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Include Page
_Micro-head-en
_Micro-head-en

Button Hyperlink
iconbuild
titleFrançais
typeprimary
urlZeiss LSM-900 Airyscan

Tabs Container
idInstrument Tabs
titleZeiss Axio-Imager Z2
directionhorizontal
Tabs Page
idDescription
titleDescription
Zeiss LSM900

Zeiss LSM-900 confocal Airyscan microscope

Desmarais Building, Room 2234
Advanced Microscope Tier 2 usage price

Instrument awarded to Dr. Jean-Philippe Gratton by the Canadian Foundation for Innovation (CFI)

Applications

  • Transmitted light
  • Phase Contrast
  • Interference Contrast (DIC)
  • Phase Contrast
    • Fluorescence
    • Laser scanning confocal

    Light sources

  • 12V 100W halogen lamp for transmitted light

    • X-Cite 120LED mini for visible fluorescence
    • Airyscan super-resolution

    Zeiss LSM900Image Added

    Tabs Container
    idInstrument Tabs
    titleZeiss LSM900
    directionhorizontal
    Tabs Page
    idDescription
    titleDescription

    Light sources

    • LED lamp for transmitted light

    • Laser 405nm, 488nm, 561nm, 640nm
    Expand
    title
    X-Cite 120LED mini complete
    Complete specifications

    Emission

    peak

    (nm)

    Power

    Nominal power (mW)

    334

    405

    5

    30

    488

    • Objectives

  • 5x/0.15 Ph1 Air WD 5.30 N-AchroPlan 420931-9911

  • 10x/0.25 Ph1 WD TBD N-AchroPlan 420941-9911

  • 20x/0.80 Air WD 0.61 Plan ApoChromat 420650-9901

  • 40x/1.4 Oil WD TBD Plan ApoChromat 420762-9900

  • 63x/1.40 Oil WD 0.19 Plan ApoChromat 420782-9900

  • 40x/0.95 Air WD TBD Plan ApoChromat 420660-9970 Variable coverslip 0.13-0.21
    • Expand
    titleComplete lens specifications

    Position

    Nom

    Marque

    Nom complet

    Identifiant

    Grossissement

    Ouverture numérique

    Immersion

    Type

    Distance de travail (mm)

    Transmittance

    (% [nm])

    Technique

    Épaisseur du couvre-objet (mm)

    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

    4

    63x/1.40

    Huile

    Zeiss

    63x/1.4 DIC III

    Plan-Apochromat

    M27

    420782-9900-000

    63x

    1.4

    Note
    Huile

    Plan Apochromat

    0.19

    >80% [440-710]

    BF, DIC, Fluo

    0.17

    BF: Bright-field
    DIC: Interference contrast

    • Filter cubes
  • 38 GFP
  • 49 DAPI
  • 64 mPlum
  • DIC Analyzer
  • Empty
    • Empty
    Expand
    titleComplete filter specifications

    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

    • Detector
      • 2 GaASP PMT
    Tabs Page
    idUser Guide
    titleUser Guide
    25

    561

    		25

    640

    		45

    • X-Cite 120LED mini for visible fluorescence

      Expand
      titleComplete specifications

      Filter (nm)

      Emission Peak (nm)

      Nominal power (mW)

      Power at the sample (mW)

      DAPI

      365



      GFP

      		470

      mPlum

      		587

    Objectives

    1. 5x/0.15 Ph1 Air
    2. 10x/0.25 Ph1 Air
    3. 20x/0.80 Air
    4. 40x/0.95 Air
    5. 40x/1.4 Oil
    6. 63x/1.4 Oil
    Expand
    titleComplete specifications

    Position

    Name

    		BrandFull name

    identifier

    Magnification

    Numerical aperture

    Immersion

    Type

    Working distance (mm)

    Transmittance

    (% [nm])

    Applications

    Coverglass thickness (mm)

