Data Analysis

In addition to our state of the art instrumentation, the Advanced Light Microscopy Core also specializes in a wide variety of image analysis strategies. Get trained to use our cutting edge 2D, 3D, and 4D analysis software packages to develop efficient and time saving workflows. Or, hire us to do the analysis for you! Contact us to get started on your image analysis journey. 


In order to help our users get the most out of their data, we offer the following services:

  1. We will consult with you about choosing the most appropriate data analysis tool for your data.
  2. We are also willing to discuss open-source tools, such as FIJI/ImageJ, to find a solution that can be run on your personal computer.  
  1. We offer our expertise to develop analysis workflows for your data based on your written request and/or after free consultation with us. 
  2. We also provide guidance on what details to include in your methods section to adequately describe our equipment and provide your readers with information to reproduce your experiment. 
  3. Lastly, we also help with data presentation. Whether you are preparing your data for publication in print or for a poster or platform presentation, we are happy to offer tips and tricks on how to make your images pop. 
  1. Customers can request core staff to run analyses. Billing will be hourly through iLab. 
  2. We also offer help with figure making and creating small videos such as animations of 3D data renderings, for presentations or online distribution.

Available Image Analysis Software Packages

Each of our high-end workstations supports a different combination of the following software packages.

Imaris (Bitplane)

Our fully featured licenses of Imaris include modules for measuring different kinds of multi-dimensional phenomena, including co-localization, tracing filaments, tracking objects, and stitching files.

 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.  

Vision4D (Arivis)

Arivis Vision4D works with multi-channel 3D and 4D images of almost unlimited size, independent of available RAM. It allows visualization, annotation and analysis of multi-dimensional images regardless of their size, and features magic-wand assisted object drawing tools that allow a user to paint and erase segments with automatic interpolation between planes.

syGlass (IstoVisio)

SyGlass is a software package for visualizing large-scale volumetric data through a Virtual Reality headset! Stereoscopic vision significantly improves perception of complex 3D structures and immersive rendering allows for rapid annotation of data directly in 3D. The software also offers data presentation tools to create animations and take snapshots for publication and presentation.

MetaMorph (Molecular Devices)

MetaMorph allows users to measure and categorize objects into discreet user-definable classes based on any combination of morphometric parameters, such as shape, size, or optical density.

See a list of workstations located at our location on Marquam Hill here.

See a list of workstations located at our location at the South Waterfront here.