Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z _ __repr__() (spateo.tools.cluster.spagcn_utils.GraphConvolution method) (spateo.tools.Label method) (spateo.tools.labels.Label method) (spateo.tools.ST_regression.generalized_lm.GLM method) (spateo.tools.ST_regression.generalized_lm.GLMCV method) __str__() (spateo.get_version.Version method) (spateo.tools.Label method) (spateo.tools.labels.Label method) __sub_inde (spateo.tools.cluster_lasso.Lasso attribute) (spateo.tools.Lasso attribute) __version__ (in module spateo) (in module spateo.get_version) _augment_labels() (in module spateo.segmentation.label) _blue() (in module spateo.plotting.static.utils) _cellpose() (in module spateo.segmentation.external.cellpose) _check_index_in_adata() (in module spateo.plotting.static.three_d_plot.morphogenesis_plots) _check_key_in_adata() (in module spateo.plotting.static.three_d_plot.morphogenesis_plots) _compute_gradient_image() (spateo.preprocessing.auxseg.LiveWireSegmentation method) (spateo.tools.live_wire.LiveWireSegmentation method) (spateo.tools.LiveWireSegmentation method) _compute_graph() (spateo.preprocessing.auxseg.LiveWireSegmentation method) (spateo.tools.live_wire.LiveWireSegmentation method) (spateo.tools.LiveWireSegmentation method) _construct_arrow() (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.arrow_model) _construct_line() (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.line_model) _convert_to_geo_dataframe() (in module spateo.plotting.static.utils) _create_labels() (in module spateo.segmentation.simulation) _create_spatial_adjacency() (in module spateo.segmentation.density) _datashade_points() (in module spateo.plotting.static.utils) _deepcell() (in module spateo.segmentation.external.deepcell) _dendrogram_sig() (in module spateo.plotting.static.utils) _dotplot() (spateo.plotting.static.dotplot.Dotplot static method) _embed_datashader_in_an_axis() (in module spateo.plotting.static.utils) _expand_labels() (in module spateo.segmentation.label) _find_peaks() (in module spateo.segmentation.label) _generate_random_labels() (in module spateo.segmentation.qc) _generate_vf_class() (in module spateo.tdr.widgets.morphogenesis) _geo_projection() (in module spateo.plotting.static.utils) _get_adata_color_vec() (in module spateo.plotting.static.utils) _get_array_values() (in module spateo.plotting.static.utils) _get_default_cmap() (in module spateo.plotting.static.three_d_plot.morphogenesis_plots) _get_extent() (in module spateo.plotting.static.utils) _get_mean_var() (in module spateo.preprocessing.transform) _get_optimal_mapping_relationship() (in module spateo.tools.paste) _get_p_value() (in module spateo.tools.ST_regression.regression_utils) _grad_nl() (in module spateo.tools.ST_regression.generalized_lm) _green() (in module spateo.plotting.static.utils) _initial_nb_params() (in module spateo.segmentation.icell) _interactive_pick() (in module spateo.tdr.widgets.pick) _interactive_plotter() (in module spateo.tdr.widgets.utils) _interactive_rectangle_clip() (in module spateo.tdr.widgets.clip) _label_connected_components() (in module spateo.segmentation.label) _loss() (in module spateo.tools.ST_regression.generalized_lm) _mainplot() (spateo.plotting.static.dotplot.Dotplot method) _mask_cells_from_stain() (in module spateo.segmentation.icell) _mask_nuclei_from_stain() (in module spateo.segmentation.icell) _matplotlib_points() (in module spateo.plotting.static.utils) _nl() (in module spateo.tools.ST_regression.generalized_lm) _normalize_data() (in module spateo.preprocessing.normalize) _o3d2pv() (in module spateo.tdr.models.mesh.reconstruction_methods) _plot_colorbar() (spateo.plotting.static.dotplot.Dotplot method) _plot_legend() (spateo.plotting.static.dotplot.Dotplot method) _plot_size_legend() (spateo.plotting.static.dotplot.CCDotplot method) (spateo.plotting.static.dotplot.Dotplot method) _plot_traj() (in module spateo.plotting.static.utils) _plot_var_groups_brackets() (spateo.plotting.static.dotplot.Dotplot static method) _prox() (spateo.tools.ST_regression.generalized_lm.GLM method) _pv2o3d() (in module spateo.tdr.models.mesh.reconstruction_methods) _rand_binary_array() (in module spateo.tools.labels) _red() (in module spateo.plotting.static.utils) _replace_labels() (in module spateo.segmentation.label) _sanitize_labels() (in module spateo.segmentation.external.stardist) _scale_model_by_distance() (in module spateo.tdr.models.utilities.model_utils) _scale_model_by_scale_factor() (in module spateo.tdr.models.utilities.model_utils) _scatter_projection() (in module spateo.plotting.static.utils) _schc() (in module spateo.segmentation.density) _score_pixels() (in module spateo.segmentation.icell) _segment_densities() (in module spateo.segmentation.density) _select_font_color() (in module spateo.plotting.static.utils) _set_jupyter() (in module spateo.plotting.static.three_d_plot.three_dims_plotter) _smooth_image() (spateo.preprocessing.auxseg.LiveWireSegmentation method) (spateo.tools.live_wire.LiveWireSegmentation method) (spateo.tools.LiveWireSegmentation method) _stardist() (in module spateo.segmentation.external.stardist) _stardist_big() (in module spateo.segmentation.external.stardist) _themes (in module spateo.configuration) _threshold_gradient_image() (spateo.preprocessing.auxseg.LiveWireSegmentation method) (spateo.tools.live_wire.LiveWireSegmentation method) (spateo.tools.LiveWireSegmentation method) _to_hex() (in module spateo.plotting.static.utils) _update_var_groups() (spateo.plotting.static.dotplot.Dotplot method) _watershed() (in module spateo.segmentation.label) _z() (in module spateo.tools.ST_regression.generalized_lm) A A (class in spateo.tdr) (class in spateo.tdr.widgets) (class in spateo.tdr.widgets.interpolation_nn) acceleration() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.morphogenesis_plots) ADATA_AGG_TYPE (spateo.configuration.SpateoAdataKeyManager attribute) ADATA_DEFAULT_TYPE (spateo.configuration.SpateoAdataKeyManager attribute) adata_is_type() (spateo.configuration.SpateoAdataKeyManager method) adata_to_frame() (in module spateo.plotting.static.dotplot) ADATA_TYPE_KEY (spateo.configuration.SpateoAdataKeyManager attribute) ADATA_UMI_TYPE (spateo.configuration.SpateoAdataKeyManager attribute) add_contours() (in module spateo.tools.roi) add_contrastive_label() (in module spateo.tools.spatial_impute.impute) add_dendrogram() (spateo.plotting.static.dotplot.Dotplot method) add_eh_boundary() (in module spateo.digitization.utils) add_gh_boundary() (in module spateo.digitization.utils) add_image_layer() (in module spateo.io.image_utils) add_legend() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plotter) add_model() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plotter) add_model_labels() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.label_utils) add_num_legend() (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plotter) add_outline() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plotter) add_str_legend() (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plotter) add_text() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plotter) adjusted_rand_score() (in module spateo.segmentation.benchmark) affine_transform() (in module spateo.tools.utils) AffineTrans() (in module spateo.tools) (in module spateo.tools.coarse_align) align_slices_pca() (in module spateo.tools) (in module spateo.tools.coarse_align) AlignmentRefiner (class in spateo.segmentation.align) all_senders_effect_on_receiver() (spateo.tools.ST_regression.spatial_regression.Base_Model method) alpha_shape() (in module spateo.io) (in module spateo.io.bbs) (in module spateo.plotting.static.utils) alpha_shape_mesh() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.reconstruction_methods) Application (in module spateo.segmentation.external.deepcell) apply_threshold() (in module spateo.segmentation.utils) archetypes() (in module spateo.tools) (in module spateo.tools.architype) archetypes_genes() (in module spateo.tools) (in module spateo.tools.architype) arrowed_spines() (in module spateo.plotting.static.utils) assignment() (spateo.segmentation.vi.NegativeBinomialMixture method) augment_labels() (in module spateo.segmentation) (in module spateo.segmentation.label) AUGMENTED_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) average_precision() (in module spateo.segmentation.benchmark) AvgReadout (class in spateo.tools.spatial_impute.impute_model) axolotl() (in module spateo.sample_data) B B (class in spateo.tdr) (class in spateo.tdr.widgets) (class in spateo.tdr.widgets.interpolation_nn) ball_pivoting_mesh() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.reconstruction_methods) base (spateo.plotting.static.dotplot.CCDotplot attribute) Base_Model (class in spateo.tools.ST_regression.spatial_regression) batch_grad() (in module spateo.tools.ST_regression.generalized_lm) beta0_ (spateo.tools.ST_regression.generalized_lm.GLM attribute) (spateo.tools.ST_regression.generalized_lm.GLMCV attribute) beta_ (spateo.tools.ST_regression.generalized_lm.GLM attribute) (spateo.tools.ST_regression.generalized_lm.GLMCV attribute) bin_adata() (in module spateo.preprocessing.aggregate) bin_indices() (in module spateo.io.utils) bin_matrix() (in module spateo.io.utils) binary_morani_result() (in module spateo.segmentation.moran) BINS_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) box_qc_regions() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.agg) bright_10 (in module spateo.plotting.static.colorlabel) button_pressed() (spateo.preprocessing.auxseg.LiveWireSegmentation method) C cal_cell_area() (in module spateo.segmentation.utils) cal_ncenter() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.tree) calc_1nd_moment() (in module spateo.tools.ST_regression.generalized_lm) (in module spateo.tools.ST_regression.spatial_regression) (in module spateo.tools.utils) calc_tree_length() (in module spateo.tdr.widgets.changes) calculate_adj_matrix() (in module spateo.tools.cluster.spagcn_utils) calculate_distance() (in module spateo.tools.find_neighbors) calculate_p() (in module spateo.tools.cluster.spagcn_utils) Category_Model (class in spateo.tools), [1] (class in spateo.tools.ST_regression) (class in spateo.tools.ST_regression.spatial_regression) CCDotplot (class in spateo.plotting.static.dotplot) cell_directions() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) cell_marginals() (in module spateo.segmentation.bp) cellbin_morani() (in module spateo.tools) (in module spateo.tools.spatial_degs) Cellpose (in module spateo.segmentation.external.cellpose) cellpose() (in module spateo.segmentation) (in module spateo.segmentation.external.cellpose) center_align() (in module spateo.tools) (in module spateo.tools.paste) center_NMF() (in module spateo.tools.paste) center_to_zero() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.model_utils) centroids() (in module spateo.io.utils) changes_along_branch() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.changes) changes_along_line() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.changes) changes_along_shape() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.changes) check_adata_is_type() (spateo.configuration.SpateoAdataKeyManager method) check_backend() (in module spateo.tools.paste) check_colornorm() (in module spateo.plotting.static.utils) check_exp() (in module spateo.tools.paste) check_spatial_coords() (in module spateo.tools.paste) circle() (in module spateo.segmentation.utils) clahe() (in module spateo.segmentation.utils) classification_stats() (in module