    1

    5x/0.15 Ph1 Air

    Zeiss

    5x/0.15 Ph1 Air
    N-AchroPlan

    420931-9911-000

    5x

    0.15

    Air

    N-AchroPlan

    12.0

    Not Available

    BF, PhC, Fluo

    0.17

    2

    		10x/0.25 Ph1 Air

    Zeiss

    		10x/0.25 Ph1 Air
    N-AchroPlan

    420941-9911-000

    10x

    0.25

    Air


    N-AchroPlan

    6.5

    Not Available

    BF, PhC, Fluo

    0.17

    3

    20x/0.8 Air 

    Zeiss

    20x/0.8 Air
    Plan-Apochromat

     420650-9901-000

    20x

    0.8

    Air

    Plan-Apochromat

    0.55 

    >90% [400-800]

    BF, DIC, Fluo

    0.17

    4

     40x/0.95 Air

    Zeiss

    40x/0.95 Air
    Plan-Apochromat

    420660-9970-000 

    40x

    0.95

    Air

    Plan-Apochromat

     0.25

    >80% [410-820]

     BF, DIC, Fluo

    Variable
    0.13-0.21

    5

     40x/1.4 Oil

    Zeiss

    40x/1.4 Huile
    Plan-Apochroma    t

    420762-9900-000

    40x

    1.4

    Oil

    Plan-Apochromat

     0.13

    >80% [500-850] 

     BF, DIC, Fluo

    0.17

    6

    63x/1.4 Oil

    Zeiss

    63x/1.4 Huile
    Plan-Apochroma    t

     420782-9900-799

    63x

    1.4

    Oil

    Plan-Apochromat 

     0.19

     >80% [440-710]

     BF, DIC, Fluo, Super-Resolution
    Strehl ratio >90%.

    0.17

    BF: Bright-field
    PhC: Contraste de phase
    DIC: Interference contrast

     Filter cubes

    1. GFP
    2. DAPI
    3. mPlum
    4. DIC Analyzer
    5. Empty
    6. Empty
    Expand
    titleComplete specifications

    Position

    Name

    		Brand

    Identifier

    Excitation

    Dichroic

    Emission

    Graph

    1

    		GFP
    Filter Set 38    		Zeiss000000-1031-346BP 470/40FT 495BP 525/50

    Zeiss Filter Set 38 GFPImage Added

    2

    		DAPI
    Filter Set 49    		Zeiss

    488049-9901-000

    		G 365FT 395BP 445/50

    Zeiss Filter Set 49 DAPIImage Added

    3

    		mPlum
    Filter Set 64 HE    		Zeiss489064-0000-000BP 587/25 (HE)FT 605 (HE)BP 647/70 (HE)

    Zeiss Filter Set 64 HE mPlumImage Added

    4

    		DIC AnalyzerZeiss424937-9901-000----

    5

    		Vide------

    6

    Vide

    		-----

    -

    Detectors

    • 2x Gallium Arsenide Phosphid (GaAsP) Photomultiplier Tube (PMT)
    • 1x transmitted light Electronically Switchable Illumination and Detection module (ESID)
    • 1x Airyscan detector for 63x objective
    Tabs Page
    idUser Guide
    titleUser Guide
    UI Expand
    expandedtrue
    titleStartup
    1. If not already done, turn on the computer (#1) and use your UdM credentials to log in to Windows
    2. Remove the dust cover from the microscope

    3. Turn

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

    1. on the System (#2) and Components (#3) switches in the rack

    on the left of the

    1. below microscope

    2. Turn on the laser key (#4) in the rack

    on

    1. below the

    left of the

    1. microscope

    Use your UdM credentials to log in to Windows
    Note
    1. 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.
    2. Start the Zen 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.

