Examples

This section contains various short examples showcasing core squidpy functionalities.

Graph

This section contains various examples from the squidpy.gr module.

Compute centrality scores

Compute Co-occurrence probability

Compute interaction matrix

Receptor-ligand analysis

Compute Moran’s I score

Neighbors enrichment analysis

Compute Ripley’s K function

Building spatial neighbors graph

Image

This section contains various examples from the squidpy.im module.

ImageContainer object

Crop images with ImageContainer

Process a high-resolution image

Convert to grayscale

Smooth an image

Cell-segmentation for fluorescence images

Cell-segmentation for H&E stains

Extract image features

Extract summary features

Extract histogram features

Extract texture features

Extract segmentation features

Extract custom features