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

Button Hyperlink
iconbuild
titleFrançais
typeprimary
urlZeiss LSM-900 Airyscan

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 # 34992) in

2016

2015

 

Applications

  • Inverted microscope
  • Airyscan super-resolution with joint deconvolution
  • Point scanning confocal
  • Transmitted light
      • Brightfield
      • Phase contrast
      • Interference Contrast (DIC)
      • Fluorescence
    • Targeted photo-modulation FRAP
    • Incubation
    • Timelapse imaging
  • Airyscan super-resolution
    • Deconvolution
    • Extended Depth of Focus
    (see the FAQ section)

    Image Added

    Image Added

    Tabs Container

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    Instrument Tabs
    Tabs Container
    id
    directionhorizontal
    Tabs Page
    title
    idtitleDescription

    Description

    Light sources

    • LED lamp for transmitted light

    • Laser 405nm, 488nm, 561nm, 640nm
    Expand
    titleComplete specifications

    Emission (nm)

    Nominal Power (mW)

    Measured Power (mW)

    405

    5


    488

    		10

    561

    		10

    640

    		5
    • X-Cite 120LED mini for visible fluorescence
    Expand
    titleComplete specifications

    Filter (nm)

    Emission Peak (nm)

    Nominal Power (mW)

    Measured Power (mW)

    DAPI

    365



    GFP

    		470

    mPlum

    		587

    View file
    nameXCite_120LEDmini_Datasheet.pdf

    XCite_120LEDmini_User Manual.pdf

    height250

    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
    Air

    Zeiss

    5x/0.15 Ph1
    N-AchroPlan

    420931-9911-000

    5x

    0.15

    Air

    N-AchroPlan

    12.0

    Not Available

    BF, PhC, Fluo

    0.17

    2

    		10x/0.25
    Air

    Zeiss

    		10x/0.25 Ph1
    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
    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
    Plan-Apochromat

    420660-9970-000 

    40x

    0.95

    Air

    Plan Apochromat

     0.25

    >80%
    [410-820]

     BF, DIC, Fluo

    0.13-0.21

    5

     40x/1.4
    Oil

    Zeiss

    40x/1.4
    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
    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

     Filters

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

    Position

    Name

    		Brand

    ID

    Excitation

    Dichroic

    Emission

    Graph

    1

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

    Zeiss Filter Set 38 GFPImage Modified

    2

    		DAPI
    Filter Set 49    		Zeiss

    488049-9901-000

    		G 365FT 395BP 445/50

    Zeiss Filter Set 49 DAPIImage Modified

    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 Modified

    4

    		DIC AnalyzerZeiss424937-9901-000----

    5

    		-------

    6

    -

    		-----

    -

    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
    Expand
    titleComplete specifications

    Image Modified

    Tabs Page
    title
    idtitleUser Guide

    User Guide

    UI Expand
    expandedtrue
    titleStartup
    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 System (#2) and Components (#3) switches in the rack below microscope
    4. Turn on the laser key (#4) in the rack below the microscope
    5. When using the instrument for the first time, it is necessary to import the microscope configuration into the software. See the First Use section below.
    6. Start Zen
    UI Expand
    titleFirst Use

    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 Zen is open, close it and wait until it has completely shut down (this may take up to 30 seconds)

    2. On the Desktop, open the Softwares folder

    3. Double-click Zen Settings for LSM 900

    4. A script will run and a black window will appear briefly

    5. When the message Settings for Zen have been imported successfully appears, click OK to close it

    6. You can now open Zen

    UI Expand
    titleLoading samples

    During this procedure, you will:

    • Set the microscope to a safe configuration
    • Perform a calibration
    • Load your sample
    • Find and adjust the focus

    Once completed, your sample will be ready for acquisition.

    UI Expand
    titleCalibration

    This step is required to calibrate the microscope in XY and Z. Performing this calibration will significantly reduce the time needed to locate and focus on your sample.

    • If not already done, select the lowest-magnification objective. On the microscope touch screen Home > Microscope > Control > Objectives > 5x
    • In Zen, once it has started a calibration dialog should appear. Simply click Calibrate Now.
      The microscope will lower the objectives, perform an XY calibration first, followed by a Z calibration, and then return to its original position.
    Tip

    Once calibrated, the focus is typically found at Z = 1.7 mm for a microscope slide.
    The Z position can be viewed on the microscope touch screen under Home > Z-Position, as well as in Zen within the Focus tab, located on the right side of the screen.

    Expand
    titleThe calibration dialog did not appear...

    The system may already be calibrated. This can occur if a previous user calibrated the system and left it on.

