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_Micro-head-en
_Micro-head-en

Button Hyperlink
iconbuild
titleFrançais
typeprimary
urlZeiss Z1 Colibri

Zeiss

Axio

Z1-

Observer Z1

Colibri

inverted microscope

Microscope

Desmarais Building, Room 2234
Simple Microscope usage price
Instrument awarded to Dr. Audrey Claing and Dr. Jean-Philippe Gratton by the Canadian Foundation for Innovation (CFI) in 2014



Transmitted light

 

Applications

  • Inverted microscope
  • Widefield imaging

    • Brightfield
    • Phase contrast
    • Fluorescence
  • Incubation
  • Timelapse imaging
  • Incubation
    • Deconvolution
    • Extended
    Focus (see the FAQ section)
    • Depth of Focus

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    Image Added

    Tabs Container

    Zeiss Z1 ColibriImage Removed

    Instrument Tabs
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    idDescription
    titleDescription

    Description

    Light sources

    • LED lamp for transmitted light

    • Colibri 7 R[G/Y]B-UV (385/469/555-590/631) for fluorescence
    Expand
    titleComplete specifications

    Emission peak (nm)

    		Nominal Power (mW)Measured Power (mW)
    385/30150 
    469/38110 
    555/3031 
    631/3350 

    Zeiss Colibri 7 Datasheet

    View file
    nameZeiss_Colibri-7_Product Information.pdf
    height250

    Image AddedImage Removed

    Objectives

    1. 2.5x/0.075 Air

    2. 10x/0.25 Air Ph1
    3. 20x/0.5 Air Ph2

    4. 40x/0.75 Air Ph2

    5. 63x/0.75 Air Ph2 Long Distance
    6. 63x/1.4 Oil
    Expand
    titleComplete specifications
    PositionNameBrandFull nameIDMagnificationNumerical ApertureImmersionTypeWorking distance (mm)Transmittance
    (% [nm])    		TechniqueCover glass thickness (mm)
    12.5x/0.075 AirZeiss2.5x/0.075
    EC Plan-Neofluar

    M27
    420320-9901-0002.5x0.075AirPlan Neofluar9.5>80% [400-840]BF, Fluo0.17
    210x/0.25 AirZeiss10x/0.25 Ph1
    N-Achroplan

    M27 
    420941-9911-00010x0.25AirN-AchroPlan

    6.5

    		Not AvailableBF, PhC, Fluo0.17
    320x/0.5 AirZeiss20x/0.50 Ph2
    EC Plan-Neofluar

    M27

    420351-9910-000

    		20x0.50AirPlan Neofluar2.0Not AvailableBF, PhC, Fluo0.17
    4

    40x/0.75 Air

    		Zeiss40x/0.75 Ph2
    EC Plan-Neofluar

    M27

    420361-9910-000

    40x

    		0.75

    Air

    		Plan Neofluar0.71Not AvailableBF, PhC, Fluo

    0.17

    563x/0.75 Air
    		Zeiss

    63x/0.75 Corr Ph2
    LD Plan-Neofluar

    M27
    421381-9970-000

    63x

    0.75

    		AirLD Plan-Neofluar1.7 at cover glass 0.75Not AvailableBF, PhC, Fluo

    0 - 1.5

    663x/1.4 OilZeiss63x/1.4 DIC
     Plan-Apochromat Oil
    M27
    420782-9900-00063x1.4OilPlan Apochromat0.19>80% [400-700]BF, Fluo0.17

    Filter

    1. DAPI
    2. GFP
    3. Rhodamine
    4. DHE (dihydroethidium)
    5. Cy5
    6. Quadruple DAPI/GFP/Cy3/Cy5
    Expand
    titleComplete specifications
    PositionNameBrandIDExcitation filterDichroic mirrorEmission filterComments
    1DAPI
    Filter Set 49    		Zeiss

    488049-9901

    		365/50
    [325-375]    		395LP445/50
    [420-470]
    2GFP
    Filter Set 13    		Zeiss488013-0000

    470/20
    [460-480]

