Index

A

add_box() (spatialproteomics.pl.plot.PlotAccessor method) add_channel() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) add_feature() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) add_label_property() (spatialproteomics.la.label.LabelAccessor method) add_label_type() (spatialproteomics.la.label.LabelAccessor method) add_labels() (spatialproteomics.la.label.LabelAccessor method) add_labels_from_dataframe() (spatialproteomics.la.label.LabelAccessor method) add_layer() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) add_layer_from_dataframe() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) add_neighborhood_obs() (spatialproteomics.nh.neighborhood.NeighborhoodAccessor method) add_neighborhoods_from_dataframe() (spatialproteomics.nh.neighborhood.NeighborhoodAccessor method) add_obs_from_dataframe() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) add_observations() (in module spatialproteomics.pp.preprocessing) (spatialproteomics.pp.preprocessing.PreprocessingAccessor method)

add_properties() (spatialproteomics.la.label.LabelAccessor method) (spatialproteomics.nh.neighborhood.NeighborhoodAccessor method) add_quantification() (in module spatialproteomics.pp.preprocessing) (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) add_quantification_from_dataframe() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) add_segmentation() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) annotate() (spatialproteomics.pl.plot.PlotAccessor method) apply() (in module spatialproteomics.pp.preprocessing) (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) astir() (in module spatialproteomics.tl.tool) (spatialproteomics.tl.tool.ToolAccessor method) autocrop() (spatialproteomics.pl.plot.PlotAccessor method)

C

cellpose() (in module spatialproteomics.tl.tool) (spatialproteomics.tl.tool.ToolAccessor method) colorize() (spatialproteomics.pl.plot.PlotAccessor method) compute_graph_features() (spatialproteomics.nh.neighborhood.NeighborhoodAccessor method) compute_neighborhoods() (spatialproteomics.image_container.ImageContainer.ImageContainer method)

compute_neighborhoods_delaunay() (spatialproteomics.nh.neighborhood.NeighborhoodAccessor method) compute_neighborhoods_knn() (spatialproteomics.nh.neighborhood.NeighborhoodAccessor method) compute_neighborhoods_radius() (spatialproteomics.nh.neighborhood.NeighborhoodAccessor method) convert_to_8bit() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) convert_to_anndata() (spatialproteomics.tl.tool.ToolAccessor method) convert_to_spatialdata() (spatialproteomics.tl.tool.ToolAccessor method)

D

deselect() (spatialproteomics.la.label.LabelAccessor method) (spatialproteomics.nh.neighborhood.NeighborhoodAccessor method)

downsample() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) drop_layers() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method)

F

filter_by_obs() (in module spatialproteomics.pp.preprocessing) (spatialproteomics.pp.preprocessing.PreprocessingAccessor method)

G

get_bbox() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) get_channels() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) get_disconnected_cell() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method)

get_layer_as_df() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) get_neighborhood_composition() (spatialproteomics.image_container.ImageContainer.ImageContainer method) grow_cells() (in module spatialproteomics.pp.preprocessing) (spatialproteomics.pp.preprocessing.PreprocessingAccessor method)

I

ImageContainer (class in spatialproteomics.image_container.ImageContainer)

imshow() (spatialproteomics.pl.plot.PlotAccessor method)

L

LabelAccessor (class in spatialproteomics.la.label)

M

mask_cells() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) mask_region() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) merge_segmentation() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) mesmer() (in module spatialproteomics.tl.tool) (spatialproteomics.tl.tool.ToolAccessor method) module spatialproteomics.image_container.ImageContainer spatialproteomics.la.label spatialproteomics.nh.neighborhood spatialproteomics.pl.plot spatialproteomics.pp.preprocessing spatialproteomics.tl.tool

N

NeighborhoodAccessor (class in spatialproteomics.nh.neighborhood)

normalize() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method)

P

PlotAccessor (class in spatialproteomics.pl.plot) predict_cell_subtypes() (in module spatialproteomics.la.label) (spatialproteomics.la.label.LabelAccessor method)

predict_cell_types_argmax() (in module spatialproteomics.la.label) (spatialproteomics.la.label.LabelAccessor method) PreprocessingAccessor (class in spatialproteomics.pp.preprocessing)

R

remove_label_type() (spatialproteomics.la.label.LabelAccessor method) remove_outlying_cells() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) render_labels() (spatialproteomics.pl.plot.PlotAccessor method)

render_neighborhoods() (spatialproteomics.pl.plot.PlotAccessor method) render_obs() (spatialproteomics.pl.plot.PlotAccessor method) render_segmentation() (spatialproteomics.pl.plot.PlotAccessor method) rescale() (spatialproteomics.pp.preprocessing.PreprocessingAccessor method)

S

scatter() (spatialproteomics.pl.plot.PlotAccessor method) scatter_labels() (spatialproteomics.pl.plot.PlotAccessor method) set_label_colors() (spatialproteomics.la.label.LabelAccessor method) set_label_level() (spatialproteomics.la.label.LabelAccessor method) set_label_name() (spatialproteomics.la.label.LabelAccessor method) set_neighborhood_colors() (spatialproteomics.nh.neighborhood.NeighborhoodAccessor method) set_neighborhood_name() (spatialproteomics.nh.neighborhood.NeighborhoodAccessor method) show() (spatialproteomics.pl.plot.PlotAccessor method) spatialproteomics.image_container.ImageContainer module spatialproteomics.la.label module

spatialproteomics.nh.neighborhood module spatialproteomics.pl.plot module spatialproteomics.pp.preprocessing module spatialproteomics.tl.tool module stardist() (in module spatialproteomics.tl.tool) (spatialproteomics.tl.tool.ToolAccessor method)

T

threshold() (in module spatialproteomics.pp.preprocessing) (spatialproteomics.pp.preprocessing.PreprocessingAccessor method) threshold_labels() (in module spatialproteomics.la.label) (spatialproteomics.la.label.LabelAccessor method)

ToolAccessor (class in spatialproteomics.tl.tool) transform_expression_matrix() (in module spatialproteomics.pp.preprocessing) (spatialproteomics.pp.preprocessing.PreprocessingAccessor method)