Data Visualization, Processing, and Analysis

Acquiring high-quality data on our state-of-the-art instrumentation is only one chapter of your microscopy experiment. The Advanced Light Microscopy Core offers access to expertise on how to analyze a variety of image data. Get trained to use our commercial 2D, 3D, and 4D visualization and analysis packages that support sophisticated and time-saving workflows for data quantification. Or, consult with us on general approaches and tips and tricks for processing your data.  Contact us to get started on your image analysis journey.  


In order to help you get the most out of your data, we offer the following services:

  1. Free 30 min consultation and discussion about your analysis needs and our analysis platform recommendations.  

  1. One-on-one staff assistance to help develop an analysis pipeline that runs in ZEN, Arivis, or Imaris (billed at standard staff rate).  

  1. Consultation with our experts to help develop an analysis pipeline with FIJI/ImageJ (billed at consultation rate).   

  1. Help with data presentation for publication in print or for a poster or talk (billed at standard staff rate).  

  1. Help with exporting videos of 3D renderings and time-lapse data for presentations and for online distribution (billed at standard staff rate).  

  1. Staff-run analysis in ZEN or Imaris (billed at standard staff rate but contingent on staff availability). 

Data Visualization and Pre-Processing

We offer advice on common initial tasks, such as how to view multi-dimensional and large data sets, how to compare intensities, and how to pre-process data to facilitate downstream object recognition for analysis.  

We also support a set of software packages for denoising image data acquired using a variety of microscopy modalities.  

  • Imaris Clearview GPU-based deconvolution using PSF estimates for widefield, point scanning confocal, or spinning disk confocal microscopy.  

  • ZEN LSM Plus deconvolution algorithm for denoising laser-scanning confocal data. Data must be sampled at >0.6x Nyquist resolution in xy and z. 

  • ZEN GPU-based deconvolution for widefield data using theoretical and experimental PSF information.  

  • ZEN AI-based denoising of image data with no need for training sets or extensive parameter setting.   

Data Analysis Platforms

Our high-end workstations feature combinations of the following data analysis platforms. 

Our full-featured licenses of Imaris include modules for measuring different aspects of multi-dimensional data, including co-localization, tracing filaments, and tracking objects. 

 This software suite allows you to: 

  • Visualize 3D volumes and objects in real time using a rich selection of rendering modes. 
  • Assess signal or object overlap (co-localization) of channels. 
  • Trace filaments (neuronal processes, blood vessels). 
  • Track objects over time. 
  • AI and machine learning capabilities for segmentation and object classification. 
  • Identify and interact with objects based on morphology, intensity, size, and many more parameters. 
  • Extract statistics for quantitative analysis. 
  • Prepare images for publication and presentation. 
  • Further information and training videos can be found at the Imaris website.   

Our ZEN Desk software installations allow you to analyze microscopy data acquired on our many Zeiss instruments.  

  • ZEN Desk allows you to: 
  • Hierarchically segment objects for analysis using a step-by-step wizard. 
  • Assess signal overlap of channels (co-localization). 
  • Identify and interact with objects in 2D data sets using interactive pre-processing and conventional or AI-based thresholding. 
  • Classify and filter segmented objects based on morphology and intensity. 
  • Extract statistics for quantitative analysis. 

We also offer access two copies of Arivis Pro, one at our waterfront location (KCRB 3161) and one at our Marquam hill location (LBRB 481). Its flexible analysis pipelines and machine learning tools are scalable to very large data sets. Features include:

  • 2D, 3D, and 4D data compatibility.
  • A variety of approaches for image segmentation including traditional intensity based, machine leaning, and deep learning algorithms. 
  • Cellpose 2.0 trainable deep learning algorithm for faithful cell and nuclear segmentation/splitting. 
  • Custom pipeline design for flexible data pre-processing, segmentation, and feature extraction.
  • Ability to design custom excel exports. 
  • Tracking algorithms for time lapse data.
  • Neuron tracer algorithm utilizing probability maps.

syGlass (IstoVisio)

SyGlass is a software package for visualizing large-scale volumetric data through a Virtual Reality headset. Stereoscopic vision improves the perception of complex 3D structures and immersive rendering allows for rapid annotation of data directly in 3D.  

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.