Index

A

analyse() (ovrlpy.Ovrlp method)

ATERA_CTRLS (in module ovrlpy.io)

B

built-in function ovrlpy.cell_integrity_from_masks() ovrlpy.cell_integrity_from_transcripts() ovrlpy.io.read_Atera() ovrlpy.io.read_CosMx() ovrlpy.io.read_MERSCOPE() ovrlpy.io.read_Xenium() ovrlpy.plot_pseudocells() ovrlpy.plot_region_of_interest() ovrlpy.plot_signal_integrity() ovrlpy.plot_tissue() ovrlpy.plot_umap() ovrlpy.process_coordinates()

C

celltype_assignments (ovrlpy.Ovrlp attribute) celltype_centers (ovrlpy.Ovrlp attribute)

compute_VSI() (ovrlpy.Ovrlp method) COSMX_CTRLS (in module ovrlpy.io)

D

detect_doublets() (ovrlpy.Ovrlp method)

dtype (ovrlpy.Ovrlp attribute)

F

fit_pseudocells() (ovrlpy.Ovrlp method)

fit_signatures() (ovrlpy.Ovrlp method) fit_transcripts() (ovrlpy.Ovrlp method)

G

genes (ovrlpy.Ovrlp attribute)

gridsize (ovrlpy.Ovrlp attribute)

I

integrity_map (ovrlpy.Ovrlp attribute)

K

KDE_bandwidth (ovrlpy.Ovrlp attribute)

M

MERSCOPE_CTRLS (in module ovrlpy.io) min_distance (ovrlpy.Ovrlp attribute)

module ovrlpy ovrlpy.io

N

n_workers (ovrlpy.Ovrlp attribute)

O

origin (ovrlpy.Ovrlp attribute) ovrlpy module ovrlpy.cell_integrity_from_masks() built-in function ovrlpy.cell_integrity_from_transcripts() built-in function ovrlpy.io module ovrlpy.io.read_Atera() built-in function ovrlpy.io.read_CosMx() built-in function ovrlpy.io.read_MERSCOPE() built-in function

ovrlpy.io.read_Xenium() built-in function ovrlpy.Ovrlp (built-in class) ovrlpy.plot_pseudocells() built-in function ovrlpy.plot_region_of_interest() built-in function ovrlpy.plot_signal_integrity() built-in function ovrlpy.plot_tissue() built-in function ovrlpy.plot_umap() built-in function ovrlpy.process_coordinates() built-in function

P

patch_length (ovrlpy.Ovrlp attribute) pca (ovrlpy.Ovrlp attribute) pca_rgb (ovrlpy.Ovrlp attribute)

process_coordinates() (ovrlpy.Ovrlp method) pseudocell_integrity() (ovrlpy.Ovrlp method) pseudocells (ovrlpy.Ovrlp attribute)

S

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

signatures (ovrlpy.Ovrlp attribute) subset_transcripts() (ovrlpy.Ovrlp method)

T

transcripts (ovrlpy.Ovrlp attribute)

transform_pseudocells() (ovrlpy.Ovrlp method) transform_transcripts() (ovrlpy.Ovrlp method)

U

umap_2d (ovrlpy.Ovrlp attribute) UMAP_2D_PARAMS (in module ovrlpy)

umap_rgb (ovrlpy.Ovrlp attribute) UMAP_RGB_PARAMS (in module ovrlpy)

X

XENIUM_CTRLS (in module ovrlpy.io)