Data Analysis

Tissue Clearing Imaging Systems Data Analysis

SCC staff partners with the University of Minnesota's Informatics Institute to offer cutting edge technological assisstance for data analysis.

  • Deformable registration (symmetric diffeomorphism) to the Allen Brain Atlas (ABA mouse P56 and rat currently) to either deform the atlas onto the image of the brain, or normalize the image of the brain into standard space.
  • Quantification of signal abundance in each ABA region in the original image
  • Estimation of cellular bodies count in each ABA region
  • Visualization using Bitplane Imaris, FIJI and open source software solutions
  • High speed networks (GSN )to enable data transfer, visualization, and analysis
  • Optimizing data handling and remote viewing for multi-terabyte data sets

Cell Count Data Analysis with Allen Brain Atlas, Brain Render, and Brain Globe Software

Brain Render Image

 

Brain Globe Image

 

Data Analysis Screen Shot

Imaging Informatics Contact Information

Imaging Informatics: Imaging Informatics services now include image analysis across many different imaging modalities. From fluorescence microscopy, to small animal imaging, neuroimaging and material science. Dr. Thomas Pengo provides analysis support for biological images (any instrument at the University Imaging Centers). Services include 2D image analysis (morphometry, particle analysis, densiometry, etc.) and 3D image analysis (volumetric sample measurement) reconstruction and image editing. Analysis is performed with FIJI, QuPath, MATLAB, Nikon Elements, Imaris, Amira, MATLAB and Python software.Analysis tools include open-source software and customized analysis pipelines.
Contact: Thomas Pengo, Ph.d., tpengo@umn.edu. Office: 1-220 CCRB