spateo.segmentation.benchmark) clean_mesh() (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.mesh_utils) clear() (in module spateo.tools.roi) collect_models() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.model_utils) color (in module spateo.tools.roi) color_index (in module spateo.tools.roi) color_label() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.colorlabel) compare() (in module spateo.segmentation) (in module spateo.segmentation.benchmark) compute_coeff_significance() (spateo.tools.ST_regression.spatial_regression.Base_Model method) compute_pca_components() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) compute_shortest_path() (in module spateo.tools) (in module spateo.tools.live_wire) (spateo.preprocessing.auxseg.LiveWireSegmentation method) (spateo.tools.live_wire.LiveWireSegmentation method) (spateo.tools.LiveWireSegmentation method) compute_smallest_distance() (in module spateo.tools.utils) compute_spatial_weights() (spateo.tools.ST_regression.spatial_regression.Base_Model method) compute_variance_decomposition() (in module spateo.tools.gene_expression_variance) compute_wald_test() (in module spateo.tools.ST_regression.regression_utils) conditionals() (in module spateo.segmentation.em) (in module spateo.segmentation.vi) (spateo.segmentation.vi.NegativeBinomialMixture static method) confidence() (in module spateo.segmentation.em) config (in module spateo) (in module spateo.configuration) config_spateo_rcParams() (in module spateo.configuration) ConfigurationError connect() (spateo.preprocessing.auxseg.LiveWireSegmentation method) construct_align_lines() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.line_model) construct_arrow() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.arrow_model) construct_arrows() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.arrow_model) construct_axis_line() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.line_model) construct_binned_spatial_distance() (in module spateo.tools.find_neighbors) construct_bounding_box() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.uniform_model) construct_cells() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.mesh_model) construct_field() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.morphofield_model) construct_field_streams() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.morphofield_model) construct_genesis() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.morphopath_model) construct_genesis_X() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.morphopath_model) construct_geodesic_distance_matrix() (in module spateo.tools) (in module spateo.tools.find_neighbors) construct_line() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.line_model) construct_lines() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.line_model) construct_nn_graph() (in module spateo.tools) (in module spateo.tools.find_neighbors) construct_pc() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.pc) (in module spateo.tdr.models.pc.pc_model) construct_space() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.uniform_model) construct_spatial_distance_matrix() (in module spateo.tools) (in module spateo.tools.find_neighbors) construct_surface() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.mesh_model) construct_trajectory() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.morphopath_model) construct_trajectory_X() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.morphopath_model) contour_to_geo() (in module spateo.io.utils) contours() (in module spateo.plotting) (in module spateo.plotting.interactive) (in module spateo.plotting.interactive.agg) conv2d() (in module spateo.segmentation.utils) copy_adata() (in module spateo.utils) cosine_distance() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.nn_losses) COUNT_COLUMN_MAPPING (in module spateo.io.bgi) create_label_class() (in module spateo.tools) (in module spateo.tools.labels) create_line() (in module spateo.tdr.widgets.slice) create_model() (spateo.tdr.NLPCA method) (spateo.tdr.widgets.NLPCA method) (spateo.tdr.widgets.tree.NLPCA method) create_neighbor_offsets() (in module spateo.segmentation.bp) create_plotter() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plotter) curl() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.morphogenesis_plots) curvature() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.morphogenesis_plots) cyc_10 (in module spateo.configuration) cyc_20 (in module spateo.configuration) D darkblue_cmap (in module spateo.configuration) darkgreen_cmap (in module spateo.configuration) darkpurple_cmap (in module spateo.configuration) darkred_cmap (in module spateo.configuration) dataframe_to_filled_labels() (in module spateo.io.bgi) dataframe_to_labels() (in module spateo.io.bgi) DataSampler (class in spateo.tdr) (class in spateo.tdr.widgets) (class in spateo.tdr.widgets.deep_interpolation) DDRTree() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.tree) deaxis_all() (in module spateo.plotting.static.utils) deduplicate_kwargs() (in module spateo.plotting.static.utils) deep_intepretation() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.interpolations) deepcell() (in module spateo.segmentation) (in module spateo.segmentation.external.deepcell) DeepInterpolation (class in spateo.tdr) (class in spateo.tdr.widgets) (class in spateo.tdr.widgets.deep_interpolation) default_20 (in module spateo.plotting.static.colorlabel) default_28 (in module spateo.plotting.static.colorlabel) default_base (spateo.plotting.static.dotplot.Dotplot attribute) default_category_height (spateo.plotting.static.dotplot.Dotplot attribute) default_category_width (spateo.plotting.static.dotplot.Dotplot attribute) default_color_legend_title (spateo.plotting.static.dotplot.Dotplot attribute) default_color_on (spateo.plotting.static.dotplot.Dotplot attribute) default_colormap (spateo.plotting.static.dotplot.Dotplot attribute) DEFAULT_COLORS (in module spateo.plotting.static.colorlabel) default_dot_edgecolor (spateo.plotting.static.dotplot.Dotplot attribute) default_dot_edgelw (spateo.plotting.static.dotplot.Dotplot attribute) default_dot_max (spateo.plotting.static.dotplot.Dotplot attribute) default_dot_min (spateo.plotting.static.dotplot.Dotplot attribute) default_largest_dot (spateo.plotting.static.dotplot.CCDotplot attribute) (spateo.plotting.static.dotplot.Dotplot attribute) default_legends_width (spateo.plotting.static.dotplot.Dotplot attribute) default_num_colorbar_ticks (spateo.plotting.static.dotplot.Dotplot attribute) default_num_size_legend_dots (spateo.plotting.static.dotplot.Dotplot attribute) default_plot_x_padding (spateo.plotting.static.dotplot.Dotplot attribute) default_plot_y_padding (spateo.plotting.static.dotplot.Dotplot attribute) default_quiver_args() (in module spateo.plotting.static.utils) default_size_exponent (spateo.plotting.static.dotplot.Dotplot attribute) default_size_legend_title (spateo.plotting.static.dotplot.Dotplot attribute) default_smallest_dot (spateo.plotting.static.dotplot.Dotplot attribute) default_wspace (spateo.plotting.static.dotplot.Dotplot attribute) delaunay() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.bbs) dendrogram() (in module spateo.plotting.static.utils) denormalize_y() (spateo.plotting.static.utils.Loess method) despline() (in module spateo.plotting.static.utils) despline_all() (in module spateo.plotting.static.utils) dev (spateo.get_version.Version attribute) deviance() (in module spateo.tools.ST_regression.generalized_lm) device (in module spateo.tdr.widgets.deep_interpolation) digitize() (in module spateo.digitization) (in module spateo.digitization.grid) Discriminator (class in spateo.tools.spatial_impute.impute_model) dist() (spateo.segmentation.vi.NegativeBinomialMixture method) DISTANCES_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) div_blue_black_red_cmap (in module spateo.configuration) div_blue_red_cmap (in module spateo.configuration) divergence() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.morphogenesis_plots) domain_heat_eqn_solver() (in module spateo.digitization.utils) Dotplot (class in spateo.plotting.static.dotplot) dotplot() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.dotplot) download_data() (in module spateo.sample_data) drag_mode() (in module spateo.tools.roi) draw_init() (in module spateo.tools.roi) draw_seg_grid() (in module spateo.digitization.utils) drosophila() (in module spateo.sample_data) E ecp_silhouette() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) effective_L2_error() (in module spateo.digitization.utils) ElPiGraph_tree() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.changes) Encoder (class in spateo.tools.spatial_impute.impute_model) estimate() (spateo.plotting.static.utils.Loess method) euclidean_dist() (in module spateo.digitization.utils) euclidean_distance() (in module spateo.tdr.widgets.slice) expand_labels() (in module spateo.segmentation) (in module spateo.segmentation.label) (in module spateo.tools.labels) EXPANDED_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) extend_contours() (in module spateo.tools.roi) extend_layer() (in module spateo.digitization.utils) EXTEND_WIDTH (in module spateo.tools.roi) extract_cluster_contours() (in module spateo.digitization) (in module spateo.digitization.contour) F fdr_correct() (in module spateo.tools.cci_fdr) feature() (in module spateo.plotting.static.three_d_plot.morphogenesis_plots) field_contour_line() (in module spateo.digitization.utils) field_contours() (in module spateo.digitization.utils) fill (in module spateo.tools.roi) fill_contours() (spateo.preprocessing.auxseg.LiveWireSegmentation static method) fill_grid_label() (in module spateo.digitization.utils) fill_mask_color() (in module spateo.tools.roi) filter_by_coordinates() (in module spateo.preprocessing.filter) filter_cell_labels_by_area() (in module spateo.segmentation.utils) filter_cells() (in module spateo.preprocessing.filter) filter_common_genes() (in module spateo.tools.paste) filter_genes() (in module spateo.preprocessing.filter) find_all_cluster_degs() (in module spateo.tools) (in module spateo.tools.cluster_degs) find_cci_two_group() (in module spateo.tools) (in module spateo.tools.cci_two_cluster) find_cluster_degs() (in module spateo.tools) (in module spateo.tools.cluster_degs) find_intersection() (in module spateo.tdr.widgets.slice) find_model_outline_planes() (in module spateo.tdr.widgets.slice) find_peaks() (in module spateo.segmentation) (in module spateo.segmentation.label) find_peaks_from_mask() (in module spateo.segmentation) (in module spateo.segmentation.label) find_peaks_with_erosion() (in module spateo.segmentation) (in module spateo.segmentation.label) find_plane_equation() (in module spateo.tdr.widgets.slice) find_spatial_archetypes() (in module spateo.tools) (in module spateo.tools.architype) find_spatial_cluster_degs() (in module spateo.tools) (in module spateo.tools.cluster_degs) find_spatially_related_genes() (in module spateo.tools) (in module spateo.tools.architype) fire_cmap (in module spateo.configuration) fit() (spateo.tdr.NLPCA method) (spateo.tdr.widgets.NLPCA method) (spateo.tdr.widgets.tree.NLPCA method) (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) (spateo.tools.cluster.spagcn_utils.simple_GC_DEC_PyG method) (spateo.tools.ST_regression.generalized_lm.GLM method) (spateo.tools.ST_regression.generalized_lm.GLMCV method) fit_glm() (in module spateo.tools) (in module spateo.tools.ST_regression.generalized_lm) fit_predict() (spateo.tools.ST_regression.generalized_lm.GLM