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Button Hyperlink
iconbuild
titleFrançais
typeprimary
urlhttps://wiki.umontreal.ca/display/Microscopie/Nikon+Eclipse+E600pages/viewpage.action?pageId=189567128


Filters

  • DAPI/Hoechst/AMCA

  • FITC/EGFP

  • TRITC/Rhodamine

  • TexasRed

Detector

  • Color Camera Nikon DS-Ri2 Serial 701234

Workstation

  • HP Z440 Workstation
  • Intel Xeon E5-1630 v3 @ 3.7GHz
  • RAM 32 GB DDR4 2133 MHz  (4 x 8 GB)
  • OS 256GB SSD 550 MBs
  • 2TB HD Data Storage 150 MBs
  • Video Card NVIDIA Quadro K620 2 GB DDR3 dedicated memory
  • Monitor HP Z24i display 24' 1920x1200

Consumables

Tabs Container
idInstrument Tabs
titleHP Z840 Deconvolution and Image Analysis Workstation
directionhorizontal


Tabs Page
idDescription
titleDescription


HP Z840 Deconvolution

and Image Analysis

Workstation

Roger Gaudry Building, Room R-619
Instrument awarded to Dr Paradis-Bleau by the Canadian Foundation for Innovation (CFI)
Workstation usage price

  • Applications

    • 2D and 3D Deconvolution

    • Image processing

    • Image Analysisanalysis

    • Quantification

  • Processor

    • 2 x Intel Xeon E5-2623 v4 2.60 GHz 

  • RAM

    • 128 GB (8x16GB) ECC DDR4 2400 MHz

  • Drives

    • 512 GB OS 512GB NVMe at 2500 MB/s OS
    • Data Storage 4TB 4 TB (2x2TB) at 170 MB/s spanned volume for storage(2x2TB spanned volumes)

  • Video Card

    • NVidia nVidia GTX 1080 with 8GB DDR5 dedicated memory

  • Monitor

    • HP Z24n 24" IPS display native resolution 1920 x 1200

  • OS
    • Windows 10 21H1
  • Softwares

    • ImageJ

    • FIJI

    • Microsoft Office 2016

    • NIS-Elements AR v5.02 64-bits

    • NIS-Elements Offline Deconvolution v4.11 64-bits


Tabs Page
idUser Guide
titleUser Guide


UI Expand
expandedtrue
titleStartup
  1. Turn on the computer
  2. Turn on the monitor
  3. Log in Windows using your UdM credentials
  4. Start-up NIS-Elements Offline Deconvolution


UI Expand
titleShutdown
  1. Save your data
  2. Close NIS-Elements
  3. Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive


UI Expand
titleStorage Management
  • 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).
Remarque

In any case, your files should be removed from the C: drive.




Tabs Page
idManuals
titleManuals

Manuals


Tabs Page
idLog
titleLog


UI Expand
expandedtrue
titleTo do
  • Bring a network cable to connect directly to Ti2 microscope workstationNothing


UI Expand
expandedtrue
title20212022-0709-20
  • Windows 10 UdeM Image installation
  • Change the 2nd network adapter configuration with fix IP to enable for computer to computer communication
  • Change sharing policies of public document folder
22
  • Added network cable between Nikon Ti2 microscope workstation
  • Added shared public document shortcuts in Desktop\Documentation


UI Expand
title2021-07-20
  • Change GPO
  • Computer Configuration → Administrative Templates → All Settings
    • Do not display the lock screen Enabled
    • Set an active Power plan Enabled High Performance
    • Select the Power button action (plugged in) Enabled Take no action
    • Specify a custom active power plan Enabled
    • Specify the unattended sleep time out (plugged in) Enabled 0
    • Turn off the display (plugged in) Enabled 0
    • Turn off the hard disk (plugged in) Enabled 0
  • User Configuration → Administrative Templates → All Settings
    • Enable screen saver Disabled
    • Desktop Wallpaper Enabled C:\Admin Files\Source Files\DesktopBG.jpg Fit
    • Screen saver timeout Enabled 0
    • Password protect the screen saver Disabled


UI Expand
title2021-07-20
  • Windows 10 UdeM Image installation
  • Change the 2nd network adapter configuration with fix IP to enable for computer to computer communication
  • Change sharing policies of public document folder
  • Change GPO to disable screen saver



