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Deconvolution and 3D analysis workstation

Bombardier Building, Room 3023
Workstation usage price
Instrument awarded to Dr Pascal Chartrand by the Canadian Foundation for Innovation (CFI #) in 

 

Applications

  • 2D and 3D Deconvolution

  • Image processing

  • 3D Image analysis

  • Quantification

Description

Applications

  • 2D and 3D Deconvolution

  • Image processing

  • 3D Image analysis

  • Quantification

Processor

  • 2 x Intel Xeon X5675  3.1 GHz

RAM

  • 96 GB (6 x 16 GB) ECC DDR3 666 MHz

Drives

  • OS 1 TB SSD at 500 MB/s
  • Data Storage 4 TB at 170 MB/s

Video Card

  • nVidia Quadro K5000 with 4 GB DDR5 dedicated memory

Monitor

  • HP 27bw 27" 1920 x 1080

  • Dell S2721D 27" 2560 x 1440

Softwares

  • Imaris v7.5

  • Autoquant X3.13

  • Zen Lite 3.13
  • ICY
  • ImageJ
  • FIJI
  • R
  • RStudio
  • VLC
  • Bulk Rename utility

User Guide

  1. If not already done, turn on the computer (#1) and log in to Windows using your UdeM credentials
  2. Available software are located on your Desktop in the Software folder
  • 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 the software
  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

Manuals



Log

  • Migrated to Windows 11

Technical Datasheet

Workstation

  • HP Z800 Workstation Serial CZC20472MK
  • I154048-CIB
  • Motherboard HP 0AECh Chipset Intel 5520
  • BIOS 786G5 v03.61 2018-05-03
  • Processor 2 x Intel Xeon X5675 3.1 GHz 
  • RAM 96 GB (6 x 16 GB) ECC DDR3 666 MHz

  • Drives

    • OS 1 TB SSD at 500 MB/s via PCie x4 to SATA3 adapter OWC
    • Data Storage 4 TB at 170 MB/s (4 x 1 TB  RAID 10) 
  • Video Card nVidia Quadro K5000 with 4 GB GDDR5 2.1 TFLOPS

  • Monitors

    • HP 27bw 27" 1920 x 1080

    • Dell S2721D 27" 2560 x 1440

  • OS Windows 11 23H2

  • Bitplane Imaris v7.5.2 x64 Node license

  • Media Cyubernetics Autoquant X3.1 HASP Dongle License

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 contact us to request permission to the platform manager.
Please note that you can't start the software 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.

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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"