Core Facilities and Platforms

StemCore Laboratories

StemCore Laboratories

Spatial Biology

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OVERVIEW

Spatial biology preserves the tissue context of molecular measurements, revealing how cells interact within their native architecture. Rather than dissociating tissue into single cells, spatial methods map gene expression or protein abundance while maintaining positional information - critical for understanding tissue organization, cell-cell communication, and microenvironment effects.

We currently offer two complementary spatial biology platforms: Visium HD for spatial transcriptomics and CellDIVE for highly multiplexed protein imaging.

Visium HD Spatial Transcriptomics

Equipment

  • 10x Genomics Visium HD with CytAssist
    • Resolution: 2µm (typically binned to 8µm for analysis)
    • Coverage area: up to 6.5mm x 6.5mm per capture area
    • Whole transcriptome spatial gene expression
    • Compatible with fresh frozen or FFPE tissue sections via CytAssist

Applications

  • Map tumor architecture and identify spatial patterns of gene expression across malignant, stromal, and immune compartments
  • Trace developmental trajectories and tissue patterning by linking gene expression to anatomical structures
  • Define cellular niches and microenvironments by identifying spatially restricted gene programs
  • Characterize immune infiltration patterns and interface regions between tissue compartments
  • Discover region-specific biomarkers and validate spatial expression of therapeutic targets

Sample Requirements

  • Tissue sections on Superfrost Plus slides
    • Section thickness: 10-20µm
    • Fresh frozen: Any species
    • FFPE: Mouse or human only

Workflow

  1. Contact Kathy to confirm sample and workflow type
  2. QC samples to ensure sufficient RNA quality
  3. Submit request via Idea Elan Infinity
  4. Submit tissue sections
  5. Image slides and select region of interest (ROI)
  6. Prepare single-cell library from selected ROI
  7. Sequence on NovaSeq X
  8. Data delivered via BaseSpace for use in SpaceRanger and Loupe

Pricing

From $4000/slide
 

CellDIVE Multiplexed Imaging

Equipment

  • Leica CellDIVE
    • 1-60+ protein multiplexed imaging capability
      • Scale your panel as small or large as you like
    • ~235nm resolution with subcellular detail
      • Typical 20x resolution with whole slide automatic stitching
    • Cyclic staining and imaging
      • Images are built up by 4 channels at a time; Stain -> Image -> Blank -> Repeat
    • BAB200 robot for automated cyclic staining and destaining - enabling high-throughput multiplexed analysis
      • Set and forget week's worth of staining in a morning
    • Apply flow cytometry-style marker panels in spatial context

Sample Requirements

  • Tissue sections on Superfrost slides
    • Fresh frozen or FFPE tissue compatible
    • Avoid slide edges - imaging covers most of slide area but edges should be clear
       

Workflow

  1. Contact Damian to discuss your project and antibody panel design
  2. Panel optimization and validation (if needed for new markers)
  3. Submit request via Idea Elan Infinity (https://secure17.ideaelan.com/uOttawa/Public/applogin.aspx)
  4. Submit tissue sections on Superfrost slides
  5. CellDIVE imaging performed
  6. Use our AIVIA PC platform to analyze your data with AI-powered algorithms
  7. Image data and analysis delivered

Note: With appropriate training, users can operate the CellDIVE platform independently.
 

Pricing

  • CellDIVE and BAB200 access: $10/hour

  • AIVIA analysis platform: Free

Total project costs depend on panel complexity, number of slides, and imaging time required. Contact Damian for project-specific quotes.

Getting Started