method) (spateo.tools.ST_regression.generalized_lm.GLMCV method) fix_mesh() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.mesh_utils) fix_seed() (in module spateo.tools.spatial_impute.impute) flatten() (in module spateo.tools.utils) forward() (spateo.segmentation.align.AlignmentRefiner method) (spateo.segmentation.vi.NegativeBinomialMixture method) (spateo.tdr.A method) (spateo.tdr.B method) (spateo.tdr.h method) (spateo.tdr.MainFlow method) (spateo.tdr.SineLayer method) (spateo.tdr.widgets.A method) (spateo.tdr.widgets.B method) (spateo.tdr.widgets.h method) (spateo.tdr.widgets.interpolation_nn.A method) (spateo.tdr.widgets.interpolation_nn.B method) (spateo.tdr.widgets.interpolation_nn.h method) (spateo.tdr.widgets.interpolation_nn.MainFlow method) (spateo.tdr.widgets.interpolation_nn.SineLayer method) (spateo.tdr.widgets.MainFlow method) (spateo.tdr.widgets.SineLayer method) (spateo.tools.cluster.spagcn_utils.GraphConvolution method) (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) (spateo.tools.cluster.spagcn_utils.simple_GC_DEC_PyG method) (spateo.tools.spatial_impute.impute_model.AvgReadout method) (spateo.tools.spatial_impute.impute_model.Discriminator method) (spateo.tools.spatial_impute.impute_model.Encoder method) forward_with_intermediate() (spateo.tdr.SineLayer method) (spateo.tdr.widgets.interpolation_nn.SineLayer method) (spateo.tdr.widgets.SineLayer method) FOV_PARSER (in module spateo.io.nanostring) G gaussian_blur() (in module spateo.segmentation.utils) gaussian_weight_2d() (in module spateo.tools.find_neighbors) gen_cluster_image() (in module spateo.digitization) (in module spateo.digitization.contour) gen_new_layer_key() (spateo.configuration.SpateoAdataKeyManager method) gen_rotation_2d() (in module spateo.tools.utils) generalized_procrustes_analysis() (in module spateo.tools) (in module spateo.tools.paste) generate_batch() (spateo.tdr.DataSampler method) (spateo.tdr.widgets.DataSampler method) (spateo.tdr.widgets.deep_interpolation.DataSampler method) generate_edges() (in module spateo.tdr.models.morpho_models) (in module spateo.tdr.models.morpho_models.line_model) generate_normalized_onehot() (spateo.tools.Label method) (spateo.tools.labels.Label method) generate_onehot() (spateo.tools.Label method) (spateo.tools.labels.Label method) generate_random_labels() (in module spateo.segmentation) (in module spateo.segmentation.qc) generate_random_labels_like() (in module spateo.segmentation) (in module spateo.segmentation.qc) generate_spatial_distance_graph() (in module spateo.tools.find_neighbors) generate_spatial_weights_fixed_nbrs() (in module spateo.tools) (in module spateo.tools.find_neighbors) generate_spatial_weights_fixed_radius() (in module spateo.tools) (in module spateo.tools.find_neighbors) genewise_variance_decomposition() (in module spateo.tools.gene_expression_variance) geo() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.geo) get_adata() (in module spateo.sample_data) get_adata_type() (spateo.configuration.SpateoAdataKeyManager method) get_agg_bounds() (spateo.configuration.SpateoAdataKeyManager method) get_align_labels() (in module spateo.tools) (in module spateo.tools.three_dims_align) get_all_dependencies_version() (in module spateo.get_version) get_aug_feature() (in module spateo.tools.spatial_impute.impute) get_axes() (spateo.plotting.static.dotplot.Dotplot method) get_bin_props() (in module spateo.io.utils) get_borderline() (in module spateo.digitization) (in module spateo.digitization.borderline) get_cluster_num() (in module spateo.tools.cluster.spagcn_utils) get_concave_hull() (in module spateo.io) (in module spateo.io.bbs) get_coords_labels() (in module spateo.io.utils) get_effect_sizes() (spateo.tools.ST_regression.spatial_regression.Base_Model method) get_fisher_inverse() (in module spateo.tools.ST_regression.regression_utils) get_genes_from_spatial_archetype() (in module spateo.tools) (in module spateo.tools.architype) get_label_props() (in module spateo.io.utils) get_mapper() (in module spateo.tools.utils) get_min_range() (spateo.plotting.static.utils.Loess static method) get_normalized_onehot() (spateo.tools.Label method) (spateo.tools.labels.Label method) get_onehot() (spateo.tools.Label method) (spateo.tools.labels.Label method) get_params() (spateo.segmentation.align.AlignmentRefiner method) (spateo.segmentation.align.NonRigidAlignmentRefiner method) (spateo.segmentation.align.RigidAlignmentRefiner method) (spateo.segmentation.vi.NegativeBinomialMixture method) get_points_props() (in module spateo.io.utils) get_uns_spatial_attribute() (spateo.configuration.SpateoAdataKeyManager method) get_version() (in module spateo) (in module spateo.get_version) get_version_from_dirname() (in module spateo.get_version) get_version_from_git() (in module spateo.get_version) get_version_from_metadata() (in module spateo.get_version) get_weights() (spateo.plotting.static.utils.Loess static method) get_X_Y_grid() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.interpolations) glasbey_dark_cmap (in module spateo.configuration) glasbey_white_cmap (in module spateo.configuration) GLM (class in spateo.tools.ST_regression.generalized_lm) glm_ (spateo.tools.ST_regression.generalized_lm.GLMCV attribute) glm_degs() (in module spateo.tools) (in module spateo.tools.glm) glm_fit() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.glm) glm_test() (in module spateo.tools.glm) GLMCV (class in spateo.tools.ST_regression.generalized_lm) GLMCV_fit_predict() (spateo.tools.ST_regression.spatial_regression.Base_Model method) GM_lag_model() (in module spateo.tools) (in module spateo.tools.lisa) godsnot_102 (in module spateo.plotting.static.colorlabel) GraphConvolution (class in spateo.tools.cluster.spagcn_utils) grid_borderline() (in module spateo.digitization) (in