📅 Day 1: Foundations – Spatial Biology, Tissue Architecture & Digital Histopathology
- Core concepts of spatial biology: tissue architecture, cellular organization, and why location matters in health and disease
- Fundamentals of digital histopathology and how whole-slide images capture morphology
- Introduction to spatial omics and the Tumor Microenvironment (TME): heterogeneity, cellular neighborhoods, and key biological patterns
- How AI assists interpretation of tissue-level data (conceptual overview only – no algorithms)
🛠️ Hands-on
- Guided exploration of the Human Protein Atlas: locate and compare protein-expression patterns across normal and disease tissues
- Interpret spatial organization and note 2–3 biologically meaningful differences under mentor guidance
📅 Day 2: AI-Enabled Analysis – Tissue Image Interpretation & Spatial Omics
- Practical role of AI and computer vision in digital pathology: cell segmentation, pattern recognition, and image embeddings (high-level)
- Reading spatial gene-expression data: cellular heterogeneity and neighborhood analysis
- Linking imaging features with molecular (spatial omics) information for biomarker clues
- Live mentor walkthrough of interpretation logic using public datasets
🛠️ Hands-on
- Explore cell populations and spatial gene-expression patterns in CellxGene (public spatial datasets)
- Interpret a NanoString GeoMx spatial dataset: identify one clear biological pattern or neighborhood and record key observations
📅 Day 3: Application & Integration – From Spatial Insights to Precision Pathology Workflows
- AI-supported computational pathology in cancer and complex diseases: digital biomarkers and patient stratification
- Combining histopathology + spatial omics + AI insights for translational questions
- Designing a simple, realistic Spatial AI → Biomarker → Precision Medicine workflow
- Clinical relevance, current limitations, and emerging trends (foundation models at a conceptual level)
🛠️ Hands-on
- Work through a provided case-based AI spatial pathology workflow (tissue architecture → key findings → biomarker hypothesis)
- Complete a one-page conceptual workflow template for a research or clinical question of interest and receive brief mentor feedback
