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Zeiss Axio-Observer Z1 inverted microscope

Roger Gaudry Building, Room R-421
Simple Microscope usage price

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

  • Applications
    • Bright-field
    • Phase contrast
    • Fluorescence

  • Light sources

    • LED lamp for transmitted light

    • Colibri

  • Objectives

    1. 2.5x/0.085 Air WD 8.8

    2. Empty

    3. 10x/0.25 Air Ph1 WD 6.5

    4. Empty
    5. 20x/0.5 Air Ph2 WD 2.0
    6. 40x/0.95 Air WD 0.25
PositionNameBrandFull nameIDMagnificationNumerical ApertureImmersionTypeWorking distance (mm)Transmittance
(% [nm])		TechniqueCover glass thickness (mm)
120x/0.5 AirZeiss20x/0.50 Ph2
EC Plan-Neofluar
M27		420351-991020x2.0AirPlan Neofluar2.0Not AvailableBF, PhC, Fluo0.17
2

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3

40x/0.95

Zeiss40x/0.95
Plan-Apochromat Corr
M27		420660-9970

40x

0.95

Air

Plan ApoChromat0.25>80% [400-840]BF, Fluo

0.13 - 0.21
Correction ring

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52.5x/0.085 AirZeiss2.5x/0.085
EC Plan-Neofluar
M27 		420320-99022.5x0.085AirPlan Neofluar8.8>95% [400-750]BF, Fluo0.17
610x/0.25 AirZeiss10x/0.25 Ph1
N-Achroplan
M27 		420941-991110x0.25AirAchroPlan

6.5

Not availableBF, PhC, Fluo0.17
  • Filter cubes
    1. DAPI
    2. GFP
    3. Rhodamine
    4. DHE (dihydroethidium)
    5. Cy5
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]
3Rhodamine
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]


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  • Détector
    • Zeiss AxioCam MR R3 CCD Camera 1388 x 1040 pixels, 12-bit, 13 images/s at full resolution, detector size 8.9 mm x 6.7 mm

  1. Remove the dust cover from the microscope

  2. Turn on the computer (#1)

  3. Turn on the power bar at the bak f the computer monitor (#2)

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

  5. Log in Windows using your UdM credentials

    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.

  6. Startup Zen Blue

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-Osberver Z1
  4. A script will run and a black window will appear briefly
  5. You can then reopen the Zen Blue software

  • 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.

  1. Save your data
  2. Close 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. Turn off the microscope power bar (#2)

  5. Turn off the computer
  6. Cover the microscope

Important Reminders

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


The following schematics depict the light path for transmitted (bright-field and Phase Contrast) and reflected (fluorescence) lights.

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  • Check stage tilt
  • Ask for Colibri Remote
  • Ask for fluorescence backlight from LED
  • Computer replacement
  • Added Colibri
  • Added startup procedure
  • Parafocality and paracentrality
  • Added complete description
  • Added to wiki

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
    • TBD Filters
  • X-Cite 120Q Serial: TBD

Condenser

  • Manual condenser Product number: TBD, Serial: TBD

  • 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

  • 2.5x/0.085 Air WD 8.8

  • Empty

  • 10x/0.25 Air Ph1 WD 6.5

  • Empty
  • 20x/0.5 Air Ph2 WD 2.0
  • 40x/0.95 Air WD 0.25

Stage

  • Motorized stage Marzhauser Sensotech, Part number 432903-9011-000, #14 07 132052; 90-76-200-0820
  • Remote control joystick
  • Inserts
    • Slide combo
    • 6-well plate
    • 35 mm dish
    • Multi-well plat

Filters

  1. DAPI Filter Set 49
  2. GFP Filter Set 13
  3. Rhodamine Filter Set 43
  4. DHE (dihydroethidium)
  5. Cy5 Filter Set 50
  6. Empty

Detector

  • Zeiss AxioCam MR R3 CCD Camera 1388 x 1040 pixels, 12-bit, 13 images/s at full resolution, detector size 8.9 mm x 6.7 mm. Model: r3.1 Part Number: 426509-9901-000. Serial: 1 22 12 5537

Workstation

  • Fujitsu Esprimo P920 E90+
  • Intel Core i5-4670 @ 3.4 GHz
  • RAM 32 GB DDR3 1600 MHz ECC (4 x 8 GB)
  • OS 500 GB SSD 550 MB/s
  • 2 TB HD Data Storage (2 x 1 TB spanned volume) 110 MB/s
  • Video Card AMD FirePro V4900 1 GB DDR5 dedicated memory
  • Monitor TBD display TBD' 1920 x 1200
  • Software Zen Blue 2.0

Incubation

  • Pecon incubation
  • TBD

Consumables

  • CO2 Tank
  • N2 Tank
  • Liquid Light Guide
  • 100 W Mercury lamp

Troubleshooting

This microscope is motorized for most of its components, yet the X-Cite light source is manual. Ensure the X-Cite diaphragm (#4B) fully opened (high position).

  1. On the X-Cite lamp
  2. Turn the intensity diaphragm (#4B) up

FAQ

  • 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

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.


Core Facilities CIB               Structural Biology    |    Cytometry    |    Microscopy    |    Histology

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