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Image Analysis

Image Analysis Software

The CSIF provides several several software, such as Huygens, Imaris or Volocity, for image analysis.


Workstations available within the CSIF:

In Beckman, Room B050, available for remote access:

  • CPU: 2 Xeon E5-2650 v3 @ 2.30GHz, 25MB (20 Cores)
  • RAM: 128G, 16X8G, 2133Mhz
  • GPU: 12 GB NVIDIA Quadro M6000

In Shriram, Room B023:

  • CPU: Xeon E5-2687 v2 @ 3.4GHz, 25 MB (8 Cores)
  • RAM: 128G, 16X8G, 1866MHz DDR3
  • GPU: 4GB NVIDIA Quadro K5000


Software available within the CSIF:

Imaris (Bitplane) 3D Image Analysis Software

Bitplane Imaris (http://www.bitplane.com/imaris/imaris) is ideal for visualization and analysis of 3D data sets as well as rendering animations.

RESERVE THIS WORKSTATION

LOCATION OF THE WORKSTATION: Beckamn Center, Room B050 (Remote instructions, please contact kamanl@stanford.edu)

LOCATION OF THE WORKSTATION: Shriram Center, Room B023 (not networked)

 


 

Volocity (PerkinElemer) 3D Image Analysis Software

RESERVE THIS WORKSTATION

LOCATION OF THE WORKSTATION: Beckman Center, Room B050 (Remote access, contact kamanl@stanford.edu)

SVI Huygens 3D Image Analysis Software

RESERVE THIS WORKSTATION

LOCATION OF THE WORKSTATION: Beckamn Center, Room B050 (Remote instructions, please contact kamanl@stanford.edu)

SoftWoRx and Monet (OMX/Delta Vision)

  • Deconvolution
  • Structured Illumination Microscopy (SIM)
  • Localization super-res microscopy analysis (STORM)

LOCATION OF THE WORKSTATION: Beckman Center, Room B050 (book time on OMX system to use).


Also Available:


MATLAB

RESERVE THIS WORKSTATION

LOCATION OF THE WORKSTATION: Shriram Center, Room B023


ZENPRO

RESERVE THIS WORKSTATION

LOCATION OF THE WORKSTATION: Shriram Center, Room B023


PHOTOSHOP

RESERVE THIS WORKSTATION

LOCATION OF THE WORKSTATION: Beckman Center, Room B050


FIJI

Download ImageJ and install it.

For use in your own lab, we recommend the use of Fiji, a free software for microscope images. Fiji is just ImageJ pre-packaged with Bio-Formats and other plugins. It also checks for updates automatically.


 

MICROVOLUTION Deconvolution Software

Real-time GPU-based 3D Deconvolution

For more information relating to Microvolution, please see: http://www.microvolution.com/technology

RESERVE THIS WORKSTATION

LOCATION OF THE WORKSTATION: Shriram Center, Room B023