Nikon Deconvolution Workstation

Roger Gaudry Building, Room R-619
Workstation usage price
Instrument awarded to Dr Paradis-Bleau by the Canadian Foundation for Innovation (CFI #34495) in 2015


 

Applications

  • 2D and 3D Deconvolution

  • Image processing

  • Image analysis

  • Quantification



Applications

  • 2D and 3D Deconvolution

  • Image processing

  • Image analysis

  • Quantification

Processor

  • 2 x Intel Xeon E5-2623 v4 2.60 GHz 

RAM

  • 128 GB (8x16GB) ECC DDR4 2400 MHz

Drives

  • OS 512GB NVMe at 2500 MB/s
  • Data Storage 4TB at 170 MB/s

Video Card

  • nVidia GTX 1080 with 8GB DDR5 dedicated memory

Monitor

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

Softwares

  • ImageJ

  • FIJI

  • NIS-Elements AR v5.02 64-bits

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

  1. If not already done, turn on the computer (#1) and log in to Windows using your UdeM credentials
  2. Start-up NIS-Elements Offline Deconvolution
  • 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).

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

  1. Save your data
  2. Close NIS-Elements Offline Deconvolution
  3. Transfer your data to the D: drive (Data Storage) or to your external drive and delete it from the local C: drive
  4. Turn off the computer
  • Migrated to Windows 11
  • Added network cable between Nikon Ti2 microscope workstation
  • Added shared public document shortcuts in Desktop\Documentation
  • 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

Workstation

  • HP Z840 Workstation Serial 2UA70726TV
  • I155433-CIB
  • Motherboard HP 2129 Chipset Intel C612
  • BIOS M60 v02.59 2022-03-31
  • Processor 2 x Intel Xeon E5-2623 v4 2.60 GHz 
  • RAM 128 GB (8 x 16 GB) ECC DDR4-2400 1200 MHz
  • Drives

    • OS 512GB NVMe at 2500 MB/s PCie x4  Samsnung MZVPV512HDGL-000H
    • Data Storage 4 TB at 170 MB/s (2x2TB spanned volumes) Seagate ST2000DM001-1ER164
  • Video Card nVidia GeForce GTX 1080 with 8GB GDDR5X dedicated memory
  • Monitor HP Z24n HWP320E 24" IPS display native resolution 1920 x 1200
  • OS Windows 10 22H2

  • NIS Elements AR v5.02.01 Build 1270 HASP ID 63F02F43

  • NIS Offline Deconvolution version 4.11.01 Build 872 HASP ID 57894085
  • LIM Deconvolution 2D, 3D, Wiener

Troubleshooting

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 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

Yes! Please request permission to the platform manager.
Please note that y
ou can't start the softwares from a remote session but you can start the software locally and then connect remotely to make sure everything is running smoothly.

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)


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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"