Experimental Histopathology Data Analysis

Aperio Image Analysis Suite

The Aperio Image Analysis suite of tools will be availble to you after you log in to Spectrum (https://eslidemanager.fhcrc.org) (IP-restricted to Fred Hutch - accessible only when on campus or via VPN). A quick-start guide is available for accessing and installing Spectrum, ImageScope and Second Slide softwares. It includes the following analysis tools:

  • True stain separation
  • Nuclear quantification
  • Microvessel analysis
  • Area quantification
  • Membrane quantification
  • Rare event detection
  • Multi-stain quantification
  • Cytoplasm quantification
  • Genie histology pattern recognition

Image analysis will be accomplished using a team approach in order to ensure proper training, selection of region on interest (ROI), and full development and testing of analysis solutions. These teams will include the investigator(s), pathologists, and Experimental Histopathology staff. Please contact Experimental Histopathology to set up a meeting of your team.

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HALO Image Analysis Modules

HALO is image analysis software created by Indica Labs which use innovative algorithms to report morphological and multiplexed expression data on a cell-by-cell basis across entire tissue sections.  After running an analysis module, users can click on any cell in an image and immediately see analysis outputs for that specific cell.

Sorting and filtering capabilities allow the user to mine millions of cells while visually assessing corresponding cell populations. For example, cells can be sorted according to biomarker intensity and then immediately locate those cells with highest intensity within the image.  The algorithms are packaged as individual modules for clients to choose from.  HALO modules can analyze a variety of image formats, and include the ability to import metadata with images from some proprietary systems (i.e. Aperio or InForm).










There are several modules available to Experimental Histopathology clients for analyzing both brightfield and fluorescent images.

Current Modules Available:


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