Tabs Page
idTechnical Datasheet
titleTechnical Datasheet


Workstation

  • HP Z840 Workstation
  • 2 x Intel Xeon E5-2623 v4 2.60 GHz 
  • 128 GB (8x16GB) ECC DDR4 2400 MHz

  • Drives

    • OS 512GB NVMe at 2500 MB/s
    • Data Storage 4TB at 170 MB/s (2x2TB spanned volumes)
  • Video Card nVidia GTX 1080 with 8GB DDR5 dedicated memory
  • Monitor HP Z24n 24" IPS display native resolution 1920 x 1200
  • OS Windows 10
Tabs Page
idTechnical Datasheet
titleTechnical Datasheet

Stand

  • Nikon Eclipse E600 upright Serial 725540

Light sources

  • Transmitted light Halogen 12V 100W Serial 01875599
  • Reflected light
    • Power supply Nikon Mercury lamp Type C SHG1 Serial D12139
    • Bulb housing model LH M100C-1 Serial 039326

Condenser

  • Condenser Universal C-CU Serial 081901
  • Lens Dry NA 0.9
  • Filters: Empty, Ph1, Ph2, Ph3, DICM, DICH, Empty

Objectives

  • 10x/0.3 Plan Fluor Ph1 DLL WD 16 Air
  • 40x/0.75 Plan Fluor Ph2 DLL WD 0.72 Air with PF40 Wollaston prism
  • 100x/1.3 Plan Fluor Ph3 DLL WD 0.2 Oil with PF/PA 100 Oil Wollaston prism
  • Empty
  • Empty
  • Empty
Développer
titleObjectives complete specifications
PositionNameBrandIDMagnificationNumerical ApertureImmersionTypeWorking distance (mm)Transmittance
(% [nm])		TechniqueCover glass thickness (mm)
110x/0.3 AirNikon10x/0.3 Air Plan Fluor Ph1 DLL10x0.3AirPlan Fluor16>75% [400-800]BF, Pol, PhC, Fluo0.17
2

40x/0.75 Air

Nikon40x/0.75 Air Plan Fluor Ph2 DLL40x

0.75

Air

Plan Fluor0.72>80% [400-750]BF, Pol, PhC, Fluo0.17
3

100x/1.3 Oil

Nikon100x/1.3 Oil Plan Fluor Ph3 DLL

100x

1.3
Remarque
Oil
Plan Fluor0.2>75% [400-800]BF, Pol, PhC, Fluo0.174Empty5Empty6Empty
Développer
titleFilters complete specifications
PositionCube nameBrandIDExcitation FilterDichroic mirrorEmission Filter
1DAPI/Hoechst/AMCAChromaCube set 31000v2350/50x [325-375]400LP460/50m [435-485]
2FITC/EGFPChromaCube set 41001

480/40x [420-500]

505LP

535/50m [510-560]
3TRITC/RhodamineChroma

Cube set 41002c

545/30x [530-560]570LP620/60m [590-650]
4Texas RedChroma

Cube set 41004

560/55x [532-588]

595LP645/75m [607-682]
5Empty6Empty


Tabs Page
idFAQ
titleTroubleshooting & FAQ


Troubleshooting

true.
UI Expand
expanded
titleTroubleshootingDeconvolution processing not giving expected results..

This usually happens when the image files do not contain the correct metadata.

  • Make sure to save the files with all available metadata on the microscope used for the acquisition.
    This usually requires to save the files in the software propriatery proprietary format (.nd for NIS-Elements and Metamorph, .czi for Zen,...)
  • You can always add the correct calibration values after acquisition (pixel size in XY and Z, wavelength, Z-step)


FAQ

UI Expand
titleFAQCan I use this workstation remotely?

Yes and No. You can't

use

start the software remotely but you can start the software locally and then connect remotely to make sure all is running smoothly. To do so you need to request permission to the platform manager.


UI Expand
titleWhich deconvolution method should I use?

There is no single answer

  • If you have a single plan you should choose 2D-deconvolution
  • If you have a Z-stack you should pick 3D-deconvolution.
  • If you want to have a quick view of the result you should use Fast Deconvolution.

Quality wise, the best results are achieved using blind and Landweber. However these methods required a long processing time (several hours for big files)

For more information about deconvolution method refer to paragraph 1.2.2 Choosing the deconvolution Method of the NIS Offline Deconvolution Manual (pdf)





Tabs Container
idDemo Image
titleHP Z840 Deconvolution Workstation
directionhorizontal


Tabs Page
idDemo ImagesImage
titleDemo ImagesImage

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