    495LP

    		517/25
    [505-530]
    3DsRed
    Filter Set 43    		Zeiss

    000000-1114-101

    		545/25
    [533-567]    		570LP605/70
    [570-640]
    4DHECustom

    Custom

    500/50
    [475-525]

    		540LP580/20
    [570-590]    		Undefined specifications
    Best guess values
    5Cy5
    Filter Set 50    		Zeiss488050-9901640/30
    [625-655]    		660LP

    690/50
    [665-715]


    6Quadruple
    DAPI/GFP/Cy3/Cy5
    FS90 HE LED    		Zeiss489090-9110-000


    		QBS
    405+493+575+653

    QBP 425/30+514/30+592/25+709/100

    		Excitation filters included in the light source FS90 HE LED

    Detectors

    • PCO Edge 5.5Zeiss AxioCam MRm
      Expand
      titleComplete specifications
      Camera
    Zeiss AxioCam MRm
    • PCO Edge 5.5

      Sensor Type

    CCD
    • sCMOS

      Sensor Category

      		Monochrome

      Nb Pixels

    1
    • 5.
    4
    • 5 M

      Pixel Layout

    1388
    • 2560 x
    1040
    • 2160

      Pixel size

      		 6.
    45
    • 5 um

      Sensor size

    8
    • 16.
    9
    • 6 mm
    x 6
    • x  14.
    7
    • 0 mm

      Sensor diameter

    11
    • 21.8 mm

      Bit depth

    12
    • 16-bit
      Speed at full resolution
    13
    • 100 images/s

      Max QE

     55
    •  60 % at 600 nm
    Readout
    • Reading noise
     8
    •  1.0 e⁻

      Cooling

    Pelletier
    • Forced air +7C

      Dark Current

      		0.
    7
    • 6 e⁻/pixel/sec

      Full well capacity

    17
    • 30 000 e-

      Dynamic Range

      		1:
    2000
    • 30000

      Interface

    FireWire (IEEE 1394a)
    • Dual Camera Link PCIe

      Mount

      		C-mount

    • Image Added

      View file
      namePCO_Edge 5.5

    Image Removed

    Zeiss_AxioCam MRm

    • _Datasheet.pdf

    • height250

      • PCO Edge 5.5
    • Zeiss Axiocam MRm (not installed)

    Expand
    titleComplete specifications
    sCMOS55 2560 21605 16 mm x  140 21.8 16100
    CameraPCO Edge 5.5Zeiss Axiocam MRm

    Sensor Type

    		CCD

    Sensor Category

    		Monochrome

    Nb Pixels

    		1.4 M

    Pixel Layout

    		1388 x 1040

    Pixel size

    		 6.45 um

    Sensor size

    		8.9 mm x 6.7 mm

    Sensor diameter

    		11 mm

    Bit depth

    		12-bit
    Speed at full resolution13 images/s

    Max QE

    		 60  55 % at 600 nm
    Reading Readout noise 1.0  8 e⁻

    Cooling

    		Forced air +7CPelletier

    Dark Current

    		0.6 7 e⁻/pixel/sec

    Full well capacity

    		30 17 000 e-

    Dynamic Range

    		1:300002000

    Interface

    Dual Camera Link PCIe    		FireWire (IEEE 1394a)

    Mount

    		C-mount

    Image Removed


    Image Added

    View file
    nameZeiss_AxioCam MRm
    PCO_Edge 5.5
    _Datasheet.pdf
    height250

    Tabs Page
    idUser Guide
    titleUser 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. If incubation is required, turn on the incubation power bar (#2) on the desk near the computer and open the CO₂ cylinder (#2B) near the sink
      Note

      Make sure the humidifier is properly filled with distilled water.