    Note

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

    1. If open, close the Zen software and wait for it to close completely (up to 30 seconds)
    2. On the Desktop open the Documentation folder
    3. Double-click Zen Settings for
    LSM800
    1. LSM900
    2. A script will run and a black window will appear briefly
    3. Click OK to close the message Settings for Zen have been imported successfully.
    4. You can then
    reopen
    1. open the Zen 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
    1. objectives to
    its
    1. the lowest position
    2. Press Set Work Position to store this position
    3. If necessary, move the focus slightly up to remove the
    “Lower
    1. Lower Z limit
    reached”
    1. reached message displayed on the touchscreen
    Press
    1. If not already done, press Home>Microscope>Control>Objectives>5x to select the 5x objective
    2. If asked, tap Done to remove the oil lens cleaning warning
    3. Press Home>Microscope>XYZ>Position>Z-Position>Set zero>Auto to perform focus calibration
    4. Press OK to start the focus calibration procedure
    5. Wait a few seconds for the calibration to be completed
    Note

    Once calibrated, the focus can be found at Z = 1.

    6 Press 5x

    7 mm). The Z value can be found on the microscope touch screen Home>Z-Position

    UI Expand
    titleFirst focus
    Warning
    titleImportant

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

    On the microscope touch screen:

  • Press Home>Microscope>Turret>Objectives
    1. If not already done, press Home>Microscope>Turret>Objectives>5x to select the 5x
    lens
    1. objective
      Info

      The 5x objective is

    the safest

    1. the safest because it has the longest working distance (

    TBD mm

    1. 12mm). 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

    1. parafocal, focusing with the safest objective will then allow you to easily find your sample with

    another objective.

    1. another objective. The 10x objective is also safe because its working distance is 6.5 mm.

    2. If not done already, press
    Press
    1. Home>Load Position to lower the
    stage
    1. objective to
    its
    1. the lowest position
    Press
    1. and press Set Work Position to store this position
    2. If necessary, move the focus slightly up to remove the
    “Lower
    1. Lower Z limit
    reached”
    1. reached message displayed on the touchscreen
    2. Place the test slide on the microscope stage with the coverslip toward the objective
      Note
      titleImportant

      Always use the test slide to perform the first focus.

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

    On the computer:

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

      Note

      Once calibrated, the focus can be found at Z = 1.

    6

    1. 7 mm). The Z value can be found on the microscope touch screen Home>Z-Position


    2. In the Locate tab, select Off to turn off the illumination
    UI Expand
    titleSeconday focus
    Warning
    titleImportant

    First focus with the safest

    lens

    objective 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>
    1. Home>Microscope>Control>Objectives
    Press
    1. , press 10x, 20x or 40x to select the desired
    lens
    1. objective
      Info
      The 40x objective is the best Air objective because it has the greatest number of optical corrections (Plan Apochromat) and the largest numerical aperture (0.95)
    . It offers a lateral resolution of 420nm at a wavelength of 550nm.
    1. but has a smaller field of view.
      The 20x/0.8 objective offers the best compromise between Resolution and Field of View
      Note

      There are two (2) 40x objectives, make sure you select the Air

    one

    1. 40x


    In Zen software :

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


    UI Expand
    titleFocusing with oil
    lenses
    objectives

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

    1. Press Home>Microscope>Turret>Objectives

    2. Press 63x Oil, 40x Oil to select the desired

    lens

    1. objective. The microscope will automatically lower the stage so that the sample is accessible.

      Info

      The 40x

    objective is the best oil objective because it has the most optical corrections (Plan Apochromat) and the largest

    1. and 63x oil objectives provide the same spatial resolution because they have the same numerical aperture (1.4).

    It


    1. The 40x oil objective offers a

    lateral resolution of 240nm at a wavelength of 550nm.
    Note

    There are two (2) 40x objectives, make sure you select the OIL one

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

    1. larger field of view and transmits light slightly better beyond 700nm.
      The 63x oil objective transmits light slightly better in the visible spectrum (440-710 nm) and has a better Strehl ratio (90%). It is particularly suited for super-resolution imaging, but its field of view is smaller.

      Note

      There are two (2) 40x objectives, make sure you select the 40x Oil


    2. Place a single drop of oil on the objective
    3. Press Done. The microscope will automatically return the objective to its original position

    In Zen software:

    1. In the Locate tab, select BF or the desired fluorescence (DAPI, GFP, mPlum) 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!

