Examples

This section contains various short examples showcasing core squidpy functionality.

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 statistics

Compute Sepal score

Building spatial neighbors graph

Image

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

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

Plot features in adata.obsm

ImageContainer

This section contains various examples for the squidpy.im.ImageContainer class, which is the underlying data structure for the squidpy.im module. See ImageContainer object for an entry point to the squidpy.im.ImageContainer.

Show layers of the ImageContainer

Crop images with ImageContainer

Plotting

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

Plot scatter plot in spatial coordinates

Plot segmentation masks