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id | Description |
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title | Description |
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| Zeiss Axio-Observer Z1 inverted microscopeRoger Gaudry Building, Room R-421
Access upon request to the platform manager. Consult the Link in New Window |
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href | https://pharmacologie-physiologie.umontreal.ca/wp-content/uploads/sites/38/2017/05/tarification-2017.pdf |
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linkText | Phamarcology and Physiology Department Microscopy Platform |
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| .Serial Camera 1 22 12 5537 r3.1 426509-9901-000 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
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
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title | Objectives complete specifications |
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Position | Name | Brand | Full name | ID | Magnification | Numerical Aperture | Immersion | Type | Working distance (mm) | Transmittance (% [nm]) | Technique | Cover glass thickness (mm) |
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1 | 20x/0.5 Air | Zeiss | 20x/0.50 Ph2 EC Plan-Neofluar M27 | 420351-9910 | 20x | 2.0 | Air | Plan Neofluar | 2.0 | Not Available | BF, PhC, Fluo | 0.17 | 2 | Empty |
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| 3 | | Zeiss | 40x/0.95 Plan-Apochromat Corr M27 | 420660-9970 | 40x | 0.95 | | Plan ApoChromat | 0.25 | >80% [400-840] | BF, Fluo | 0.13 - 0.21 Correction ring | 4 | Empty |
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| 5 | 2.5x/0.085 Air | Zeiss | 2.5x/0.085 EC Plan-Neofluar M27 | 420320-9902 | 2.5x | 0.085 | Air | Plan Neofluar | 8.8 | >95% [400-750] | BF, Fluo | 0.17 | 6 | 10x/0.25 Air | Zeiss | 10x/0.25 Ph1 N-Achroplan M27 | 420941-9911 | 10x | 0.25 | Air | AchroPlan | 6.5 | Not available | BF, PhC, Fluo | 0.17 |
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- Filter cubes
- DAPI
- GFP
- Rhodamine
- DHE (dihydroethidium)
- Cy5
- Quadruple DAPI/GFP/Cy3/Cy5
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title | Filters complete specifications |
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Position | Name | Brand | ID | Excitation filter | Dichroic mirror | Emission filter | Comments |
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1 | DAPI Filter Set 49 | Zeiss | 488049-9901 | 365/50 [325-375] | 395LP | 445/50 [420-470] |
| 2 | GFP Filter Set 13 | Zeiss | 488013-0000 | 470/20 [460-480] | 495LP | 517/25 [505-530] |
| 3 | Rhodamine Filter Set 43 | Zeiss | 000000-1114-101 | 545/25 [533-567] | 570LP | 605/70 [570-640] |
| 4 | DHE | Custom | Custom | 500/50 [475-525] | 540LP | 580/20 [570-590] | Undefined specifications Best guess values | 5 | Cy5 Filter Set 50 | Zeiss | 488050-9901 | 640/30 [625-655] | 660LP | 690/50 [665-715] |
| 6 | Quadruple DAPI/GFP/Cy3/Cy5 FS90 HE LED |
| 489090-9110-000
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| QBS 405 + 493 + 575 + 653 | QBP 425/30+514/30+592/25+709/100 | Excitation filters included in the light source FS90 HE LED |
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- 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
Identifiant système 1024979772. |
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id | User Guide |
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title | User Guide |
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| UI Expand |
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expanded | true |
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title | Start-up | Startup |
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| Remove the dust cover from the microscope Turn on the computer (#1) Turn - If necessary, turn on the microscope power bar (#2)
If incubation is required, turn on the Okolab - for the incubation module (
#3A) and the Lauda water-bath (#3B- #2A) and open the CO2 cylinder (
#3C) and N2 (#3D) tanks Avertissement | Make sure the humidifier and the water bath are clean and properly filled with distilled water.- #2B)
Turn on the power bar at the left of the computer monitor (#3) Press the microscope start button located on the rear left of the microscope (#4) - Log in Windows using your UdM credentials
Remarque |
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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. |
- Start -up NIS-Elements
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The first time you use the instrument, you need to import the microscope settings into the software. To do this follow the instructions Software setup. |
- the Zen 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. Remarque |
