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id | Description |
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title | Description |
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| Zeiss Axio-Observer spinning-disk microscopeJ-A Bombardier Building, Room 3223-01 Advanced Microscope Tier 2 usage price Instrument awarded to Dr. Daniel Zenklusen by the Canadian Foundation for Innovation (CFI) - Applications
- Transmitted light
- Interference Contrast (DIC)
- Fluorescence
Light sources 12V 100W halogen lamp for transmitted light Lumencor SOLA for visible fluorescence
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title | Lumencor SOLA complete specifications |
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| Emission peak (nm) | Power (mW) |
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334 | 5 | 365 | 20 | 405 | 19 | 436 | 22 | 546 | 21 | 579 | 18 |
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4 lasers 405, 488 561 638 Expand |
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title | Laser complete specifications |
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| Laser line (nm) | Nominal Power (mW) |
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405 | 50 | 488 | 100 | 561 | 50 | 639 | 50 |
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100x/1.46 Oil WD 0.11 TIRF Divergence adjusting aid - TIRF Angle adjusting aid
63x/1.46 Oil WD 0.1 10x/0.3 Air WD 5.2 - Empty
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title | Full lens specifications |
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| Position | Nom | Marque | Nom complet | Identifiant | Grossissement | Ouverture numérique | Immersion | Type | Distance de travail (mm) | Transmittance (% [nm]) | Technique | Épaisseur du couvre-objet (mm) |
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1 | 100x/1.46 Oil | Zeiss | 100x/1.46 DIC I Alpha Plan-ApoChromat M27 | 420792-9800 | 100x | 1.46 | | Plan Apochromat | 0.11 | >70% [410-800] | BF, DIC, Fluo | 0.17 | 2 | TIRF Divergence adjusting aid | Zeiss |
| 423682-8801-000 |
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| 3 | TIRF Angle adjusting aid | Zeiss |
| 423682-8802-000 |
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| 4 | 63x/1.46 Oil | Zeiss | 63x/1.46 DIC III Alpha Plan-Apochromat Korr TIRF M27 | 420780-9970-000 | 63x | 1.46 | | Plan Apochromat | 0.10 | >80% [500-800] | BF, DIC, Fluo | 0.15-0.19 | 5 | 10x/0.3 Air
| Zeiss | 10x/0.3 EC Plan-NeoFluar | 420340-9901 | 10x | 0.3 | Air | Plan-NeoFluar | 5.2 | >90% [450-750] | BF, DIC, Fluo | 0.17 | 6 | Empty |
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BF: Bright-field DIC: Interference contrast |
- Empty
- BS_455
- LSM TFT80/20 1447-381
- BF RL TIRF Calibration 424928
- Set 76 C/G/Dr
- Set 77 G/R/A6
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title | Complete filter specifications |
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Position | Nom | Marque | Identifiant | Filtre d'excitation | Miroir dichroïque | Filtre d'émission | Commentaire |
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1 | Empty |
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| 2 | BS_455 | Zeiss |
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| 455LP |
| To be used with FRAP 405 | 3 | LSM Duo T20/R80 UV | Zeiss |
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| 4 | Brightfield Ref Light | Zeiss |
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| 5 | Set 76 CFP GFP DsRed | Zeiss | 489076-0000-000 | 390-422 484-501 549-573 | 427 503 578 | 448-472 512-538 585-631 |
| 6 | Set 77 GFP/RFP/Alexa633 | Zeiss | 489077-0000-000 | 469-497 552-577 629-650 | 506 582 659 | 510-542 587-614 665-711 |
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id | User Guide |
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title | User Guide |
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UI Expand |
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| - Turn on the computer (#1)
- If required, turn on the incubation power bar
Turn on the camera and laser power bar on the left of the microscope (#2) Turn on the microscope power bar on the right of the microscope (#3) Use your UdeM credentials to log in to Windows
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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.
