IGC

Image Processing Workstations

The Advanced Imaging unit has several bioimage processing workstations with specialized software (both open source and commercial). Any of these workstations can be used for FIJI, Ilastik, QuPath and other open source toolboxes (ask!). Upon request, some of these can also be acessible remotely (ask!). List of available workstations:

Imaris | Reservation

This workstation has the newest version of Imaris (v 9) installed. Imaris makes working with 3D bioimage data easier and quicker; it allows basic processing and advanced analysis such as cell tracking, 3D reconstruction and rendering, animations, etc, all in 3D, as opposed to ImageJ/Fiji or Huygens which are less intuitive and easy to use for 3D datasets.

Priority is for using the Imaris software!

You can find excellent tutorials for Imaris here.

Workstation specifications:

  • CPU: Intel Xeon E5-1650 v3 @ 3.5GHz
  • RAM: 96 GB DDR3
  • Graphics: nVidia GeForce GTX 1070 - 6 GB VRAM
  • OS: Windows10 64 Bits
  • HDD space 1: 1x SSD 500 GB
  • HDD space 2: 1x HDD 4 TB - ONLY FOR TEMP STORAGE!
  • Software: Imaris v9, FIJI (ImageJ), Leica LAS AF lite, ...

Speak with the Advanced Imaging staff for help and tutorials on how to use the Imaris software and problem solving.

Huygens | Reservation

This workstation has the latest version of Huygens Pro deconvolution software installed, which allows robust image restoration through deconvolution. Currently it includes support for widefield, confocal, spinDisk and two-photon datasets (including time-lapse), and other restoration tools such as automatic chromatic shift and bleedthrough correction. It also includes PSF distiller for generating empirical (instead of theoretical) PSFs.

For datasets smaller than 4Gb processing is done in GPU which is 3-4 times faster.

Priority of this workstation is for bioimage restoration with Huygens or FIJI! You can find excellent tutorials for Huygens here.

Computer specifications:

  • CPU: Intel i7 4.2GHz
  • RAM: 128 GB DDR3
  • Graphics: nVidia GeForce GTX 1050 Ti - 4 GB VRAM
  • OS: Windows 10 64 Bits
  • SSD space: 1Tb (For temp storage only - cleaned regularly!)
  • Software installed: Huygens Professional, FIJI

Speak with the Advanced Imaging staff for some and tutorials on how to use the Huygens software and suggestions on how to deconvolve images using this software.

Amira | Reservation

This workstation has the latest version of the Amira software for 3D image processing and analysis. This workstation can also be booked for processing demanding FIJI, QuPath and Ilastik operations. It is currently our faster workstation for processing with FIJI or GPU operations (eg ML).

Python, TensorFlow+CUDA are also installed.

Priority is for using the Amira software! You can find excellent tutorials for Amira here.

Computer specifications:

  • CPU: Intel i9 9900X (10x2 cores) @3.5GHz (max 4.4Ghz!)
  • RAM: 128 GB DDR4
  • Graphics: nVidia GeForce RTX2070 - 8 GB VRAM
  • OS: Windows10 Pro 64-Bit
  • HDD: 8Tb
  • Software: Amira, Fiji, QuPath, Ilastik, Icy, Ilastik, Python, TensorFlow+CUDA, others upon request...

Speak with the Advanced Imaging staff for help and tutorials on how to use the Amira software and suggestions.

Z2 BigData processing workstation | Reservation

This workstation has the Arivis, Zeiss and FIJI sofware installed and is one of two workstations capable of processing large "BigData" datasets (eg Z.1 light-sheet / SPIM datasets).

Priority is for using Zeiss Zen and FIJI software!

Computer specifications:

  • CPU: 2x Xeon E5.2620 (2x6x2 cores) @2.4GHz
  • RAM: 192 GB DDR4
  • Graphics: nVidia Quadro P4000 - 8 GB VRAM
  • OS: Windows10 Pro 64 Bits
  • SDD: 2x256Tb (system+software and temp storage)
  • HHD(RAID5): 36Tb (NOT for permanent storage!)
  • Software: Zen, Arivis, FIJI others upon request...

Speak with the Advanced Imaging staff for aceessing and using this workstation.

Z3 BigData processing workstation | Reservation

This workstation has the Zeiss and FIJI sofware installed and is one of two workstations capable of processing large "BigData" datasets (eg Z.1 light-sheet / SPIM datasets).

Computer specifications:

  • CPU: 2x Xeon E5.2620 (2x6x2 cores) @2.4GHz
  • RAM: 128 GB DDR4
  • Graphics: nVidia Quadro P4000 - 8 GB VRAM
  • OS: Windows10 Pro 64 Bits
  • SDD: 2x256Tb (system+software and temp storage)
  • HHD(RAID5): 36Tb (NOT for permanent storage!)
  • Software: Zen, Arivis, FIJI others upon request...

Speak with the Advanced Imaging staff for help using this worksation.

Taiko | Reservation

This machine is exclusive for dSTORM reconstruction and analysis.

Computer specifications:

  • CPU: Intel Xeon E5-2620 2.0GHz
  • RAM: 96 GB DDR3/EEC
  • Graphics: nVidia GForce GTX 970 - 4 GB VRAM
  • OS: Win 7 64bits
  • Software: FIJI (NanoJ etc...), ...

Speak with the Advanced Imaging staff for help using this workstation.

DeltaVision Worstation | Reservation

The DeltaVision workstaion is equiped with the Applied Precision software SoftWorx, similar to the Deltavision microscope software, which can be used for image processing and deconvolution of widefield Deltavision datasets.

Computer specifications:

  • CPU: Intel Xeon 5660 2.8GHz
  • RAM: 16 GB DDR3/EEC
  • Graphics: nVidia GForce GT 520 - 1 GB VRAM
  • OS: Linux CentOS
  • HDD space: 1 TB
  • Software: softWorx, FIJI (ImageJ), ...

Speak with the Advanced Imaging Staff for support with this workstation (currently limited support with SoftWorx software).