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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 # 33122) in 2015

 Applications

  • Inverted microscope
  • Widefield imaging
    • Brightfield
    • Pseudo phase contrast and DIC
    • Fluorescence
  • Swept-field imaging
    • Fluorescence
  • High-throughput imaging


Description

Light sources

    • LED for transmitted light

    • Toptica iChrome MLE for fluorescence

      Source

      Polychroic

      Excitation (nm)

      Fluorophores

      Nominal Power

      (mW)

      Measured Power (mW)

      405nm

      390/40

      [370-410]

      DAPI, Hoechst

      50


      488nm

      482/18

      [473-491]

      FITC, GFP, YFP

      25


      561nm

      564/9

      [559-569]

      Cy3, DsRed, TxRed

      30


      642nm

      640/14

      [632-647]

      Cy5, Cy5.5

      50


Objectives

  1. 10x/0.45
  2. 20x/0.75
  3. 40x/0.6
  4. 60x/0.95
    PositionNameBrandFull nameIdentifierWorking distance (mm)Transmittance
    (% [nm])    		TechniquesCover glass thickness (mm)
    110x/0.45
    Air    		Nikon

    10x/0.45 Air
    Plan Apo

    		MRD001014.0
    		BF, p-PhC, p-DIC, Fluo0.17
    2

    20x/0.75
    Air

    		Nikon20x/0.75 Air
    Plan Apo
    DIC N2    		MRD002011.0
    		BF, p-PhC, p-DIC, Fluo0.17
    3

    40x/0.6
    Air

    		Nikon40x/0.6
    Plan Fluor ELWD    		MRH084302.7-3.7
    		BF, p-PhC, p-DIC, Fluo0.17
    460x/0.95
    Air     		Nikon60x/0.95 Air 
    Plan Apo    		MRD006000.15
    		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 filterEffective 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

  • PCO.edge 5.5

Camera

PCO Edge 5.5

Sensor Type

sCMOS

Sensor Category

Monochrome

Nb Pixels

5.5 M

Pixel Layout

2560 x 2160

Pixel size

 6.5 um

Sensor size

16.6 mm x  14.0 mm

Sensor diameter

21.8 mm

Bit depth

16-bit
Speed at full resolution100 images/s

Max QE

 60 % at 600 nm
Reading noise 1.0 e⁻

Cooling

Forced air +7C

Dark Current

0.6 e⁻/pixel/sec

Full well capacity

30 000 e-

Dynamic Range

1:30000

Interface

Dual Camera Link PCIe

Mount

C-mount

User Guide

  1. If not already done, turn on the microscope (#1) (the switch is not easily accessible and is located on the back of the right side of the device)

  2. If not already done, turn on the computer (#2) and log in to Windows using your UdeM credentials

  3. Start INCell Analyzer 6000

During this procedure, you will:

  • Load your sample

  • Create and configure a template

  • Create an acquisition protocol

Once completed, your sample will be ready for acquisition.

  1. Within the software, 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

    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 instrument for the first time, it is necessary to define the type of plate used. This procedure is usually carried out during the training session but can also be performed if you are using a different multi-well plate.

During this procedure, you will:

  • Create a new plate map

  • Measure the A1 well offset

  • Measure and compute the inter-well distance

  • Measure the plate bottom height and thickness

If you need help, feel free to ask for support. We are always happy to help.

  1. In the software, 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 are 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
  1. In the software, if necessary, click on the Dashboard > Objective Lens> 10x to 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

  1. In the software, if necessary, click on the Dashboard > Objective Lens> 10x to 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 bottom right Well 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

This diagram explains how the Laser Autofocus measure and estimate the position of the sample.


  1. In the software, if necessary, click on the Dashboard > Objective Lens> 10x to select the 10x objective
  2. On the plate map, click on the center of a well containing a sample to center this well on the objective
  3. In the Dashboard menu select Plate/Slide
  4. Click Verify LAF
  5. 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
  6. 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 until the peak are detected successfully
  7. 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).

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

  1. Click Eject to open the access door
  2. Collect your samples
  3. Click Load to close the access door
  4. Select the 10x objective
  5. Close the software
  6. Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
  7. Turn off the computer
  • Collect your samples, especially those in the microscope
  • Leave the microscope and workspace clean

Log


Migrated to windows 11

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

Technical Datasheet

Instrument Serial W24318-1493815 BK02029

Service Password apiAWL

Workstation

  • HP Z230 Workstation Serial
  • I139539-CIB
  • Motherboard HP 1905 Chipset Intel C226
  • BIOS L51 v01.62 v03.61 2019-10-06
  • Processor Intel Core i7-4790 3.6 GHz 
  • RAM 16 GB (4 x 16 GB) DDR3 600 MHz

  • Drives

    • OS 1 TB SSD at 530 MB/s
    • Data Storage 2 TB at 170 MB/s (2 x 1 TB  spanned volume) 
  • Video Card integrated Intel HD Graphics 4600

  • Monitor

    • HP Zr 24w 24" 1920 x 1200

  • OS Windows 11 23H2

  • GE InCell ANalyzer 6000 v7.2 License files for temperature, transmitted light 

Troubleshooting

Usually, this microscope displays a green light when operational and an orange light when in use. A red light 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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Content published under CC BY-SA 4.0. Sharing allowed under the same license with attribution: "Original content by l'Institut Courtois d'innovation biomédicale, used under CC BY-SA 4.0"