Centre for High-Throughput Phenogenomics

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Data Analysis Room

Data RoomWorkstations

The Centre for High-Throughput Phenogenomics provides free access to a variety of image analysis software packages. From popular open source software, to advanced software specific to particular imaging modalities, our workstations can cover a range of applications. Workstations are available for CHTP users from Monday to Friday between the hours of 8am and 6pm and can be reserved in advance. For specific information about the different workstations and associated software packages, please see the information below.

Windows Workstation #1

  • HP ZX800 (Windows 7)
  • Intel Xeon Quad-Core CPU X5672 with 3.2 GHz 12 MB cache and 1333 MHz memory
  • 12 GB installed RAM
  • Nividia Quadro 4000 video card
  • Software: Amira (multiple versions, most recent v6.0.1), ImageQuest, Fiji/ImageJ, 3D_Slicer, and Image Composite Editor.

This computer is primarily devoted to Amira, an extremely robust software package that allows for detailed data visualization and analysis.

Windows Workstation #2

  • HP EliteDesk 800 G1 TWR (Windows 7)
  • Intel Core i7-4790 CPU 3.60 GHz
  • 16 GB installed RAM
  • Nividia Quadro 4000 video card
  • Software: ImageJ, 3D_Slicer, Leica LAS-AF Lite, FEI MAPS, Image Composite Editor, Nikon EZ-C1 Free Viewer, TSL OIM, as well as msIQuant for MALDI quantitation.

This Windows computer is the most recent addition to our data analysis room and will be available for users who would like to transfer or analyze data in a Windows environment. This computer is equipped with a range of software packages, from general open source software such as ImageJ, to more advanced software packages specific to particular imaging modalities (e.g. FEI MAPS).

Linux Workstation #1

  • HP Z1
  • Intel Xeon CPU E3-1245 V2 3.40 GHz
  • 32 GB installed RAM
  • VESA framebuffer graphics card
  • Software: ImageJ, MicroView, GIMP, Matlab

This powerful computer is equipped with a high resolution 27" monitor (2560x1440 resolution, 60Hz refresh rate), making it an excellent choice for image analysis. CHTP users can login with their individual CWL credentials, establishing an automatic connection to their Teamshare folder, which allows for quick and easy access to the required data. Currently installed software packages include ImageJ, MicroView, and GIMP (similar to Photoshop).

Linux Workstation #2

  • HP Z1
  • Intel Xeon CPU E3-1245 V2 3.40 GHz
  • 16 GB installed RAM
  • VESA framebuffer graphics card
  • Software: ImageJ, MicroView, GIMP, Matlab

This powerful computer is equipped with a high resolution 27" monitor (2560x1440 resolution, 60Hz refresh rate), making it an excellent choice for image analysis. CHTP users can login with their individual CWL credentials, establishing an automatic connection to their Teamshare folder, ultimately allowing for quick and easy access to the required data. Currently installed software packages include ImageJ, MicroView, and GIMP (similar to Photoshop).

Scanco Workstation (OpenVMS)

This workstation is connected to the specimen micro-CT scanner for convenient analysis of micro-CT data. When the micro-CT images have finished reconstructing, the 3D dataset can be quickly accessed from the Scanco Workstation. This software allows users to segment and analyze their data in a quantitative manner, as well as generate 3D images of the scanned specimen. This software is particularly excellent for bone analysis, including volumetric bone mineral density calibrated to mg HA/cm3, as well as measurements of bone microarchitecture.

For users who require micro-CT scans, but prefer to analyze their data in different software, images can be converted to many different file formats including TIFF and DCM for subsequent analysis.

Software Links:

Amira: fei.com/software/amira-3d-for-life-sciences/

ImageJ: imagej.nih.gov/ij/

MicroView: microview.sourceforge.net

GIMP: gimp.org

3D_Slicer: slicer.org

Image Composite Editor: research.microsoft.com/en-us/um/redmond/projects/ice/

Leica LAS-AF Lite: leica-microsystems.com/products/microscope-software/software-for-life-science-research/las-x-powerful-and-flexible/

FEI MAPS: fei.com/software/maps/

Nikon EZ-C1 Free Viewer: nikon.com/products/microscope-solutions/support/download/software/confocal/c1_freevw_v390.htm

TSL OIM: edax.com/Products/EBSD/OIM-Data-Analysis-Microstructure-Analysis.aspx

msIQuant: maldi-msi.org/index.php?option=com_content&view=article&id=297&Itemid=96

 

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UBC Centre for High-Throughput Phenogenomics
2405 Wesbrook Mall | Vancouver, BC | Canada | V6T 1Z3
Tel: 604-822-6641

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