HTRC Core Facility User Guide – Download guide to see annotated notes.

• LabVantage: Registering and Documenting Consent
  LabVantage: Reporting Features
  LabVantage: Creating Requests (Withdrawal of Samples)  Note: If you are requesting cancer specimens from biobanks, then you are required to submit and receive approval from the University of Chicago Comprehensive Cancer Center (UCCCC) Biospecimen Committee (UCCCC Biospecimen Request) PRIOR to submitting the withdrawal request in LabVantage.
• If in-person training is needed, it is provided free of charge by an HTRC staff member.
• Contact LabVantage@bsd.uchicago.edu for training.

• Materials provided include: charged slides, OCT, brushes, pencils, coverslips.
• Pen and paper recommended for taking notes.
• For training fees, please see our fee schedule.
• Contact mcheng1@bsd.uchicago.edu for training.

General Information:

• A viewing software is required to open the Aperio image files. ImageScope is a free viewing software provided by Leica.
  • Please review installation instructions prior to downloading ImageScope.
  • Download ImageScope software
  • Please review the ImageScope User Manual
  • Please note that ImageScope requires Windows OS.
  • ImageScope On Mac

Quantitative Analysis Information:

• If you would like to use the Aperio Analysis Software for quantitative analysis, you must complete training with the HTRC prior to use of the software. The software is complex, so please plan accordingly.
• Aperio Analysis Software training is provided by Dr. Christopher Weber, Assistant Professor of Pathology. Please email Dr. Weber to schedule a training session.
• Your slides must be scanned prior to Aperio Analysis Software training.
• Topics available for training include:
  • Algorithms (nuclear, membrane, microvessel, cytoplasmic, or stain intensity analysis; stain separation; rare event detection)
    Nuclear Algorithm Manual
    Membrane Algorithm Manual
    Colocalization Algorithm Manual
    Color Deconvolution Algorithm Manual
    Microvessel Algorithm Manual
    Cytoplasmic Algorithm Manual
    Rare Event Detection Algorithm Manual
    Positive Pixel Count Algorithm Manual
  • TMA Lab Manual (designed specifically for working with tissue microarrays)
  • Genie Manual (advanced training in histology pattern recognition software used to recognize and identify the histological patterns present in tissue)

  *Please review digital pathology fees for slide scanning and Quantitative Analysis training.

• For training fees, please see our fee schedule.
• Pen and paper recommended for taking notes.
• Contact mcheng1@bsd.uchicago.edu for training.

• LCM User Manual
  LCM Preparation for Frozen Sections
  Materials Needed for LCM
  H&E Frozen LCM
  H&E Paraffin LCM
• Materials provided include reagents for LCM H&E staining of frozen or formalin-fixed paraffin embedded slides.
• For training fees, please see our fee schedule.
• Contact DigitalPathology@bsd.uchicago.edu for training.