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Start the Zen Blue software
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| 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 |
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Please note, this procedure will delete all your experiment protocols and restore the software to its original settings. |
- If open, close the Zen Blue software and wait for it to close completely (up to 30 seconds)
- On the Desktop open the Documentation folder
- Double-click Settings for Axio-Observer Z1
- A script will run and a black window will appear briefly
- You can then reopen the Zen Blue software
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| 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 |
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| On the microscope touch screen: - Press Home>Load Position to lower the stage to its lowest position
- Press Set Work Position to store this position
- If necessary, move the focus slightly up to remove the “Lower Z limit reached” message displayed on the touchscreen
- Press Home>Microscope>Turret>Objectives>10x to select the 10x objective
- If asked, tap Done to remove the oil lens cleaning warning
- Press Home>Microscope>XYZ>Position>Z-Position>Set zero>Auto to perform focus calibration
- Press OK to start the focus calibration procedure
- Wait a few seconds for the calibration to be completed
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Once calibrated, the focus can be found at Z = 5 mm). The Z value can be found on the microscope touch screen Home>Z-Position |
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| Warning |
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Make sure to calibrate the focus before performing the first focus. |
On the microscope touch screen: - Press Home>Microscope>Turret>Objectives
- Press 10x to select the 10x lens
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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. |
- Press Home>Load Position to lower the stage to its lowest position
- Press Set Work Position to store this position
- If necessary, move the focus slightly up to remove the “Lower Z limit reached” message displayed on the touchscreen
- Place the test slide on the microscope stage with the coverslip toward the objective
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Always use the test slide to perform the first focus. |
- If necessary, move the stage so that the sample is centered on the objective
On the computer: - Open the Zen Blue software
- In the Locate tab, select BF or the desired fluorescence ((CFP/GFP/DsRed ou GFP/RFP/Cy5, etc…) to activate the configuration
- Adjust the focus with the main dial while looking through the eyepieces until the image is perfectly sharp
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Once calibrated, the focus can be found at Z = 5 mm). The Z value can be found on the microscope touch screen Home>Z-Position |
- In the Locate tab, select Off to turn off the illumination
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| Warning |
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| First focus with the safest lens before selecting another lens and continuing with secondary focus. |
UI Expand |
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title | Focusing with air objectives |
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| This microscope does not have additional air objectives. However, if there were, the procedure would be as follows: After performing the first focus, on the microscope touch screen: - Press Home>Microscope>Turret>Objectives
- Press on the desired lens
In Zen Blue software: - In the Locate tab, select BF or the desired fluorescence (CFP/GFP/DsRed ou GFP/RFP/Cy5, etc…) to activate the configuration
- Adjust the focus with the precision dial while looking through the eyepieces until the image is perfectly sharp
- In the Locate tab, select Off to turn the illumination off
- Your sample is ready for acquisition!
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title | Focusing with oil lenses |
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| After performing the first focus, on the microscope touch screen:
- Press Home>Microscope>Turret>Objectives
Press 63x Oil (1.4)or 100x Oil (1.4) to select the desired lens. The microscope will automatically lower the stage so that the sample is accessible.
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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. |
- Remove your sample from the microscope
- Place a drop of oil on the objective
- Replace your sample from the microscope
- Press Done. The microscope will automatically return the sample to its original position
In Zen Blue software: - In the Locate tab, select BF or the desired fluorescence (CFP/GFP/DsRed ou GFP/RFP/Cy5, etc…) to activate the configuration
- Adjust the focus with the precision dial while looking through the eyepieces until the image is perfectly sharp
- In the Locate tab, select Off to turn the illumination off
- Your sample is ready for acquisition!
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| - 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).
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In any case, your files should be removed from the C: drive. |
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| - Save your data
- Close the software Zen Blue
- Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
- If used, turn of the incubation power bar
- If used, clean oil lenses with lens cleaner and paper
Turn off the microscope power bar on the right of the microscope (#3) - Turn off the camera and laser power bar on the left of the microscope (#2)
- Turn off the computer
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| - Take back your samples including ones in the microscope
- Leave the microscope and the working area clean
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id | Light Path |
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title | Light Path |
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| The following diagrams allow you to follow the light path in transmitted light (bright field, DIC) and in reflected light (fluorescence).
