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Virtual Microscopy / Image Analysis

PRECISION Image Analysis Toolbox:

We recently purchased the PRECISION Image Analysis Toolbox. This sophisticated software package will allow us to take our digital slide scanning to a whole new level by offering image analysis options. We are able to perform relative quantification of histochemical and immunohistochemical stains. Contact the Image Analysis Specialist ( to set up a consultation and obtain pricing.

Area Quantification

Module includes brightfield color deconvlution and colocalization tools. Separate multiple stains in brighfield whole slide images. Once separated, intensity, stain area, and colocalization of each stain is calculated.

Whole Cell Quantification

Includes nuclear, membrane, and cytoplasmic analysis tools. Count stained cells or nuclei and measure stain intensity within nuclei, membranes, or cytoplasm.

Object Quantification

Includes Microvessel analysis and rare event detection. Measure Microvessel density (MVD), vessel area, vessel perimeter, and measure lumen. Find rare stained cells on a slide, locate objects using x-y coordinates on slide, sort by size or intensity.

Application of Algorithms (

  • Genie : Histology pattern recognition tool
    • Automate selection ov viable tumor for analysis in xenografts
    • Automatically select tumor cells for analysis and exclude stroma in IHC stained tissue sections
    • Measure glomerular area in IHC-stained kidney section
  • Colocalization
  • Color Deconvolution
    • Automate selection of viable tumor for analysis in xenografts
    • Comparing amount of fibrosis in mouse heart between treatment groups
    • Quantification of area and intensity of beta-amyloid staining in mouse brain
    • Separation of three stains in pancreatic tissue selection
  • Membrane
    • Quantification of Her2-positive cells in breast tumor
  • Nuclear
    • Count number of Ki-67 positive nuclei to quantify cell proliferation in breast tumor
    • Automatically select tumor cells for analysis and exclude stroma in IHC stained tissue
  • Microvessel Density
    • Calculate microvessel density within viable tumor of CD34-stained xenografts
  • Rare Event Detection
  • TMALab II : Tissue Micro Array Analysis
    • The auto-segmentation feature within Aperio’s TMALab module is used to segment tissue cores on four slides cut from the same TMA block. Once all four slides are segmented, any TMA core can be selected from the TMA map to view the four stained spots associated with that core.

** Positive Pixel Count is offered free to everyone and the user guide is available here (insert link to pdf)


Submitting Slides for Scanning:

All services requests are performed electronically through our online submission system eRAMP which is interfaced to eREQUEST.  



  • Link to our Spectrum website:
  • Contact Jenny Bolon for log in information and password resets.
  • Creating Publication Quality Images (link .pdf)
  • Download ImageScope Software free from Aperio and click on Download ImageScope at the very top of the page.