module spateo.digitization.borderline) gridit() (in module spateo.digitization) (in module spateo.digitization.grid) H h (class in spateo.tdr) (class in spateo.tdr.widgets) (class in spateo.tdr.widgets.interpolation_nn) harmony_debatch() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) has_uns_spatial_attribute() (spateo.configuration.SpateoAdataKeyManager method) high2low() (spateo.tdr.DeepInterpolation method) (spateo.tdr.widgets.deep_interpolation.DeepInterpolation method) (spateo.tdr.widgets.DeepInterpolation method) I image (spateo.preprocessing.auxseg.LiveWireSegmentation property) (spateo.tools.live_wire.LiveWireSegmentation property) (spateo.tools.LiveWireSegmentation property) img_segmentation() (in module spateo.tools.roi) impute_and_downsample() (in module spateo.tools), [1] (in module spateo.tools.spatial_impute) (in module spateo.tools.spatial_impute.run_impute) imshow() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.agg) in_concave_hull() (in module spateo.io.utils) in_convex_hull() (in module spateo.io.utils) in_hull() (in module spateo.tools.utils) init_adata_type() (spateo.configuration.SpateoAdataKeyManager method) init_best_params() (spateo.segmentation.vi.NegativeBinomialMixture method) init_mean_variance() (spateo.segmentation.vi.NegativeBinomialMixture method) init_uns_pp_namespace() (spateo.configuration.SpateoAdataKeyManager method) init_uns_spatial_namespace() (spateo.configuration.SpateoAdataKeyManager method) init_weights() (spateo.tdr.SineLayer method) (spateo.tdr.widgets.interpolation_nn.SineLayer method) (spateo.tdr.widgets.SineLayer method) integrate() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) interactive() (in module spateo.plotting.static.utils) interactive_box_clip() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.clip) interactive_pick() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.pick) interactive_rectangle_clip() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.clip) interactive_slice() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.slice) interlabel_connections() (in module spateo.tools.labels) interpolate_model() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.vtk_interpolate) intersect_lsts (in module spateo.tools.paste) iou() (in module spateo.segmentation.benchmark) IOWarning is_cell_anno_column() (in module spateo.plotting.static.utils) is_gene_name() (in module spateo.plotting.static.utils) is_layer_keys() (in module spateo.plotting.static.utils) is_list_of_lists() (in module spateo.plotting.static.utils) J jacobian() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.morphogenesis_plots) K kernel_interpolation() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.interpolations) key_pressed() (spateo.preprocessing.auxseg.LiveWireSegmentation method) kl_divergence_backend() (in module spateo.tools.paste) knee_threshold() (in module spateo.segmentation.utils) L L1_L2_penalty() (in module spateo.tools.ST_regression.regression_utils) L1_penalty() (in module spateo.tools.ST_regression.regression_utils) L2_penalty() (in module spateo.tools.ST_regression.regression_utils) Label (class in spateo.tools) (class in spateo.tools.labels) label_connected_components() (in module spateo.segmentation) (in module spateo.segmentation.label) label_overlap() (in module spateo.segmentation.utils) labeling_stats() (in module spateo.segmentation.benchmark) labels (spateo.get_version.Version attribute) LABELS_LAYER_KEY (spateo.configuration.SpateoAdataKeyManager attribute) LABELS_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) Lagged_Model (class in spateo.tools), [1] (class in spateo.tools.ST_regression) (class in spateo.tools.ST_regression.spatial_regression) lamtheta_to_muvar() (in module spateo.segmentation.em) lamtheta_to_r() (in module spateo.segmentation.em) Lasso (class in spateo.tools) (class in spateo.tools.cluster_lasso) legend() (spateo.plotting.static.dotplot.Dotplot method) ligrec() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.interactions) line_ls (in module spateo.tools.roi) line_mode() (in module spateo.tools.roi) LineDDA() (spateo.preprocessing.auxseg.LiveWireSegmentation static method) lisa() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.lisa) lisa_geo_df() (in module spateo.tools) (in module spateo.tools.lisa) lisa_quantiles() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.lisa) live_wire() (in module spateo.tools) (in module spateo.tools.live_wire) LiveWireSegmentation (class in spateo.preprocessing.auxseg) (class in spateo.tools) (class in spateo.tools.live_wire) load() (spateo.tdr.DeepInterpolation method) (spateo.tdr.widgets.deep_interpolation.DeepInterpolation method) (spateo.tdr.widgets.DeepInterpolation method) local_moran_i() (in module spateo.tools) (in module spateo.tools.lisa) Loess (class in spateo.plotting.static.utils) log1p() (in module spateo.preprocessing) (in module spateo.preprocessing.transform) log1p_anndata() (in module spateo.preprocessing.transform) log1p_array() (in module spateo.preprocessing.transform) log1p_sparse() (in module spateo.preprocessing.transform) log_likelihood() (in module spateo.tools.ST_regression.generalized_lm) logger_manager (in module spateo.logging) logging_level (spateo.configuration.SpateoConfig property) loss() (spateo.segmentation.align.AlignmentRefiner method) loss_function() (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) low2high() (spateo.tdr.DeepInterpolation method) (spateo.tdr.widgets.deep_interpolation.DeepInterpolation method) (spateo.tdr.widgets.DeepInterpolation method) lrt() (in module spateo.tools.glm) M mad() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.nn_losses) mae() (in module spateo.tools.ST_regression.regression_utils) main() (in module spateo.tools.roi) MainFlow (class in