Usage

Launch jupyter lab or notebook and navigate to Griottes/example notebooks folder Try interactive version in Binder

• Working with 2D labels
  • I. Building graph
    • 1. Load image and mask of nuclei
    • 2. Generating a contact graph
    • 3. Plotting a representation of the graph
  • II. Estimating the properties of the tissue graphs
    • 1. Geometric graphs
    • 2. Delaunay graphs
    • 3. Comparing graph construction properties
    • 4. Populating nodes with different cell types
• Working with 3D spheroid data
  • I. Build the graph
    • 1. Load image and mask of nuclei
    • 2. Extracting single-cell fluorescence data
    • 3. Network representation of tissues in 3D
  • II. Spatial analysis of MSC spheroids
    • 1. Attributing layers to spheroids
    • 2. Comparing graph properties between spheroids
    • 3. Looking at the link statistics
    • 4. Looking at statistics over individual cells in the network
• Working with the 3D coordinates
  • I. Build the graph
    • 1. Load image and mask of nuclei
    • 2. Create Delaunay network
    • 3. Plot the graph
  • II. Analyzing the network properties
    • 1. Tissue composition
    • 2. Degree distribution within the tissue
    • 3. Subgraph clusters