    UI Expand
    titleVerifying if the system is already calibrated

    In Zen, within the Focus tab, located on the right side of the screen:

    1. Click Load to lower the objective

    2. The Z position is indicated below Current
    3. If Z position value is less than 100 um the system is calibrated

    On the microscope touch screen:

    1. Lower the objective by pressing Home > Load Position

    2. Press Set Work Position to store this position

    3. If necessary, slightly adjust the focus upward to clear the Lower Z Limit Reached message displayed on the touch screen

    4. The Z position value is indicated
    5. If the value is less than 0.1 mm then the system is calibrated
    UI Expand
    titleManual calibration with the software

    In Zen, within the Stage tab, located on the right side of the screen:

    1. If not already done, check the Show All option

    2. At the bottom of the tab click Calibrate

    3. A warning message will show up click Continue

    4. The microscope will lower the objectives and perform a XY stage calibration and then return to its original position.

    In Zen, within the Focus tab, located on the right side of the screen:

    1. If not already done, check the Show All option

    2. At the bottom of the tab click Calibrate

    3. A warning message will show up click Continue

    4. The microscope will then perform a Z calibration and then return to its original position

    XY and Z calibrations are now complete

    UI Expand
    titleManual calibration with the microscope touch screen

    On the microscope touch screen:

    1. Navigate to Home > Microscope > XYZ > Position > Z-Position > Set Zero > Auto to perform focus calibration

    2. Press OK to start the calibration procedure

    3. Wait a few seconds for the calibration to complete

    4. Lower the objective by pressing Home > Load Position

    5. Press Set Work Position to store this position

    6. If necessary, slightly adjust the focus upward to clear the Lower Z Limit Reached message displayed on the touch screen

    7. Navigate to Home > Microscope > XYZ > Position > XY-Position > Set Zero > Auto to perform a stage calibration

    8. Press OK to start the calibration procedure

    9. Wait a few seconds for the calibration to complete

    XY and Z calibrations are now complete

    UI Expand
    titleEnsuring the calibration dialog is displayed at startup

    In Zen:

    1. In the menu bar, navigate to Tools > Options

    2. Select Startup/Shutdown

    3. Under Stage/Focus Calibration, ensure Request Stage/Focus Calibration on Startup is checked

    4. Click OK to close the Options dialog

    UI Expand
    titleInitial focus
    Warning
    Ensure that the calibration has been completed beforehand. Calibration will significantly reduce the time required to locate and focus on your sample.

    On the microscope touch screen:

    1. If not already done, select the lowest-magnification objective Home > Microscope > Control > Objectives > 5x
    Info

    The 5× objective is the safest to use due to its  long working distance (12 mm). The sample will appear in sharp focus well before the objective approaches it. It is recommended to always focus using the safest objectives first. Since the objectives are parafocal, focusing with the safest objectives will facilitate locating the sample when switching to higher-magnification objectives.

    1. Lower the objective by pressing Home > Load Position

    2. Press Set Work Position to store this position

    3. If necessary, slightly adjust the focus upward to clear the Lower Z Limit Reached message displayed on the touch screen

    4. Place the test slide on the microscope stage with the coverslip facing the objective
    Note

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

    1. If necessary, adjust the stage to ensure that the sample is centred under the objective

    In Zen:

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

    Once calibrated, the focus is typically found at Z = 1.7 mm for a microscope slide.
    The Z position can be viewed on the microscope touch screen under Home > Z-Position, as well as in Zen within the Focus tab, located on the right side of the screen.

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

    Perform the initial focus using the safest objective before switching to higher-magnification objectives.

    UI Expand
    titleFocusing with air objectives

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

    1. Press Home>Microscope>Control>Objectives
    2. Press 10x, 20x, 40x (0.95) to select the desired objective
    Info

    The 40× (0.95) Air objective is the best air objective because it has the highest number of optical corrections (Plan Apochromat) and the largest numerical aperture (0.95), but it has a smaller field of view.
    The 20×(0.8) objective offers the best compromise between resolution and field of view.

    Warning

    There are two (2) 40x objectives, make sure you select the 40x Air (0.95)

    In Zen:

    1. In the Locate tab, select BF or the desired fluorescence (DAPI, GFP or 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 off the illumination

    Your sample is ready for acquisition!

    UI Expand
    titleFocusing with oil objectives

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

    1. Press Home>Microscope>Turret>Objectives
    2. Press 40x Oil (1.4) or 63x Oil (1.4)to select the desired objective. The microscope will automatically lower the stage so that the sample becomes accessible.
    Info

    The 40× and 63× oil objectives provide the same spatial resolution because they share the same numerical aperture (1.4).
    The 40× oil objective offers a larger field of view and transmits light slightly better beyond 700 nm.
    The 63× oil objective transmits light slightly better within the visible spectrum (440–710 nm) and has a higher Strehl ratio (90%). It is particularly well suited for super-resolution imaging, although its field of view is smaller.

