkfield
    3. DIC III #426706
    4. Ph3
    5. DICII #426702

    6. Ph 2

    7. DIC 426701
    8. Ph 1

Objectives

  1. 10x/0.30 Air WD 5.30 DIC I  Plan-NeoFluar M27 420340-9901-000

  2. 20x/0.80 Air WD 0.61 DIC II Plan-Apochromat W0.8x1/36" 440640-9903-000

  3. 40x/0.75 Air WD 0.71 DIC II EC Plan-NeoFluar M27 420360-9900-000

  4. 63x/1.40 Oil WD 0.19 DIC III Plan-Apochromat M27 420782-9900-000

  5. 100x/1.30 Oil WD 0.20 DIC III Plan-NeoFluar M27 420490-9900-000

  6. 100x/1.40 Oil WD 0.17 DIC III Plan-Apochromat M27 420792-9900-000 

Stage

  • Motorized stage Zeiss AIM System #2502000124
  • Remote control joystick
  • Inserts
    • Slide only

Filters

10-positions motorized filter wheel #424913 #424905-0160-810

  1. DAPI Zeiss Filter Set 49 cube 424933
  2. GFP Zeiss  Filter Set 38 cube 424933
  3. YFP Zeiss  Filter Set 46 cube 424933
  4. DsRed Zeiss  Filter Set 43 cube 424933
  5. TxRed Zeiss  Filter Set 45 cube 424933
  6. Cy3.0 Chroma #SP102v1 C162410
  7. Cy3.5 Chroma #SP103v1 C162411
  8. Cy5 Chroma #49009 C162412
  9. DIC Analyzer Zeiss 424932-01
  10. Empty

Detector

  • Photometrics Prime Camera sCMOS 2048 x 2048 pixels, 16-bit, 30 images/s at full resolution, detector size 13.312mm x 13.312mm (18.8 mm diagonal). Serial: A18B202001. Cameralink cable and PCIe adapter available for imaging 100 images/s

Workstation

  • HP Z800 Workstation Serial: CZC1473Y0Q Part number: WJ112ECJ#AK6
  • 2 x Intel Xeon X5650 2.66 GHz
  • RAM 24 GB DDR3 1333 MHz ECC (12 x 2 GB)
  • OS 500 GB SSD 410 MB/s
  • 2 TB HD Data Storage (2 x 1 TB spanned volume) 110 MB/s
  • Video Card ATI FirePro V5800 1 GB DDR5
  • Monitor Dell ST2410  24' 1920 x 1080
  • Software Zen Blue 2.6 Hotfix 12

Incubation

  • None

Consumables

Troubleshooting

I don't see any fluorescence!

The best way to solve a problem in Microscopy is to follow the light path. You will find in the Light path tab of this page, the diagrams which will allow you to follow the light all along its path through the microscope.

  1. Open the light path file
  2. Starting from the light source and moving towards the detector, verify that there is indeed light after each component of the microscope

FAQ

Can I use this microscope to observe cells in culture?
No. It is an upright microscope designed for the observation of specimens between a slide and a coverslip (thickness 0.17mm).


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