    4. Turn on the microscope power bar (#3) on the desk near the computer

    5. When using the instrument for the first time, it is necessary to import the microscope configuration into before starting the software. See the 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 Axio-Observer Zeiss Z1-Colibri

    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 > 2.5x
    • 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.
    Infotip

    Once calibrated, the focus is typically found at Z = 1.1 mm for a microscope slide.
    The Z position can be viewed on the microscope touch For a multi-well plate the focus is generally around Z = 3 mm but this is highly dependent on your multi-well plate.
    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
    titleImportant
    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 . On the microscope touch screen Home > Microscope > Control > Objectives > 2.5x
    Info

    The 2.5× and 10× objectives are the safest to use due to their long working distance (>6 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
      titleImportant

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

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

    In Zen:

    1. In the Locate tab, select BF or the desired fluorescence (Fluo, DAPI, GFP, Cy3, Cy5) to activate the configuration
    2. Adjust the focus with the main dial while looking through the eyepieces until the image is perfectly sharp
    Info

    Once calibrated, the focus is typically found at Z = 1.1 mm for a microscope slide. For a multi-well plate the focus is generally around Z = 3 mm but this is highly dependent on your multi-well plate.
    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 Locate tab, select Off to turn off the illumination
    UI Expand
    titleSeconday focus
    Warning
    titleImportant

    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 or 63x (0.75) to select the desired objective
    Info
    The 40x objective is the best Air objective because it has the largest Numerical aperture (0.75) together with a wider field of view (40x).

    In Zen:

    1. In the Locate tab, select BF or the desired fluorescence (Fluo, DAPI, GFP, Cy3, DsRed, Cy5) 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 63x Oil (1.4)to select the desired objective. The microscope will automatically lower the stage so that the sample becomes accessible.

    3. Place a single drop of oil on the objective
    4. 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 (Fluo, DAPI, GFP, Cy3, DsRed, Cy5) 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 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 2.5x lowest magnification objective and press load position to place the objectives in a safe position

    6. If used, turn off the incubation module power strip (#2A) and close the CO2 cylinder (#2B)

    7. Turn off the microscope power bar (#3)

    8. Turn off the computer
    9. Cover the instrument with the protective dust cover
    Note
    titleReminder
    • Take back your samples including ones in the microscope
    • Leave the microscope and the working area clean

    Log
    Tabs Page
    titleidLog

    Log

    UI Expand
    title
    To be done
    • Measure Power output
    • Modify camera power supply cable
    UI Expand
    title2025-09-01 Camera upgrade10-22 Windows 11 and more
    • Installation of Windows 11
    • Added CO2 connection to incubation module
    • Cable management
    • Replaced video card
      • AxioCam replacement with PCO Edge 5.5
    UI Expand
    title2025-09-01 Camera upgrade
    • Added compressed air connexion to the anti-vibration table
    UI Expand
    title2025-09-01 Camera upgrade
    • AxioCam replacement with PCO Edge 5.5
    UI Expand
    title2025-08-08-21 Wiki Updated
    • Updated wiki with complete specifications
    UI Expand
    title2024-02-22 Microscope Firmware update
    • Microscope Firmware update to add Colibri to the touchscreen
    • Zen 3.5 HotFix 10
    UI Expand
    title2022-05-09
    • Computer replacement
    • Added Colibri
    • Added startup procedure
    • Parafocality and paracentrality
    UI Expand
    title2022-03-17
    • Added complete description
    UI Expand
    title2021-09-27
    • Added to wiki
    Tabs Page
    title
    idtitleTechnical Datasheet

    Technical Datasheet

    Stand

    • Zeiss Axio-Observer Z1 inverted Serial: 3851001242 Part Number: 431007-9902-000
      System ID: 1024979772

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

    Light sources

    • Transmitted LED light
    • Colibri 7 R(G/Y)B-UV 423052-9730-000 Serial 5440000661

