Index

B

built-in function ovrlpy.compute_VSI() ovrlpy.detect_doublets() ovrlpy.get_pseudocell_locations() ovrlpy.io.read_CosMx() ovrlpy.io.read_MERFISH() ovrlpy.io.read_Xenium() ovrlpy.plot_region_of_interest() ovrlpy.plot_signal_integrity() ovrlpy.pre_process_coordinates() ovrlpy.run() ovrlpy.sample_expression_at_xy()

C

celltype_centers (ovrlpy.Visualizer attribute) celltype_class_assignments (ovrlpy.Visualizer attribute) celltyping_min_distance (ovrlpy.Visualizer attribute) celltyping_min_expression (ovrlpy.Visualizer attribute)

colors (ovrlpy.Visualizer attribute) colors_min_max (ovrlpy.Visualizer attribute) COSMX_CTRLS (in module ovrlpy.io) cumap_kwargs (ovrlpy.Visualizer attribute)

E

embedder_2d (ovrlpy.Visualizer attribute)

embedder_3d (ovrlpy.Visualizer attribute) embedding (ovrlpy.Visualizer attribute)

F

fit_pseudocells() (ovrlpy.Visualizer method)

fit_signatures() (ovrlpy.Visualizer method) fit_transcripts() (ovrlpy.Visualizer method)

G

genes (ovrlpy.Visualizer attribute)

I

integrity_map (ovrlpy.Visualizer attribute)

K

KDE_bandwidth (ovrlpy.Visualizer attribute)

M

MERFISH_CTRLS (in module ovrlpy.io) module ovrlpy ovrlpy.io

N

n_components_pca (ovrlpy.Visualizer attribute)

O

ovrlpy module ovrlpy.compute_VSI() built-in function ovrlpy.detect_doublets() built-in function ovrlpy.get_pseudocell_locations() built-in function ovrlpy.io module ovrlpy.io.read_CosMx() built-in function ovrlpy.io.read_MERFISH() built-in function

ovrlpy.io.read_Xenium() built-in function ovrlpy.plot_region_of_interest() built-in function ovrlpy.plot_signal_integrity() built-in function ovrlpy.pre_process_coordinates() built-in function ovrlpy.run() built-in function ovrlpy.sample_expression_at_xy() built-in function ovrlpy.Visualizer (built-in class)

P

pca_2d (ovrlpy.Visualizer attribute) pca_3d (ovrlpy.Visualizer attribute) plot_fit() (ovrlpy.Visualizer method) plot_region_of_interest() (ovrlpy.Visualizer method) plot_tissue() (ovrlpy.Visualizer method)

plot_umap() (ovrlpy.Visualizer method) pseudocell_df() (ovrlpy.Visualizer method) pseudocell_expression_samples (ovrlpy.Visualizer attribute) pseudocell_locations_x (ovrlpy.Visualizer attribute) pseudocell_locations_y (ovrlpy.Visualizer attribute)

S

SCALEBAR_PARAMS (in module ovrlpy) signal_map (ovrlpy.Visualizer attribute)

signatures (ovrlpy.Visualizer attribute) subsample_df() (ovrlpy.Visualizer method)

T

transform_pseudocells() (ovrlpy.Visualizer method)

transform_transcripts() (ovrlpy.Visualizer method)

U

UMAP_2D_PARAMS (in module ovrlpy)

umap_kwargs (ovrlpy.Visualizer attribute) UMAP_RGB_PARAMS (in module ovrlpy)

X

XENIUM_CTRLS (in module ovrlpy.io)