Imaging workstations

Last modified by Jussi Kenkkilä on 2024/03/13 13:29

When you want to use an imaging workstation, please make a reservation in the online reservation system (Open IRIS) and mark in the Comments field which software you are going to use. This will let BIU follow which software is being used and which is not.

Ima­ging work­sta­tion 1-2

Imaging_Workstation_1_1920_1200.jpg

Configuration: Lenovo workstation with Windows 10, Intel Xeon W-2135 3.7 GHz CPU, 128 GB RAM and NVidia Quadro P2000 graphics card.

Main use: General use workstation for image processing and analysis (also in 3D and 4D).

Software:

  • Zen (blue and black edition, full version) by Carl Zeiss Microscopy
  • Leica Application Suite X (LAS X) 3.0.1 by Leica Microsystems
  • NIS Viewer
  • Pannoramic Viewer and CaseViewer 2.4 by 3DHistech
    • QuantCenter plugin
  • Matlab by MathWorks
  • Fiji/ImageJ, image processing and analysis
  • CellProfiler, image processing and analysis
  • Imaris converter
  • Aura by Spectral Imaging Instruments for Lago image analysis
  • AngioTool for analyzing vessels (Quick guide)
  • Ilastik
  • Qupath
  • HCS studio
  • MetaXpress
  • Origin 2020
  • PicoQuant
  • R and RStudio

Imaging workstation 3

Imaging_Workstation_3_1920_1200.jpg

New workstation installed 5.2.2024

Configuration: Lenovo p620 Windows 10 workstation with 512 GB RAM and NVIDIA RTX A5000 graphics card.

Main use: 3D and 4D data visualization and analysis (Imaris, Huygens); deconvolution (Huygens).

Software:

  • Imaris by Bitplane, 3D and 4D data visualization and analysis, co-localization and volume rendering
  • Huygens Professional by Scientific Volume Imaging, 3D and 4D data deconvolution with confocal, wide-field and time modules; data visualization and analysis
  • Huygens Localizer by Scientific Volume Imaging, SMLM localization
  • Zen lite by Carl Zeiss Microscopy
  • Leica Application Suite X (LAS X) by Leica Microsystems
  • NIS-Elements AR
  • Fiji/ImageJ, image processing and analysis
  • CellProfiler, image processing and analysis
  • 3D Slicer
  • Analyze 14.0

Remote Desktop BIU 3D VM

Configuration: 128GB memory and half a Grid P100 graphics card

Main use: 3D and 4D data visualization and analysis (Imaris, Huygens); deconvolution (Huygens).

Using the remote desktops.

Software:

  • Zen by Carl Zeiss Microscopy (blue lite)
  • QuPath 0.2.3, for digital pathology and whole slide image analysis
  • Fiji/ImageJ, image processing and analysis
  • Imaris by Bitplane, 3D and 4D data visualization and analysis, co-localization and volume rendering
  • Huygens Professional by Scientific Volume Imaging, 3D and 4D data deconvolution with confocal, wide-field and time modules; data visualization and analysis
  • Huygens Localizer
  • CellProfiler, image processing and analysis
  • Ilastik, image processing software mainly for classification and segmentation.
  • NIS Viewer by Nikon
  • Matlab by MathWorks
  • Anaconda
  • R and R studio, statistical analysis

Remote Desktop BIU VM 2

Main use: General use virtual workstation mostly for BIU internal testing and running scripts.

Using the remote desktops.

Total system failure 27.3.2023, system reinstalled from scratch

Software:

  • Huygens Professional by Scientific Volume Imaging, 3D and 4D data deconvolution.
  • Huygens Localizer
  • Fiji/ImageJ, image processing and analysis
  • CellProfiler, image processing and analysis
  • Olympus OlyVIA freeware