Index

A

add_img() (squidpy.im.ImageContainer method)

apply() (squidpy.im.ImageContainer method)

C

calculate_image_features() (in module squidpy.im) centrality_scores() (in module squidpy.gr) (in module squidpy.pl) co_occurrence() (in module squidpy.gr) (in module squidpy.pl) compute() (squidpy.im.ImageContainer method) concat() (squidpy.im.ImageContainer class method)

connectivities (squidpy.gr.SpatialNeighborsResult attribute) copy() (squidpy.im.ImageContainer method) count() (squidpy.gr.NhoodEnrichmentResult method) (squidpy.gr.SpatialNeighborsResult method) counts (squidpy.gr.NhoodEnrichmentResult attribute) crop_center() (squidpy.im.ImageContainer method) crop_corner() (squidpy.im.ImageContainer method)

D

data (squidpy.im.ImageContainer property)

distances (squidpy.gr.SpatialNeighborsResult attribute)

E

extract() (in module squidpy.pl)

F

features_custom() (squidpy.im.ImageContainer method) features_histogram() (squidpy.im.ImageContainer method) features_segmentation() (squidpy.im.ImageContainer method)

features_summary() (squidpy.im.ImageContainer method) features_texture() (squidpy.im.ImageContainer method) four_i() (in module squidpy.datasets) from_adata() (squidpy.im.ImageContainer class method)

G

generate_equal_crops() (squidpy.im.ImageContainer method)

generate_spot_crops() (squidpy.im.ImageContainer method)

I

ImageContainer (class in squidpy.im) imc() (in module squidpy.datasets) index() (squidpy.gr.NhoodEnrichmentResult method) (squidpy.gr.SpatialNeighborsResult method)

interaction_matrix() (in module squidpy.gr) (in module squidpy.pl)

L

library_ids (squidpy.im.ImageContainer property) ligrec() (in module squidpy.gr) (in module squidpy.pl)

load() (squidpy.im.ImageContainer class method)

M

mask_graph() (in module squidpy.gr) merfish() (in module squidpy.datasets) mibitof() (in module squidpy.datasets) module squidpy squidpy.datasets squidpy.gr squidpy.im squidpy.pl squidpy.read squidpy.tl

N

nanostring() (in module squidpy.read) nhood_enrichment() (in module squidpy.gr) (in module squidpy.pl)

NhoodEnrichmentResult (class in squidpy.gr)

P

process() (in module squidpy.im)

R

rename() (squidpy.im.ImageContainer method)

ripley() (in module squidpy.gr) (in module squidpy.pl)

S

save() (squidpy.im.ImageContainer method) sc_mouse_cortex() (in module squidpy.datasets) segment() (in module squidpy.im) (squidpy.im.SegmentationCustom method) (squidpy.im.SegmentationModel method) (squidpy.im.SegmentationWatershed method) SegmentationCustom (class in squidpy.im) SegmentationModel (class in squidpy.im) SegmentationWatershed (class in squidpy.im) sepal() (in module squidpy.gr) seqfish() (in module squidpy.datasets) shape (squidpy.im.ImageContainer property) show() (squidpy.im.ImageContainer method) slideseqv2() (in module squidpy.datasets) sliding_window() (in module squidpy.tl) spatial_autocorr() (in module squidpy.gr) spatial_neighbors() (in module squidpy.gr)

spatial_scatter() (in module squidpy.pl) spatial_segment() (in module squidpy.pl) SpatialNeighborsResult (class in squidpy.gr) squidpy module squidpy.datasets module squidpy.gr module squidpy.im module squidpy.pl module squidpy.read module squidpy.tl module subset() (squidpy.im.ImageContainer method)

U

uncrop() (squidpy.im.ImageContainer class method)

V

var_by_distance() (in module squidpy.pl) (in module squidpy.tl) visium() (in module squidpy.datasets) (in module squidpy.read) visium_fluo_adata() (in module squidpy.datasets) visium_fluo_adata_crop() (in module squidpy.datasets)

visium_fluo_image_crop() (in module squidpy.datasets) visium_hne_adata() (in module squidpy.datasets) visium_hne_adata_crop() (in module squidpy.datasets) visium_hne_image() (in module squidpy.datasets) visium_hne_image_crop() (in module squidpy.datasets) vizgen() (in module squidpy.read)

Z

zscore (squidpy.gr.NhoodEnrichmentResult attribute)