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| Check Loss of 488nm laser power |
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expanded | true |
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title | 2024-03-04 |
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| Corrected Trigger Module configuration for the BackCam - reassigned each camera with its own trigger module in MTB config
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| - DualCam calibration parameters set, using beads
- Realigned Lasers:
- Laser output measured in spinning disk mode at the sample with 10x objective, 1x Extended tubelens, 100% laser power and ALL lasers ON:
- 405nm: 0.70 mW before => 0.66 mW after
- with laser 488 OFF: 0.81 mW before => 0.83 mW after
- 488nm: 3.75 mW before => 4.17 mW after
- with laser 405 OFF: 3.95 mW before => 4.33 mW after
- 561nm: 2.1 mW before => 2.37 mW after
- 639nm: 0.9 mW before => 1.1 mW after
- NOTE: AOTF2 for FRAP
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| For FRAP, the illumination is strongest with the AOTF2 at 60% and not 100% |
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| FRAP/SD illumination switching triggers an error message " 'MTBAOTF2LaserLine6' is not supported by the current hardware" |
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| - Error when the definite focus is used (unexpected error the definite focus did not respond)
- To solve it:
- Turn off the Zen Software
- Turn off the microscope power bar (#3)
- Turn off the definite focus by pressing and holding the definite focus button
- Turn on the definite focus by pressing once the definite focus button
- Wait until the definite focus display shows "Detecting stand"
- Turn on the microscope power bar (#3)
- Confirm that the definite focus is showing in the microscope tactile display
- Open Zen software and run an experiment using the definite focus to confirm it is fully functional
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id | Technical Datasheet |
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title | Technical Datasheet |
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| Stand- Zeiss AxioObserver Z1 upright System ID: 1023798490; Serial number: 3834004569
Left imaging port camera adapter Model 60N-C, 2/3", 1x, Model: 426118-9000 for Yokogawa spinning disk - Yokogawa Spining disk CSU-X1 Serial 175116
Manual Field diaphragm for transmitted light - Right imaging port camera adapter witth slider 423685-9000 Axicam MRm r3.1 426509-9901-000 Serial 1-44-11-5127
Light sources- LED lamp for transmitted light 423053-9080
- Lumencor SOLA V-nIR Serial 27536
Condenser- Empty
- Empty
- Empty
- Empty
- Empty
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Objectives10x/0.30 Air WD 5.30 63x/1.46 Oil WD 0.19 100x/1.46 Oil WD 0.17
Stage- Motorized stage ASI MIV-2000
- Remote control joystick ASI MS-2000 #1111-2112-3426-2020 Model WK-XYB-AV200-PZ
- Remote touch screen 432907-9901
- Inserts
- Combo Slide and petri ASI I-3091
- Plate ASI I-3020
Filters6-positions motorized filter wheel Detector- 2 camera Evolve 512 Serial A10G104008 A16F104001
- Definite Focus 1
Workstation- HP Z840 Workstation Serial: CZC7498KCQ
- 2 x Intel Xeon E5-2623 v3 3.0 GHz
- RAM 64 GB DDR4 1200 MHz ECC (4 x 16 GB)
- OS 1 TB SSD 550 MB/s
- 4 TB HD Data Storage (2 x 2 TB spanned volume) 110 MB/s
- Video Card NVIDIA Quadro K2200 4 GB DDR5
- Monitor HP ZR24W 24' 1920 x 1200
- Software Zen Blue 2.6 Hotfix 12
Incubation- Zeiss Incubation Pecon XL Multi S1 Dark LS Serial 0509311 Zeiss #411857-9540-000
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id | FAQ |
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title | Troubleshooting & FAQ |
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| Troubleshooting UI Expand |
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title | I don't see my sample |
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| The spinning disk is a multipoint confocal. Outside the focal plane the sample disappears completely. It is therefore easier to find your sample through the eyepieces. Follow the tuning procedure to achieve this. |
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title | I don't see any fluorescence! |
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| 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. - Open the light path file
- Starting from the light source and moving towards the detector, verify that there is indeed light after each component of the microscope
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FAQ UI Expand |
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title | Can I use this microscope to look at cell in a dish? |
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| Yes. It is an inverted microscope designed for the observation of living specimens. The spinning disk is particularly appreciated for its limited phototoxicity. 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. |
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