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
• Built-in processing functions
• Custom processing functions
• Convert to grayscale
• Smooth an image
• Cell-segmentation for fluorescence images
• Cell-segmentation for H&E stains
• Extract image features
• Specify crop appearance
• Parallelization
• 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 {class}`squidpy.im.ImageContainer` class, which is the underlying data structure for the squidpy.im module.

• Show layers of the ImageContainer
• Crop images with ImageContainer
• Convert to grayscale using the apply method
• Generate cropped images from spots

Tools

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

• Calculate distances to a user-defined anchor point

Plotting

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

• Plot scatter plot in spatial coordinates
• Plot segmentation masks