OHSU

Data Analysis

To view images acquired on our instruments on your own workstations, we encourage you to install open-source software, such as ImageJ or  FiJi, to run on your computers.  We also offer installation packages for free viewers of the manufacturer's software where available.

For more involved analysis of your imaging data we offer training on the high-end software packages available on our offline workstations in the facility.

 

 

Imaris (Bitplane)

We have a package of the following Imaris modules -

  • Imaris Basic
  • Measurement Pro
  • Imaris Coloc
  • Imaris Track
  • Filament Tracer
  • Imaris XT
  • Imaris In Press

 

 

 

 

This software suite allows users to

  • Visualize volume images and objects in real time using a rich selection of rendering modes.
  • Identify objects based on morphology, intensity, size and many more parameters.
  • Validate segmentation by superimposing objects on the original volume image.
  • Interact dynamically with individual objects.
  • Extract statistics for quantitative analysis.
  • Prepare images for publication and presentation.

Further information can be found at the Imaris website.  

 

 

SoftWoRx (Applied Precision)

The heart of this software package is its market-leading image restoration module for deconvolving 3D image stacks with a constrained iterative algorithm that retains quantitative image information for analysis. 

Further information can be found at the SoftWoRx website.

 

 

MetaMorph (Molecular Devices)

Some of the tools included with this package allow users to

  • Overlay or separate color channels
  • Color align images
  • Measure colocalization
  • Enhance contrast
  • Identify and measure objects
  • Create intensity profiles
  • View multi-dimensional data sets
  • View orthogonal planes
  • Stitch images
  • Create movies of time lapse and Z-series
  • Analyze motion using kymographs
  • Track objects

 

 

 

 

 

Further information can be found at the MetaMorph website.