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GE INCell Analyzer 6000 High content microscope

JA Bombardier Building, Room 3129
Advanced Microscope Tier 2 usage price

Instrument awarded to Dr. Steve Michnick by the Canadian Foundation for Innovation (CFI)

  • Applications
    • Transmitted light, Bright-field
    • Pseudo phase contrast and DIC
    • Fluorescence
    • High-throughput imaging

  • Light sources

    • LED for transmitted light

    • Toptica iChrome MLE for fluorescence

      SourcePolychroicExcitation wavelength (nm)Compatible fluorophoresNominal Power
      (mW)
      405nm390/40[370-410]DAPI, Hoechst50
      488nm

      482/18

      		[473-491]FITC, GFP, YFP

      25

      561nm

      564/9

      		[559-569]

      Cy3, DsRed, TxRed

      		30
      642nm640/14[632-647]

      Cy5, Cy5.5

      50


  • Objectives

    1. 10x/0.45 Air WD 4.0
    2. 20x/0.75 Air WD 1.0
    3. 40x/0.6 Air WD 2.7-3.7
    4. 60x/0.95 Air WD 0.15

      PositionNameBrandFull nameIdentifierWorking distance (mm)Transmittance
      (% [nm])      		TechniquesCover glass thickness (mm)
      110x/0.45 AirNikon

      10x/0.45 Air
      Plan Apo
      M25x0.75

      		MRD001014.0>80% [TBD-TBD]BF, p-PhC, p-DIC, Fluo0.17
      2

      20x/0.75 Air

      		Nikon20x/0.75 Air
      Plan Apo
      DIC N2
      M25x0.75      		MRD002011.0>80% [TBD-TBD]BF, p-PhC, p-DIC, Fluo0.17
      3

      40x/0.6 Air

      		Nikon40x/0.6 Air
      Plan Fluor ELWD
      M25x0.75      		MRH084302.7-3.7>80% [TBD-TBD]BF, p-PhC, p-DIC, Fluo0.17
      460x/0.95 Air Nikon60x/0.95 Air 
      Plan Apo
      M25x0.75      		MRD006000.15>80% [TBD-TBD]BF, p-PhC, p-DIC, Fluo0.17

      BF: Bright-field
      p-PhC: Pseudo-phase contrast
      p-      DIC: Pseudo-Differetial interference contrast

  • Filters

    1. DAPI

    2. GFP

    3. Cy3

    4. Cy5

    5. Cy5.5

      PositionNameBrandIdentifier

      Polychroic (Transmission)

      		Emission filterEfective bandwith (nm)
      1DAPITBDTBDBP 420/20
      [430-462]      		455/50
      [430-480]      		[430-480]
      2GFPTBDTBD

      BP 446/32; 524/42; 600/36; 732/137

      		525/20
      [515-535]      		[515-535]
      3Cy3TBD

      TBD

      		BP 446/32; 524/42; 600/36; 732/137605/52
      [579-631]      		[582-618]
      4

      Cy5

      		TBD

      TBD

      		BP 446/32; 524/42; 600/36; 732/137707/72
      [671-743]      		[671-743]
      5

      Cy5.5

      		TBDTBDBP 446/32; 524/42; 600/36; 732/137720/60
      [690-750]      		[690-750]

  • Detector
    • sCMOS Monochrome 2560 x 2160 pixels, 16-bit, pixel 6.5um x 6.5um, sensor 16.6mm x 14.0mm

  1. Turn on the microscope (#1) – (if needed) 

    Note

    The switch is not easily accessible and is located on the back of the right side of the device.

  2. Turn on the computer (#2)
  3. Use your UdeM credentials to log in to Windows

  4. Start the software IN Cell Analyzer 6000

Within the software IN Cell Analyzer:

  1. Click Eject to open the access door
  2. Insert your sample in the space provided for this purpose, respecting the orientation indicated

  3. Click Load to close the access doors

    First use

    During the training you will follow the First use protocol

    For use with the 60x objective it is absolutely necessary to use a multi-well plate with a glass bottom. The glass thickness should be 0.17mm. We recommend the following plates:

When using the microscope for the first time, it is necessary to define the type of plate used. You will usually do this during the training session .This procedure can also be performed if you are using a different multi-well plate.



