Examples and Tutorials

Welcome to the tutorials and getting started guide for GRIDGENE!

Case Studies:

• Derive cancer and stroma masks in CosMx data
• Derive cancer and stroma masks in Xenium data
• Influence of Kernel size parameter
• Analysis of Cancer Stroma Interface in Xenium
• Identify specific populations and expand these masks - Single object
• Identify specific populations and expand these masks - multiobject
• Integration of GRIDGEN with cell segmentation
• Alternative ways of masking - SOM
  • SOM-based Cancer Stroma Identification
• Alternative ways of masking - KDTree
• General aspects of the pipeline
  • Define Cancer Stroma based on density of genes
  • How the same analysis look like using SOM.
• Tutorial Hierarchy analysis