spateo.tdr) (class in spateo.tdr.widgets) (class in spateo.tdr.widgets.interpolation_nn) make_figure() (spateo.plotting.static.dotplot.Dotplot method) make_grid_spec() (in module spateo.plotting.static.dotplot) map2color() (in module spateo.plotting.static.utils) map_gene_to_branch() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.changes) map_points_to_branch() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.changes) mapping_aligned_coords() (in module spateo.tools) (in module spateo.tools.paste) mapping_center_coords() (in module spateo.tools) (in module spateo.tools.paste) marching_cube_mesh() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.reconstruction_methods) MARKERS_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) mask_cells_from_stain() (in module spateo.segmentation) (in module spateo.segmentation.icell) mask_fill() (in module spateo.tools.roi) mask_nuclei_from_stain() (in module spateo.segmentation) (in module spateo.segmentation.icell) MASK_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) match_groups() (in module spateo.get_version) match_label_series() (in module spateo.tools.labels) match_labels() (in module spateo.tools.labels) mclose_mopen() (in module spateo.segmentation.utils) median_blur() (in module spateo.segmentation.utils) merfish() (in module spateo.sample_data) merge_animations() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plots) merge_densities() (in module spateo.segmentation) (in module spateo.segmentation.density) merge_models() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.model_utils) min_figure_height (spateo.plotting.static.dotplot.Dotplot attribute) minimal_xticks() (in module spateo.plotting.static.utils) minimal_yticks() (in module spateo.plotting.static.utils) model_morphology() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphology) models_align() (in module spateo.tools) (in module spateo.tools.three_dims_align) models_align_ref() (in module spateo.tools) (in module spateo.tools.three_dims_align) models_center_align() (in module spateo.tools) (in module spateo.tools.three_dims_align) models_center_align_ref() (in module spateo.tools) (in module spateo.tools.three_dims_align) module spateo spateo.configuration spateo.cs spateo.data_io spateo.dd spateo.digitization spateo.digitization.borderline spateo.digitization.contour spateo.digitization.grid spateo.digitization.utils spateo.errors spateo.get_version spateo.io spateo.io.bbs spateo.io.bgi spateo.io.image spateo.io.image_utils spateo.io.merfish spateo.io.nanostring spateo.io.seqfish spateo.io.seqscope spateo.io.slideseq spateo.io.starmap spateo.io.tenx spateo.io.utils spateo.logging spateo.pl spateo.plotting spateo.plotting.interactive spateo.plotting.interactive.agg spateo.plotting.static spateo.plotting.static.agg spateo.plotting.static.align spateo.plotting.static.bbs spateo.plotting.static.colorlabel spateo.plotting.static.contour spateo.plotting.static.dotplot spateo.plotting.static.geo spateo.plotting.static.glm spateo.plotting.static.interactions spateo.plotting.static.lisa spateo.plotting.static.polarity spateo.plotting.static.position spateo.plotting.static.scatters spateo.plotting.static.space spateo.plotting.static.three_d_plot spateo.plotting.static.three_d_plot.morphogenesis_plots spateo.plotting.static.three_d_plot.three_dims_plots spateo.plotting.static.three_d_plot.three_dims_plotter spateo.plotting.static.utils spateo.pp spateo.preprocessing spateo.preprocessing.aggregate spateo.preprocessing.auxseg spateo.preprocessing.filter spateo.preprocessing.image spateo.preprocessing.normalize spateo.preprocessing.transform spateo.sample_data spateo.segmentation spateo.segmentation.align spateo.segmentation.benchmark spateo.segmentation.bp spateo.segmentation.density spateo.segmentation.em spateo.segmentation.external spateo.segmentation.external.cellpose spateo.segmentation.external.deepcell spateo.segmentation.external.stardist spateo.segmentation.icell spateo.segmentation.label spateo.segmentation.moran spateo.segmentation.qc spateo.segmentation.simulation spateo.segmentation.utils spateo.segmentation.vi spateo.tdr spateo.tdr.models spateo.tdr.models.mesh spateo.tdr.models.mesh.mesh_model spateo.tdr.models.mesh.mesh_utils spateo.tdr.models.mesh.reconstruction_methods spateo.tdr.models.morpho_models spateo.tdr.models.morpho_models.arrow_model spateo.tdr.models.morpho_models.line_model spateo.tdr.models.morpho_models.morphofield_model spateo.tdr.models.morpho_models.morphopath_model spateo.tdr.models.morpho_models.uniform_model spateo.tdr.models.pc spateo.tdr.models.pc.pc_model spateo.tdr.models.utilities spateo.tdr.models.utilities.io spateo.tdr.models.utilities.label_utils spateo.tdr.models.utilities.model_utils spateo.tdr.models.voxel spateo.tdr.models.voxel.voxel_model spateo.tdr.widgets spateo.tdr.widgets.changes spateo.tdr.widgets.clip spateo.tdr.widgets.deep_interpolation spateo.tdr.widgets.interpolation_nn spateo.tdr.widgets.interpolations spateo.tdr.widgets.morphogenesis spateo.tdr.widgets.morphology spateo.tdr.widgets.nn_losses spateo.tdr.widgets.pick spateo.tdr.widgets.slice spateo.tdr.widgets.tree spateo.tdr.widgets.utils spateo.tdr.widgets.vtk_interpolate spateo.tl spateo.tools spateo.tools.architype spateo.tools.cci_fdr spateo.tools.cci_two_cluster spateo.tools.cell_communication spateo.tools.cluster spateo.tools.cluster.cluster_spagcn spateo.tools.cluster.find_clusters spateo.tools.cluster.spagcn_utils spateo.tools.cluster.utils spateo.tools.cluster_degs spateo.tools.cluster_lasso spateo.tools.coarse_align spateo.tools.find_neighbors spateo.tools.gene_expression_variance spateo.tools.glm spateo.tools.labels spateo.tools.lisa spateo.tools.live_wire spateo.tools.paste spateo.tools.roi spateo.tools.spatial_degs spateo.tools.spatial_impute