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Button Hyperlink
iconbuild
titleFrançais
typeprimary
urlhttps://wiki.umontreal.ca/display/Microscopie/GE+InCell+Analyzer+6000



FirstUse
Tabs Container
idInstrument Tabs
titleInCell Analyzer
directionhorizontal


Tabs Page
idDescription
titleDescription

GE

InCell

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)

Advanced Microscope Tier 2 usage price

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

  • Light sources

    • LED for transmitted light

    • Toptica iChrome MLE for fluorescence

      Développer
      titleToptica iChrome complete specifications
      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

      Développer
      titleObjective specifications


      PositionNameBrandFull nameIdentifier
Workinf
    1. Working distance (mm)Transmittance
      (% [nm])
Technic
    1. Techniques
Coverslip
    1. Cover 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

      Développer
      titleFilter specifications


      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


  • Files can be saved temporarily (during acquisition) to local disk C: (desktop)
  • At the end of each session, copy your data to your external drive and delete it from local drive C:
  • You can store your files on disk D: (Data Storage). If using this disk, please create one folder per laboratory using the principal investigator's last name. Inside, create a folder per user (First Name_Last Name).
Tabs Page
idUser Guide
titleUser guideGuide
UI Expand
expandedtrue
titleStartup

  1. If necessary, turn Turn on the microscope microscope (#1) – (if needed) 

    Info
    titleNote

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


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

  4. Start the software IN Cell Analyzer 6000

UI Expand
titleSet up

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

    Info
    titleFirst use

    During the training you will follow the First use protocol


    Remarque
    titleImportant

    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:

    • Link in New Window
      linkTextGreiner SensoPlate plus 96-well plate #655891
      hrefhttps://shop.gbo.com/en/row/products/bioscience/microplates/sensoplate-glass-bottom-plates/bs-sensoplate-plus/655891.html
    • Link in New Window
      linkTextNunc Optical CVG 96-well 164588
      hrefhttps://www.thermofisher.com/order/catalog/product/164588


  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 your external hard drive and delete it from local disk C:
  5. Turn off the computer
UI Expand
UI Expand
titleClosure
Remarque
titleImportant reminders
  • Collect your samples, especially those in the microscope
  • Leave the microscope and workspace clean
UI Expand
titleStorage management
Remarque
titleImportant

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

titleFirst use
Ancre
FirstUse

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.



UI Expand
titleCreate a new 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


UI Expand
Measure the bottom height and thickness of the plate bottom
titleMeasure A1 well offset

In the INCell Analyzer software:

C
  1. if necessary, click on the Dashboard
In
  1. > 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
plan
  1. map, click on the real center of
a
  1. well
containing a sample
  1. A1 to center this well on the objective

  2. In the Dashboard menu select Plate/Slide

  3. Click Edit Plate then Define Upper Left Well

  4. Click

Verify LAF

  1. Yes

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

  3. Click Yes

UI Expand
titleCompute the inter-well distance
  • 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
  • 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
  • Close the Laser Autofocus Plate/Slide Verification window
    • Measure A1 well offset

    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
    A1

    2. Click on preview (on the acquisition panel at the top right of the screen)
    3. Wait for the preview to be generated
    4. On the plate map, click on the real center of well A1 to center this well on the objective

    5. In the Dashboard menu select Plate/Slide

    6. Click Edit Plate then Define

    Upper Left

    1. bottom right Well

    2. Click Yes

    3. The inter-well distance will then be automatically calculated
    4. Check that the yellow
    circle
    1. circles matches the edges of the
    well
    1. wells

    2. Click Yes

    Compute the inter-well distance

  • Repeat the offset measurement steps for the bottom right well

    • The inter-well distance will then be automatically calculated

    UI Expand
    titleMeasure the bottom height and thickness of the plate bottom

    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


    UI Expand
    titleStorage management
    • 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).
    Remarque
    titleImportant

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

    UI Expand
    titleShutdown
    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
    Remarque
    titleImportant Reminders
    • Collect your samples, especially those in the microscope
    • Leave the microscope and workspace clean
    Tabs Page
    idLight path
    titleLight path

    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.

    View file
    namePlate_Diagram.pdf
    height250


    Tabs Page
    idManuals
    titleManuals

    Available manuals


    Tabs Page
    idLog
    titleLog
    UI Expand
    titleTo do

    UI Expand
    title2022-12

    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.

    UI Expand
    title2021-10-26

    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


    UI Expand
    title2021-09-27
    • Added to wiki


    Tabs Page
    idTechnical datasheetDatasheet
    titleTechnical datasheetDatasheet

    Instrument Serial W24318-1493815 BK02029

    Service Password apiAWL


    Tabs Page
    idFAQ
    titleTroubleshooting & FAQ

    Troubleshooting

    UI Expand
    titleThe microscope does not show the usual green light, what should I do?

    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

    UI Expand
    titleCan I use this microscope to observe cells in culture?

    Can I use this microscope to look at cell in a dish?

    NoYes.This a microscope designed to acquire images of specimen is designed for high-throughput acquisition of specimens in multi-well platesYou may also image . 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 0.17mm thick coverslipcoverslip (thickness 0.17mm).
    UI Expand
    titleHow to turn off the microscope?

    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


    Tabs Container
    idDemo Image
    titleInCell Analyzer
    directionhorizontal


    Tabs Page
    idDemo Image
    titleDemo Image




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