    Condenser

    • Manual condenser

    • Lens NA 0.35 WD 70 mm Part Number: 424241

    • Filter turret 6 positions manual

      1. H

      2. Ph0

      3. Ph1

      4. Ph2

      5. DIC

      6. DUC

    Objectives

    1. 2.5x/0.075 Air 420320-9901-000

    2. 10x/0.25 Air Ph1 420941-9911-000

    3. 20x/0.5 Air Ph2 420351-9910-000

    4. 40x/0.75 Air Ph2 420361-9910-000

    5. 63x/0.75 Air Ph2 Long Distance 421381-9970-000

    6. 63x/1.4 Oil 420782-9900-000

    Stage

    • Motorized stage Marzhauser Scan IM 130x100-2mm 90-24-550-0000 Serial 16053038
      Stage Controller 90-76-024-1803 Serial 14 04 1 2040 SMC 2009 432929-9011-000
    • Remote control joystick 2-Axis 90-76-200-0820 Zeiss Article 432903-9011-000 Serial 1615142059
    • Inserts
      • Slide combo
      • Multi-well plate

    Filters

    1. DAPI Filter Set 49 488049-9901
    2. GFP Filter Set 13 488013-0000
    3. Rhodamine Filter Set 43 000000-1114-101
    4. DHE (dihydroethidium) 424931
    5. Cy5 Filter Set 50 488050-9901
    6. Multiband FS90 HE LED 489090-9110-000

    Detector

    • Zeiss AxioCam MRm Model: r3.1 Part Number: 426509-9901-000. Serial: 1 22 12 5537
    • PCO Edge 5.5 Model pco.API.Air.BX Serial 6000001404

    Workstation

    • Computer
      • Fujitsu Esprimo P920 E90+ Model MI5W Serial YLPS036541

    • Intel Core i5-4670 @ 3.4 GHz
    • Motherboard
      • Fujistsu D3222-A1 (1 PCIe Gen3 x16, 1 PCIe Gen 2 x16 (x4 lanes), 2x PCIe Gen2 x1
      • Chipset Intel Q87
      • BIOS UEFI compatible American Trend v4.6.5.4 R1.47.0 for D3222-A1x 2019-08-26 
    • Processor
      • Intel Core i5-4670 @ 3.4 GHz
    • RAMRAM
        • 24 GB DDR3 800 MHz
        ECC
        • (3 x 8 GB)
      • OS 500 GB Drive
        • 1 TB SSD 550 MB/s
        • Win 11 23H2
      • Storage
        • 2 TB HD
        Data Storage (2 x 1 TB spanned volume)
        • 110 MB/s
      • Video Card AMD Card
        • AMD FirePro V4900 1 GB
        DDR5 dedicated memory
        • DDR5 0.768 TFLOPS 1x PCIe gen2 x16
      • Monitor
        • LG Flatron E2711 27' 1920 x 1080
        and
        • LG W2442 1920 x1080
      • Software
        • Zen Blue 3.5
        SN=
        • Serial 1121159628-524292
        • HASP
        =
        • 1798977001
        • Extended Focus
        ,
        • Measurements
        ,
        • Multi-Channel
        ,
        • Panorama
        ,
        • Software autofocus
        ,
        • Time Series
        ,
        • Z-stack 

      Incubation

      • Pecon stage top incubation

      Consumables

      Anti-vibration table

      • TMC Model 63 512 Serial 933240
      • Plain table top

      Consumables

      • CO
      • CO2 Tank
      • N2 Tank
      • Oil
      • Lens Cleaner

      Manuals

    FAQ
    Tabs Page
    Tabs Page
    id
    titleTroubleshooting & FAQ

    Troubleshooting

    UI Expand
    titleI don't see any fluorescence!

    Technical support is free and unlimited. Contact us !

    UI Expand
    titleI see a high background in fluorescence

    This happens in the following conditions at

    • At 2.5x using the DAPI or GFP channel
    • At 10x using the GFP channel
    • At 20x using the GFP channel

     To solve this you can use any of the following option:

    • Tilt the transmitted light arm backward
    • Close the manual shutter between the condenser and the transmitted light
    • Use a higher magnification objective

    FAQ

    UI Expand
    titleCan I use this microscope to look at cell in a dish?

    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.

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

    Yes, but... This microscope has an incubation module to maintain temperature, humidity and gas. Yet it does not have a Definite focus which can maintain focus throughout time. Therefore, it is possible to loose the focus over long period. You can always do a software autofocus 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

    Include Page
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    Plateformes:_Plat-foot-en