    In Zen software:

    1. In the Locate tab, select BF or the desired fluorescence (DAPI, GFP, mPlum) 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).
    NoteIn any case, your files should be removed from the C: drive.
    UI Expand
    title
    Shutdown
  • Save your data
  • Close the software Zen
    • Storage management
    • Files can be saved temporarily (during acquisition) on the local C: drive (desktop)
    • At the end of each session, copy your data
    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 lenses with lens cleaner and paper
  • Select the 5x objective and press load position to place the objectives in a safe position
  • Turn off the laser key (#4) in the rack on the left of the microscope
  • Turn off the System (#2) and Components (#3) switches in the rack on the left of the microscope

  • Turn off the computer

  • Cover the microscope
    • 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).
    Note

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

    UI Expand
    titleShutdown
    1. Save your data
    2. Close the software Zen
    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. Select the 5x objective and press load position to place the objectives in a safe position
    6. Turn off the laser key (#4) in the rack below the microscope
    7. Turn off theComponents (#3) and System (#2) switches in the rack below the microscope

    8. Turn off the computer

    9. Cover the microscope
    Note
    titleImportant Reminders
    • Take back your samples including ones in the microscope
    • Leave the microscope and the working area clean
    Note
    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). Tabs Page
    idManuals
    titleManuals
    Zen quick start guide.pdf
    Tabs Page
    idLog
    titleLog
    UI Expand
    titleTo do
    • Quality control for Illumination, Liquid light guide and filters quality.
    UI Expand
    title2024-09-19 Joystick replacement
    • Joystick replaced
    UI Expand
    title2024-09-03 Airyscan upgrade
    • Installation Airyscan upgrade. New workstation. New detector. New casing.
    UI Expand
    title2024-07-08 Joystick issue
    • Issue when the joystick is at the rest position. If it is slightly to the left, the stage will move while the image is acquired. Temporary fix: Make sure the joystick is slightly to the right when it is resting.
    UI Expand
    title2024-02-14 Added to wiki
    • User guide added to Wiki French and english version

    UI Expand
    title2021-10-20
    • Zen 2.6 updated hotfix 12
    • Microsoft Windows updated

    UI Expand
    title2021-09-27
    • Added to wiki
    Tabs Page
    idTechnical Datasheet
    titleTechnical Datasheet

    Stand

    • Zeiss AxioObserver LSM900 Serial: 2633000272

    • Manual Field diaphragm for transmitted light

    • Manual polarizer
    • Left imaging port with LSM900 confocal 
    • Manual Aperture diaphragm
    • Manual Fluorescence field diaphragm
    • 6x motorized nosepiece
    • 6x Motorized reflector changer
    • 3x Motorized sideport turret (100% Visible, 100% Left (confocal), 100% right (empty)
    • TL Motorized shutter
    • RL Motorized shutter

    Light sources

    • Transmitted LED light
    • X-Cite 120LED mini Serial XT120LM-0279 RS232 COM Port 6
    • Laser URGB 400102-9300-000 Serial 2631000466  Toptica iChrome-ZLE-4_40407 v3.1 Aug 2016

    Condenser

    • Manual condenser

    • Condenser Lens NA 0.55 WD 26mm

    • Manual polarizer

    • Filter turret 6 positions manual

      1. H Empty

      2. Ph1
      3. Ph2
      4. Ph3
      5. DIC II #426702
      6. DIC III #426706

    Objectives

    1. 5x/0.15 Ph1 Air WD 5.6 N-AchroPlan 420931-9911-000

    2. 10x/0.25 Ph1 WD 6.0 N-AchroPlan 420941-9911-000

    3. 20x/0.80 Air WD 0.61 Plan-Apochromat 420650-9901-000

    4. 40x/0.95 Air WD 0.25 Plan-Apochromat 420660-9970-000 Variable coverslip 0.13-0.21
    5. 40x/1.4 Oil WD 0.13 Plan-Apochromat 420762-9900-000