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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 software and wait for it to close completely (up to 30 seconds)
- On the Desktop open the Documentation folder
- Double-click Settings for Axio-Osberver Z1
- A script will run and a black window will appear briefly
- You can then reopen the Zen 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 = 1.5 mm). The Z value can be found on the microscope touch screen Home>Z-Position |
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| Avertissement |
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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 (6.5 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 software
- In the Locate tab, select BF or the desired fluorescence (GFP, DsRed, DAPI, 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 = 1.5mm). 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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| Avertissement |
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| First focus with the safest lens before selecting another lens and continuing with secondary focus. |
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title | Focusing with air objectives |
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| After performing the first focus, on the microscope touch screen: - Press Home>Microscope>Turret>Objectives
- Press 20x or 40x to select the desired lens
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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. |
- Adjust the focus with the precision dial while looking through the eyepieces until the image is perfectly sharp
- Your sample is ready for acquisition!
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title | Focusing with oil lenses |
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| This microscope does not have oil immersion 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 63x Oil, 100x Oil (1.3) ou 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. |
- Place a drop of oil on your sample
- 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 (GFP, DsRed, DAPI, 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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| - Save your data
- Close NIS-Elements
- Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
- Turn off the computer
- If oil objectives were used, clean it with lens cleaner and lens paper (not Kimwipes)
- If incubation was used, turn off the Okolab incubation module (#3A) and Lauda water-bath (#3B) and close the CO2 (#3C) and N2 (#3D) tanks
- Turn off the microscope power bar (#2)
- Cover the microscope
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| Take back your samples including ones in the microscopeLeave the microscope and the working area clean |
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| - 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).
Remarque |
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In any case, your files should be removed from the C: drive. |
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title | Software setup | | Shutdown |
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| - Save your data
- Close the Zen software
- 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 off the incubation module power strip (#2A) and close the CO2 cylinder (#2B) Select the 10x objective and press load position to bring the objectives to the bottom position
Turn off the microscope power bar (#3) - Turn off the computer
- Cover the instrument with the protective dust cover
Remarque |
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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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The first time you use the instrument, you need to import the microscope settings into the software. You will usually do this during the training session. This procedure can also be performed if something is not working properly and if you want to reset the software to its original settings. Remarque |
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This process will delete all experiment protocols and reset the software to the original settings for this specific microscope. | If open, close NIS-Elements and wait until it is completely closed (up to 30 seconds)On your Desktop open the Softwares folderOpen NIS Settings UtilityClick on the Import tabClick on BrowseNavigate to your DesktopSelect the file Nikon-Ti2 Settings.binClick SelectSelect all itemsClick ImportClick OKClose the NIS SettingsYou can now reopen NIS-Elements |
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id | Lightpath |
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title | Lightpath |
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| The following schematics depict the light path for transmitted (bright-field and Phase Contrast) and reflected (fluorescence) lights.Nikon Ti2 Lightpath (pdf) PDF |
