Index

_

__call__() (squidpy.gr.neighbors.DistanceIntervalPostprocessor method) (squidpy.gr.neighbors.PercentilePostprocessor method) (squidpy.gr.neighbors.TransformPostprocessor method)

A

add_img() (squidpy.im.ImageContainer method) alpha (squidpy.experimental.im.MacenkoParams attribute)

apply() (squidpy.im.ImageContainer method) assign_stitch_groups() (in module squidpy.experimental.tl)

B

beta (squidpy.experimental.im.MacenkoParams attribute) (squidpy.experimental.im.VahadaneParams attribute) build() (squidpy.gr.neighbors.DelaunayBuilder method) (squidpy.gr.neighbors.GraphBuilder method) (squidpy.gr.neighbors.GraphBuilderCSR method) (squidpy.gr.neighbors.GridBuilder method) (squidpy.gr.neighbors.KNNBuilder method) (squidpy.gr.neighbors.RadiusBuilder method)

build_graph() (squidpy.gr.neighbors.DelaunayBuilder method) (squidpy.gr.neighbors.GraphBuilder method) (squidpy.gr.neighbors.GraphBuilderCSR method) (squidpy.gr.neighbors.GridBuilder method) (squidpy.gr.neighbors.KNNBuilder method) (squidpy.gr.neighbors.RadiusBuilder method)

C

calculate_image_features() (in module squidpy.experimental.im) (in module squidpy.im) calculate_niche() (in module squidpy.gr) calculate_tiling_qc() (in module squidpy.experimental.tl) candidate_min_iou (squidpy.experimental.tl.StitchParams attribute) centrality_scores() (in module squidpy.gr) (in module squidpy.pl) close_radius (squidpy.experimental.tl.StitchParams attribute) co_occurrence() (in module squidpy.gr) (in module squidpy.pl) combine() (squidpy.gr.neighbors.DelaunayBuilder method) (squidpy.gr.neighbors.GraphBuilder method) (squidpy.gr.neighbors.GraphBuilderCSR method) (squidpy.gr.neighbors.GridBuilder method) (squidpy.gr.neighbors.KNNBuilder method) (squidpy.gr.neighbors.RadiusBuilder method)

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) decompose_stains() (in module squidpy.experimental.im) DelaunayBuilder (class in squidpy.gr.neighbors)

distance_tol (squidpy.experimental.tl.StitchParams attribute) (squidpy.experimental.tl.TilingQCParams attribute) DistanceIntervalPostprocessor (class in squidpy.gr.neighbors) distances (squidpy.gr.SpatialNeighborsResult attribute)

E

estimate_white_point() (in module squidpy.experimental.im)

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) fit_stain_reference() (in module squidpy.experimental.im) 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) GraphBuilder (class in squidpy.gr.neighbors) GraphBuilderCSR (class in squidpy.gr.neighbors)

GraphMatrixT (in module squidpy.gr) (in module squidpy.gr.neighbors) GraphPostprocessor (in module squidpy.gr.neighbors) GridBuilder (class in squidpy.gr.neighbors)

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) interval (squidpy.gr.neighbors.DistanceIntervalPostprocessor attribute)

K

KNNBuilder (class in squidpy.gr.neighbors)

L

lambda1 (squidpy.experimental.im.VahadaneParams attribute) library_ids (squidpy.im.ImageContainer property) ligrec() (in module squidpy.gr) (in module squidpy.pl)

load() (squidpy.im.ImageContainer class method) luminosity_threshold (squidpy.experimental.im.ReinhardParams attribute)

M

MacenkoParams (class in squidpy.experimental.im) mask_background (squidpy.experimental.im.ReinhardParams attribute) mask_graph() (in module squidpy.gr) max_concentrations (squidpy.experimental.im.StainReference attribute) max_contour_points (squidpy.experimental.tl.TilingQCParams attribute) merfish() (in module squidpy.datasets) method (squidpy.experimental.im.StainReference attribute) mibitof() (in module squidpy.datasets) min_area (squidpy.experimental.tl.TilingQCParams attribute) min_edge_coverage (squidpy.experimental.tl.StitchParams attribute) min_edge_length (squidpy.experimental.tl.StitchParams attribute)

min_edge_length_ratio (squidpy.experimental.tl.StitchParams attribute) module squidpy squidpy.datasets squidpy.experimental squidpy.gr squidpy.gr.neighbors squidpy.im squidpy.pl squidpy.read squidpy.tl mu (squidpy.experimental.im.StainReference attribute)

N

n_iter (squidpy.experimental.im.VahadaneParams attribute) nanostring() (in module squidpy.read) nhood_enrichment() (in module squidpy.gr) (in module squidpy.pl)

NhoodEnrichmentResult (class in squidpy.gr) normalize_stains() (in module squidpy.experimental.im)

P

percentile (squidpy.gr.neighbors.PercentilePostprocessor attribute) PercentilePostprocessor (class in squidpy.gr.neighbors) postprocessors() (squidpy.gr.neighbors.DelaunayBuilder method) (squidpy.gr.neighbors.GraphBuilder method) (squidpy.gr.neighbors.GraphBuilderCSR method) (squidpy.gr.neighbors.GridBuilder method) (squidpy.gr.neighbors.KNNBuilder method) (squidpy.gr.neighbors.RadiusBuilder method)

process() (in module squidpy.im)

R

RadiusBuilder (class in squidpy.gr.neighbors) random_state (squidpy.experimental.im.VahadaneParams attribute) ReinhardParams (class in squidpy.experimental.im)

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) sigma (squidpy.experimental.im.StainReference attribute) slideseqv2() (in module squidpy.datasets) sliding_window() (in module squidpy.tl) spatial_autocorr() (in module squidpy.gr) spatial_neighbors() (in module squidpy.gr) spatial_neighbors_delaunay() (in module squidpy.gr) spatial_neighbors_from_builder() (in module squidpy.gr) spatial_neighbors_grid() (in module squidpy.gr) spatial_neighbors_knn() (in module squidpy.gr) spatial_neighbors_radius() (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.experimental module squidpy.gr module squidpy.gr.neighbors module squidpy.im module squidpy.pl module squidpy.read module squidpy.tl module stain_matrix (squidpy.experimental.im.StainReference attribute) StainReference (class in squidpy.experimental.im) StitchParams (class in squidpy.experimental.tl) subset() (squidpy.im.ImageContainer method)

T

tiling_qc() (in module squidpy.experimental.pl) TilingQCParams (class in squidpy.experimental.tl)

transform (squidpy.gr.neighbors.TransformPostprocessor attribute) TransformPostprocessor (class in squidpy.gr.neighbors)

U

uncrop() (squidpy.im.ImageContainer class method) uns_params() (squidpy.gr.neighbors.DelaunayBuilder method) (squidpy.gr.neighbors.GraphBuilder method) (squidpy.gr.neighbors.GraphBuilderCSR method) (squidpy.gr.neighbors.GridBuilder method) (squidpy.gr.neighbors.KNNBuilder method) (squidpy.gr.neighbors.RadiusBuilder method)

V

VahadaneParams (class in squidpy.experimental.im) 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)

W

white_point (squidpy.experimental.im.StainReference attribute)

Z

zscore (squidpy.gr.NhoodEnrichmentResult attribute)