This section contains various short examples showcasing core squidpy functionality.
This section contains various examples from the squidpy.gr module.
Compute centrality scores
Compute co-occurrence probability
Compute interaction matrix
Compute Moran’s I score
Neighbors enrichment analysis
Compute Ripley’s statistics
Compute Sepal score
Building spatial neighbors graph
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
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