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name | LightPath_Zeiss_Z1.pdf |
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| Available manuals |
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| UI Expand |
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| - Check stage tilt
- Ask for Colibri Remote
- Ask for fluorescence backlight from LED
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title | 2024-02-22 Microscope Firmware update |
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| - Microscope Firmware update to add Colibri to the touchscreen
- Zen 3.5 HotFix 10
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| - Computer replacement
- Added Colibri
- Added startup procedure
- Parafocality and paracentrality
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| - Added complete descriptionNothing
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id | Technical Datasheet |
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title | Technical Datasheet |
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| StandLight sources- Transmitted LED light
- ND32 filter
- IR filter
- Manual Polarizer
- Lumencor SpectraX 6-NII-SE Serial 9409
CondenserObjectives- 20x/0.5 Air Ph1 WD 2.1
- 60x/1.4 Oil DIC WD 0.13
- 100x/1.45 Oil Ph3 WD 0.13
- 100x/1.45 Oil DIC WD 0.13
- 4x/0.2 Air WD 20
- 20x/0.75 Air DIC WD 1.0
Stage- Motorized stage Ti2 SHU compatible Serial 127808
- Remote control joystick Ti2-S-JS Serial 127976
- Inserts
- Multi-well plate Ti2-S-HW with tilt adjustment (no incubation)
- Combo slide 3cm dish Ti2-S-HU with tilt adjustment (no incubation)
- Okolab H101-CellASIC Frame with perfusion ports
- 1 x 35mm petri dish 1x35-M + cover
- 2 Chamber Slide 2xGS-M+ cover
- 1 Multi-well for oil objectives MW-OIL
- 6-well plate 6MW+ cover
- 1 CellASIC + cover
Filters - DAPI Cube Ex 383-408 DAPI-U DM 425 BA 435-485
- GFP Cube Semrock 96372 M349727 17
- Cy5 Cube Semrock 96376 M351081 8
- 77074160 Custom Quad C182279 Polychroic and quad bandpass emitter for use with the following single bandpass filters: ET395/25x, ET470/24x, ET550/15x, ET640/30x
- DIC Analyser Ti2-C-DICACL
- C197767 7707\4656 CFP\YFP\mCherry XT
Detector- Hamamatsu ORCA Flash V2 C11440-22CU CMOS Monochrome Camera 2048 x 2048 pixels, 16-bit, 30fps at full frame Serial 101081
Workstation- Colibri 7 R(G/Y)B-UV 423052-9730-000 Serial 5440000661
CondenserObjectives2.5x/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- DAPI Filter Set 49
- GFP Filter Set 13
- Rhodamine Filter Set 43
- DHE (dihydroethidium) 424931
- Cy5 Filter Set 50
- Multiband FS90 HE LED
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
- HP Z440 Workstation
- Intel Xeon E5-1620 v4 @ 3.5GHz
- RAM 32 GB DDR4 2400 MHz ECC (4 x 8 GB)
- OS 500 GB SSD 550 MB/s
- 4 2 TB HD Data Storage (2 x 2 1 TB spanned volume) 170 110 MB/s
- Video Card nVidia GTX 1080 8GB Card AMD FirePro V4900 1 GB DDR5 dedicated memory
- Monitor HP Z24i display 24' 1920x1200
- Software NIS-Elements AR v5.02
Incubation- Okolab BoldLine Temperature unit Serial 284-1058 H101 T Unit BL
- Okolab BoldLine CO2/O2 Unit 0-10/1-18 Serial 088-1102
- Okolab OkoTouch Serial 118-224
- Lauda water-bath Model Eco RE415 S LCK 4910 Serial LCK-4910-16-0006 Okolab 1322-1006 2017-05-30
- Monitor LG Flatron E2711 27' 1920 x 1080
- Software Zen Blue 3.5 HASP YRMDZ 1798977001 1798977001
Incubation- Pecon stage top incubation
Consumables- CO2 Tank
- N2 Tank
- Oil
- Lens CleanerLiquid Light Guide
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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 | Chamber does not reach the desired temperature (or is very slow to warm up) |
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| This can happen when the liquid running through the chamber is not flowing properly. - Pause your experiment
- Turn off the Okolab environment controller 3A and 3B
- Disconnect the blue end of the connection pipe (at the junction with the spring shape objective warmer)
- Place the open end into a dish to collect liquid
- Turn the Lauda water bath back ON (3B)
- The liquid should flow quite rapidly, if not proceed as follow
- Turn OFF the Lauda water bath (3B)
- Take the 20 mL syringe located inside the drawer labelled Tubing
- Connect it to the open end of the blue pipe
- Use the syringe to blow pressurized air into the pipes to clear it out
- Remove the syringe (and store it back into the Tubing drawer)
- Test if the liquid is now flowing properly by turning the Lauda water bath back ON (3B)
- If not repeat the procedure
- If so, turn OFF the Lauda water-bath (3B)
- Reconnect the blue and green pipes together
- Turn the Okolab environment controller 3A and 3B back ON
Avertissement |
