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Button Hyperlink
iconbuild
titleFrançais
typeprimary
urlhttps://wiki.umontreal.ca/display/Microscopie/Zeiss+Axio-Imager+Z2


Tabs Container
idInstrument Tabs
titleZeiss Axio-Imager Z2
directionhorizontal
Comment
Tabs Page
idDescription
titleDescription

Zeiss Axio-Imager Z2 upright microscope

J-A Bombardier Building, Room 3223-01
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

    • 12V 100W halogen lamp for transmitted light

    • 200W Exact X-Cite Lamp (340~675nm) for Fluorescence

Full specifications of the exact
    • Développer
      titleCaractéristiques complètes de la lampe X-Cite
lamp
    • exacte
Peak emission

    • Emission peak (nm)

      Power (mW)

      334

      5

      365

      20

      405

      19

      436

      22

      546

      21

      579

      18

Exact Quick Start Guide (English pdf) Exact User Guide (English pdf)
Comparison between HBO vs X-Cite Exact Mercury Lamp Emission Spectra (English) ( Source )

  • 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

WD

  1. Oil

0

  1. WD 0.19

  2. 100x/1.
30 
  1. 30 Oil WD 0.20
oil

  2. 100x/1.40 Oil WD 0.17

oil Full lens specifications



  1. Développer
    titleCaractéristiques complètes des objectifs

    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



    Remarque
    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



    Remarque
    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



    Remarque
    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
    Développer
    titleComplete filter specifications


    Position

Name

  1. Nom

Brand

  1. Marque

IdentifierExcitation filter Dichroic mirrorEmission filter

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]

FT570

  1. 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

analyzer

  1. Zeiss








    10

Empty

  1. Vide










Tabs Page
idUser Guide
titleUser Guide


UI Expand
expandedtrue
titleStartup
  1. Remove the
protective
  1. dust cover from the microscope
  2. Turn on the computer (#1)

  3. Turn on the

exact

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

    Info

    The

exact

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

    Avertissement

    The exact X-Cite lamp must be

on  for

  1. turned on for at least 30 minutes

 before

  1. before being turned

off 

  1. off and vice versa

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

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

  4. Use your UdM credentials to log in to Windows

    Remarque

    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.


  5. Start the Zen Blue software


UI Expand
titleFirst 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.

Remarque

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 theZen Blue software
. To do this, follow the First Use instructions .

  • Start the Zen Blue software


    UI Expand
    titleLoading 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.

    UI Expand
    titleFocus 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
    Remarque

    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


    UI Expand
    titleFirst focus
    Avertissement
    titleImportant

    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
      Info

      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
      Remarque
      titleImportant

      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

      Remarque

      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


    UI Expand
    titleSeconday focus
    Avertissement
    titleImportant

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


    UI Expand
    titleFocusing 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

      Info

      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!


    UI Expand
    titleFocusing 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.

      Info

      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!
    UI Expand
    titleStorage 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).
    Remarque

    In any case, your files should be removed from the C: drive.

    UI Expand
    titleShutdown
    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)

      Avertissement

      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
    Remarque
    titleImportant Reminders
    • Take back your samples including ones in the microscope
    • Leave the microscope and the working area clean
    Tabs Page
    idLight Path
    titleLight Path

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

    View file
    nameZeiss_Z2_Lightpath.pdf
    height250




    Tabs Page
    idManuals
    titleManuals


    Tabs Page
    idLog
    titleLog
    UI Expand
    titleTo do
    • Quality control for Illumination, Liquid light guide and filters quality.
    • Camera sensor clean up
    UI Expand
    title2024-06-05
    • Cy5 channel was misaligned with TXR & Cy3: switched Cy5 & TXR fllter cubes positions (7 ↔  8). Cy5 (blue signal) was shifted in y relative to TXR and AF555 channels (left), and appears to colocalize after cube slot switch (right):

    Image Added Image Added

    • Please advise platform managers if other channels appear misaligned.
    UI Expand
    title2024-02-14 Added to wiki
    • User guide added to Wiki French and english version
    UI Expand
    title2022-03-28
    • Objective 10-0.3 Plan NeoFlura NeoFluor #420340-9901-000 added
    • Parafocality adjustment using 100x-1.4 as reference
    • Condenser removed and cleaned (broken glass)
    UI Expand
    title2021-10-20
    • Zen 2.6 updated hotfix 12
    • Microsoft Windows updated
    UI Expand
    title2021-10-18
    • 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
    UI Expand
    title2021-09-27
    • Added to wiki


    Tabs Page
    idTechnical Datasheet
    titleTechnical Datasheet

    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


    Tabs Page
    idFAQ
    titleTroubleshooting & FAQ

    Troubleshooting

    UI Expand
    Troubleshooting
    titleI 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

    look at cell in a dish
    UI Expand
    titleFAQCan I use this microscope to
    observe cells in culture?
    No. This It is an upright microscope designed to look at specimen for the observation of specimens between a glass slide and a coverslip (thickness 0.17mm thick cover slip).





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    idDemo Image
    directionhorizontal


    Tabs Page
    idDemo Image
    titleDemo Image





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