    6. 63x/1.40 Oil WD 0.19 Plan Apochromat 420782-9900-799

    Stage

    • Motorized stage Marzhauser Scan IM 130x100 Serial 14032630
    • Remote control joystick Marzhauser  2-Schsen-Joystick CZ Serial 2420142128 Article 90-76-200-0820 Zeiss Serial 432903-9011-000
    • Inserts
      • Slide combo
      • 6-well plate
      • 35 mm dish
      • Multi-well plat

    Filters

    6-Position motorized Filter Turret 424947

    1. GFP Zeiss Filter Set 38 cube 424931 000000-1031-346 BP 470/40 450-490 FT 495 BP525/50 500-550
    2. DAPI Zeiss Filter Set 49 cube 424931 489064-0000-000 G365 FT 395 BP 445/50 335-383 395 420-470
    3. mPlum Zeiss Filter Set 64 HE cube 424931  489064-0000-000 BP587/25 FT605 BP647/70 574-599 605 612-682
    4. DIC Analyzer Zeiss 424937-9901
    5. Empty
    6. Empty

    Scanner

    LSM900 Scan head

    • 8x Motorized Filter wheel 1
    1. Empty
    2. SP 470 000000-2090-296 410-470 93% 480-750 0.001%
    3. SP 545 000000-2090-297 410-546 93% 557-750 0.001%
    4. SP 620 000000-2090-298 410-617 93% 630-750 0.001%
    5. Empty
    6. Empty
    7. Empty
    8. Empty
    • 8x Motorized Filter wheel 2
    1. Empty
    2. LBF 640 0000000-2090-299 410-617 93% 630-644 0.001%
    3. LP 575 0000000-2090-294 576-750 93% 410-565 0.001%
    4. LP 655 0000000-2090-295 656-750 93% 395-643 0.001%
    5. SP 620 000000-2090-298 410-617 93% 630-750 0.001%
    6. Empty
    7. Empty
    8. Empty

     Main Beam splitter

    MBS 405+488+561+640 T10/R90

    400102-9600-000

    Transmission

    • 420-471 93%
    • 502-546 93%
    • 575-618 93%
    • 656-800 93%
    • 631-642 10%

    Reflection

    • 399-410 99%
    • 481-492 99%
    • 558-564 99%
    • 631-642 90%

    Detector

    • 2 GaASp PMT
    • 1 Airyscan 2 63x Serial 2657000116
    • 1 transmitted ESID Motorized Left TL ESID LED, Right ESID Detector

    Workstation

    • HP Z2 G9 Serial CZC4027PF7 829W6EC#ABB

    • I155440-CIB

    • Motherboard HP 895C
    • BIOS version 2024-09-03
    • 1 x Intel Core i7-12700K 3.6 GHz
    • RAM 128GB DDR5 4 x 32GB no ECC
    • OS 500 GB NVMe 6 GB/s
    • 7 TB HD Data Storage 213 MB/s
    VNvidia
    • Nvidia RTX A4000 16 GB GDDR6
    • Monitor HP Z32x
    • Software Zen 3.10

    Incubation

    Consumables


    Tabs Page
    idFAQ
    titleTroubleshooting & FAQ

    Troubleshooting

    UI Expand
    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

    UI Expand
    titleCan I use this microscope to observe cells in culture?
    Yes
    it
    . It is an inverted microscope
    . Point scanning confocal induce damage so care should be taken while imaging live cells. a coverslip (thickness 0.17mm). Tabs Container
    idZeiss LSM900
    titleZeiss LSM900
    directionhorizontal
    Tabs Page
    idZeiss LSM900
    titleZeiss LSM900
    Image Removed
    designed for observing specimens in culture. The objectives are optimized for viewing through glass-bottom multi-well plates. It is also possible to observe samples between a slide and coverslip (with a thickness of 0.17mm).



    Include Page
    Plateformes:_Plat-foot-en
    Plateformes:_Plat-foot-en