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.  

Our workstations are located at KCRB 3161 at the South Waterfront, and LBRB 481 on Marquam Hill, and are also accessible remotely. Contact us for more information. 

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. Imaris' 3D and 4D data visualization is where the platform shines. The platform is great for taking snapshots and creating animations of multidimensional data. 

  • 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. 
  • Further information and training videos can be found at the Imaris website.

Arivis Pro offers traditional and AI -based image segmentation and measurement tools in a custom pipeline environment that is scalable to large data sets. Features include:

  • 2D, 3D, and 4D data compatibility.
  • Traditional intensity based, machine leaning, and deep learning algorithms for segmentation. 
  • 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.
  • Custom tabulated exports. 
  • Tracking algorithms.
  • Neuron tracing

Visiopharm is an AI-driven image analysis software for digital pathology, enabling high-throughput evaluation of tissue samples. It includes customizable deep learning tools for training models on user data and supports complex cellular phenotyping through its Phenoplexing package for multiplex datasets.

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

  • 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.

The Elements software is directly compatible with .nd2 files from Nikon instruments. The platform features manual and automated image analysis techniques and image pre-processing functions.