    Warning

    There are two (2) 40x objectives, make sure you select the 40x Oil (1.40)

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

    In Zen :

    1. In the Locate tab, select BF or the desired fluorescence (DAPI, GFP or 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 off the illumination

    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).
    Note

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

    UI Expand
    titleShutdown
    1. Save your data
    2. Close 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 objectives 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 instrument with the protective dust cover
    Note
    • Take back your samples including ones in the microscope
    • Leave the microscope and the working area clean
    Tabs Page
    idLog
    titleLog

    Log

    UI Expand
    titleTo do
    • Quality control for Illumination, Liquid light guide and filters quality.
    • Revise Technical Datasheet
    UI Expand
    title2025-10-09 20x and 40x Air objectives dirty
    • 20x/0.8 and 40x/0.95 with immersion oil on it. Cleaning objectives.
    • Added Troubleshooting
    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

    Technical datasheet

    Stand

    • Zeiss AxioObserver LSM800 System ID: 2633000272
      Serial 3851002662  431007-9902-000

    • Manual Field diaphragm for transmitted light

    • Manual polarizer
    • Left imaging port 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 with ESID 423053-9071
    • X-Cite 120LED mini Serial XT120LM 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 # 424242

    • 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
      • Multi-well plate

    Filters

    6-Position motorized Filter Turret ##424947

    1. GFP Zeiss Filter Set 38 cube 424931 000000-1031-346
    2. DAPI Zeiss Filter Set 49 cube 424931 489064-0000-000 (in MTB 488049-0000-000)
    3. mPlum Zeiss Filter Set 64 HE cube 424931  489064-0000-000
    4. DIC Analyzer Zeiss 424937-9901
    5. Empty
    6. Empty

    Scanner

    LSM 800 GaAsP-PMT 400102-9000-00000 confocal 2633000272 (in MTB LSM900 Scanhead)

    • 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 2263-682
    • 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 2024-09-0303.04.08 Rev.A 2025-07-02 
    • 1 x Intel Core i7-12700K 3.6 GHz
    • RAM 128GB DDR5 4 x 32GB no ECC
    • OS 500 GB NVMe 6 GB/s
    • Data Storage 14 TB (2 x 7 TB) HD 14 TB (2 x 7 TB) HD 213 MB/s
    • Nvidia RTX A4000 16 GB GDDR6
    • Monitor HP Z32x CNC61804QR 3840 x 2160 60 Hz CNC61804QR 3840 x 2160 60 Hz
    • Software Zen 3.10 SN=1122911743-424077 HASP=110522193
    • Zen Module Arivis Cloud Basic, Arivis Cloud Advanced, Colocalization, Data Storage, Direct Processing, Manual extended Focus, Measurements Multi-Channel. Panorama, Time Series, Advance Processing, Airyscan, Airyscan 2 Basic, Ariscan Hoiunt Deconvolution Exteneded Focus, HDR Confocal Basic, Image Analysis, Sotfware Autofocus, Tiles and Positions, Z Stack
    • Zen Module Arivis Cloud Basic, Arivis Cloud Advanced, Colocalization, Data Storage, Direct Processing, Manual extended Focus, Measurements Multi-Channel. Panorama, Time Series, Advance Processing, Airyscan, Airyscan 2 Basic, Ariscan Hoiunt Deconvolution Exteneded Focus, HDR Confocal Basic, Image Analysis, Sotfware Autofocus, Tiles and Positions, Z Stack

    Incubation

    • Pecon stage top incubation

    Consumables

    • CO2 Tank
    • N2 Tank
    • Oil
    • Lens Cleaner

    Incubation

    • Pecon stage top incubation

    Consumables

    • CO2 Tank
    • N2 Tank
    • Oil
    • Lens Cleaner

    Manuals

    Tabs Page
    Tabs Page
    idFAQ
    titleTroubleshooting & FAQ

    Troubleshooting

    UI Expand
    titleI don't see any fluorescence!

    Technical support is free and unlimited. Contact us !

    UI Expand
    titleMy image is blurry

    This can happen when objectives are dirty. this is especially true for the 20x/0.8 and 40x/0.95 which have a short working distance. If not careful immersion oil can make them dirty. If your image seems blurry with one of these objective please contact us and we will clean it for you !

    Image Added

    FAQ

    UI Expand
    titleCan I use this microscope to perform timelapse experiments?

    Yes, but... This microscope has an incubation module to maintain temperature, humidity and atmosphere. Yet, it does NOT have a module which can maintain focus throughout time. Therefore, it is possible to loose the focus over long period. You can always do a software auto-focus at different time but be aware of photo-toxicity if you are using fluorescence.

    UI Expand
    titleWhat is Extended Depth of Focus?

    Extended Focus is a method to flatten a Z-stack by keeping only the relevant information.

    In Zen:

    • Select the Processing Tab
    • Select the Extended Depth of Focus Method
    • Click Apply
    • Wait until the processing is finished
    • Save the processed image

    Z Stack animationMaximum Intensity projection of a Z-StackExtended Depth of Focus projection of a Z-Stack

    UI Expand
    titleCan I use this microscope to observe cells in culture?
    Yes. This is a inverted microscope designed to look at sample in a dish or a multi-well plate. For long timelapse, be aware of photo-toxicity.

    Include Page
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