In the INCell Analyzer software:

  1. Select from the menu Application>Plate\Slide Manager...
  2. Click on the New Plate\Slide icon
  3. Select the number of wells in your plate (6, 24, 96 etc...)
  4. Adjust the following settings:
    1. Name: Your-Name_Your-Plate
    2. Plate height, bottom thickness and well volume usually provided in the product technical sheet by the manufacturer
    3. The material used plastic or glass
    4. If necessary adjust the number of rows and columns as well as the shape of the well (round or rectangular)
  5. Click OK
  6. Close the Plate/Slide Manager window


In the INCell Analyzer software:

  1. if necessary, click on the Dashboard > Objective Lens select the 10x objective
  2. In the channel list, click the + button and add a transmitted light channel (brightfield)
  3. To the right of the plate layout, click the Setup Preview Imaging button
  4. Draw a rectangle around well A1
  5. Click on preview (on the acquisition panel at the top right of the screen)
  6. Wait for the preview to be generated
  7. On the plate map, click on the real center of well A1 to center this well on the objective

  8. In the Dashboard menu select Plate/Slide

  9. Click Edit Plate then Define Upper Left Well

  10. Click Yes

  11. Check that the yellow circle matches the edges of the well

  12. Click Yes

In the INCell Analyzer software:

  1. if necessary, click on the Dashboard > Objective Lens select the 10x objective
  2. In the channel list, click the + button and add a transmitted light channel (brightfield)
  3. To the right of the plate layout, click the Setup Preview Imaging button
  4. Draw a rectangle around the bottom right well
  5. Click on preview (on the acquisition panel at the top right of the screen)
  6. Wait for the preview to be generated
  7. On the plate map, click on the real center of well A1 to center this well on the objective

  8. In the Dashboard menu select Plate/Slide

  9. Click Edit Plate then Define bottom right Well

  10. Click Yes

  11. The inter-well distance will then be automatically calculated
  12. Check that the yellow circles matches the edges of the wells

  13. Click Yes

In the INCell Analyzer software:

  1. Click on the Dashboard
  2. In Objective Lens select the 10x objective
  3. On the plate plan, click on the center of a well containing a sample to center this well on the objective
  4. In the Dashboard menu select Plate/Slide
  5. Click Verify LAF
  6. If the 2 detected peaks (blue vertical lines) correspond to the measured peaks (black curve)
    1. Click Apply Measured Parameters
    2. Click OK
    3. Click Yes
  7. If the 2 detected peaks (blue vertical lines) do not correspond to the measured peaks (black curve)
    1. Change the bottom thickness value and repeat the operation
  8. Close the Laser Autofocus Plate/Slide Verification window
  • Files can be saved temporarily (during acquisition) to local C: drive (desktop)
  • At the end of each session, copy your data to your external drive and delete it from local C: drive
  • You can store your files on the D: drive (Data Storage). If you do, please create one folder per laboratory using the principal investigator's last name. Inside, create a folder per user using the following nomenclature (First Name_Last Name).

Important

In any case, do not store your files on the C: drive.

  1. Collect your samples
  2. Click Load to close the access door
  3. Close the INCell Analyzer software
  4. Transfer your data to disk D: (Data Storage) or to your external hard drive and delete it from local disk C:
  5. Turn off the computer

Important Reminders

  • Collect your samples, especially those in the microscope
  • Leave the microscope and workspace clean

The following diagrams allow you to follow the light path in transmitted light (bright field) and in reflected light (fluorescence). These diagrams will be available soon.


Because of an issue with the liquid handling motor, the liquid handling arm as been replaced by a standard fixed arm for the transmitted light LED. Therefore liquid handling is no longer available.

Y motor not resting when reaching the transmitted light position: This time the issue is slightly different: Y motor is homing properly during the initialization procedure but instead of resting it keeps pushing toward the home position and after a brief instant the instrument stops and the red light shows up. If the liquid handler Y motor is disabled the initialization proceed properly and the system is usable at the exception of the brightfield of course


  • Added to wiki

Instrument Serial W24318-1493815 BK02029

Service Password apiAWL

Troubleshooting

Usually, this microscope displays a green light when operational and an orange light when in use. A red light is on means the microscope is not functional. In this case please contact the platform manager.

FAQ

Yes. This microscope is designed for high-throughput acquisition of specimens in multi-well plates. The microscope can control temperature but does not have an environmental chamber. You can also acquire images of specimen mounted between a slide and a coverslip (thickness 0.17mm).

Usually the microscope remains on. However, it is best to turn it off if not in use for a long time (weeks). To do this:

  1. Navigate to the menu Application > Hardware >
  2. Click Shutdown Instrument
  3. Wait for the microscope to turn off
  4. The software closes automatically


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