ISON supports different lattice geometries for spatial transcriptomics data.
You can select the grid layout to define neighbor relationships for adjacency matrices.
| Option | Description | Default |
|---|---|---|
square |
Square grid layout | Yes |
hexagonal |
Hexagonal grid layout | |
triangle |
Triangular grid layout (same nearest-neighbor structure as hexagonal) |
Specify the lattice type using the --lattice argument when running run-ison.py:
python run-ison.py --lattice square
python run-ison.py --lattice hexagonal
python run-ison.py --lattice triangle