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Be careful not to touch your sample when performing these actions as it may displace your current acqusition |
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title | How the Okolab chamber works |
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| The liquid from the water bath enters the lead first via the red pipe - Then it goes through the lead circuitry to keep it warm
- It exists via the unlabeled tube and enters the incubation chamber main body
- It goes through the circuitry of the main body and exits via the green labelled tube
One must maintain a decent amount of liquid in the Lauda water bath to avoid bubble formation in the circuitry Because the circuitry inside the top lead and the incubation chamber main body is thin it can get clogged. The procedure above can solve this issue. UI Expand |
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title | Liquid forming inside the incubation chamber |
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| This happens when the mixed-gas humidifier is overfilled. Bubbles created by the gas going through the humidifier can bring liquid into the gas feed line. - Turn off the Okolab module and the water bath
- Remove your sample and store it properly
- Dry the incubation chamber with a clean tissue
- Carefully remove the cap of the humidifier glass bottle
Avertissement |
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Pay extra care when manipulating the humidifier bottle as it is made of glass and is very fragile |
- Remove distilled water from the humidifier
Info |
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Humidifier shouldn't be more than 2/3rd filled |
- Close the humidifier by replacing the cap
- Turn on the Okolab module and the water bath
I see a high background in fluorescence |
| The fluoresncece light source is a Colibri while the transmitted light is a LED. What happens is that the fluorescence illumination reflects and into the LED and give a high background. To solve this: - Tilt the transmitted light arm backward
or - Stop the light from entering the transmitted LED by using a cardboard
| UI Expand |
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title | Liquid forming inside the incubation chamber but the humidifier is not overfilled |
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| This can happen during long experiments. The high humidity of the gas mixture condensates in the pipe between the humidifier and the incubation chamber. - Pause your experiment
- Disconnect both ends of the yellow tube from the humidifier
- Drain the tube from any liquid
- Reconnect the yellow tube to the humidifier
- You can use a syringe or gas pressure to blow out any liquid from the incubation chamber cover
Avertissement |
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Be careful not to touch your sample when performing this action |
- Wipe any liquid with a tissue
- Reconnect the yellow tube to the incubation chamber
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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. 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
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title | How can I warm up the incubation chamber faster? | Can I use this microscope to perform timelapse experiments? |
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| 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 may use a trick to warmup the incubation chamber faster. Using this method. you should reach a stable temperature within 30 minutes. Avertissement |
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Do NOT proceed with your sample but with a blank control (dish with distilled water for example) |
- Place your blank control in the incubation chamber
- Immerge the tip of the sample temperature probe in the blank
- Set the Okolab temperature Control Mode to Chamber (Settings>Temperature>Control Mode>Chamber>Save)
- Set the Okolab temperature to 50°C (Home>Temperature>50°C>Set)
- Check the temperature of the sample (Menu Magnifier>Sample Temperature). It should take between 10 to 15 minutes for the blank to reach 30°C.
Info |
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The Lauda water bath is faster to warm up water than to cool it down. Make sure to anticipate and not pass beyond the desired temperature. If your desired temperature is 37°C, you can stop the procedure when the blank has reached 30°C. |
When the blank has reach the desired temperature Set the Okolab temperature back to 37°C (Home>Temperature>37°C>Set)Set the Okolab temperature Control Mode to Sample (Settings>Temperature>Control Mode>Sample>Save)Wait 10 to 20 minutes until the temperature stabilizesThen you can safely replace the blank with your sample |
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