spateo.tools.spatial_impute.impute spateo.tools.spatial_impute.impute_model spateo.tools.spatial_impute.run_impute spateo.tools.spatial_regression_interpretation spateo.tools.ST_regression spateo.tools.ST_regression.generalized_lm spateo.tools.ST_regression.regression_utils spateo.tools.ST_regression.spatial_regression spateo.tools.three_dims_align spateo.tools.utils spateo.utils spateo.warnings MODULES (in module spateo.segmentation.align) moran_i() (in module spateo.tools) (in module spateo.tools.spatial_degs) moranI() (in module spateo.segmentation.moran) morphofield() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) morphofield_acceleration() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) morphofield_curl() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) morphofield_curvature() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) morphofield_divergence() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) morphofield_jacobian() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) morphofield_torsion() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) morphofield_velocity() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) morphofield_X() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) morphopath() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphogenesis) mouse_event() (in module spateo.tools.roi) mouse_moved() (spateo.preprocessing.auxseg.LiveWireSegmentation method) mousebrain() (in module spateo.sample_data) mse() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.nn_losses) (in module spateo.tools.ST_regression.regression_utils) multi_slices() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.align) multiblock2model() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.model_utils) multitesting_correction() (in module spateo.tools.ST_regression.regression_utils) muvar_to_lamtheta() (in module spateo.segmentation.em) N n_iter (spateo.tools.ST_regression.generalized_lm.GLM attribute) (spateo.tools.ST_regression.generalized_lm.GLMCV attribute) n_threads (spateo.configuration.SpateoConfig property) nbn_em() (in module spateo.segmentation.em) nbn_pmf() (in module spateo.segmentation.em) NegativeBinomialMixture (class in spateo.segmentation.vi) Niche_LR_Model (class in spateo.tools), [1] (class in spateo.tools.ST_regression) (class in spateo.tools.ST_regression.spatial_regression) Niche_Model (class in spateo.tools), [1] (class in spateo.tools.ST_regression) (class in spateo.tools.ST_regression.spatial_regression) niches() (in module spateo.tools) (in module spateo.tools.cell_communication) NLPCA (class in spateo.tdr) (class in spateo.tdr.widgets) (class in spateo.tdr.widgets.tree) NonRigidAlignmentRefiner (class in spateo.segmentation.align) normalize_adj() (in module spateo.tools.find_neighbors) normalize_array() (spateo.plotting.static.utils.Loess static method) normalize_total() (in module spateo.preprocessing) (in module spateo.preprocessing.normalize) normalize_x() (spateo.plotting.static.utils.Loess method) num (in module spateo.tools.roi) O ON_RTD (in module spateo.get_version) optimizer() (spateo.segmentation.align.AlignmentRefiner method) (spateo.segmentation.vi.NegativeBinomialMixture method) order_borderline() (in module spateo.digitization) (in module spateo.digitization.utils) orth_dist() (in module spateo.tdr.widgets.tree) output_plotter() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plotter) overlap_mesh_pick() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.pick) overlap_pc_pick() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.pick) overlap_pick() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.pick) P p_equiv_radius() (in module spateo.tools.find_neighbors) pairwise_align() (in module spateo.tools) (in module spateo.tools.paste) parse() (spateo.get_version.Version static method) pc_KDE() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.morphology) pca_align() (in module spateo.tools) (in module spateo.tools.coarse_align) pca_projection() (in module spateo.tdr.widgets.tree) pca_spateo() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) pearson_residuals() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) permutation() (in module spateo.tools.spatial_impute.impute) plot_connections() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.interactions) plot_dendrogram() (in module spateo.plotting.static.utils) plot_polygon() (in module spateo.plotting.static.utils) plot_prior_vs_data() (in module spateo.tools) (in module spateo.tools.ST_regression.regression_utils) plot_variance_decomposition() (in module spateo.tools.gene_expression_variance) PlottingError PlottingWarning poisson_mesh() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.reconstruction_methods) polarity() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.polarity) polygon() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.bbs) polyhull() (in module spateo.tools.utils) position() (in module spateo.plotting.static.position) predict() (spateo.tdr.DeepInterpolation method) (spateo.tdr.widgets.deep_interpolation.DeepInterpolation method) (spateo.tdr.widgets.DeepInterpolation method) (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) (spateo.tools.cluster.spagcn_utils.simple_GC_DEC_PyG method) (spateo.tools.cluster.spagcn_utils.SpaGCN method) (spateo.tools.ST_regression.generalized_lm.GLM method) (spateo.tools.ST_regression.generalized_lm.GLMCV method) predict_ligand_activities() (in module spateo.tools) (in module spateo.tools.cell_communication) predict_target_genes() (in module spateo.tools) (in module spateo.tools.cell_communication) prepare_cci_cellpair_adata() (in module spateo.tools) (in module spateo.tools.cci_two_cluster) prepare_cci_df() (in module spateo.tools) (in module spateo.tools.cci_two_cluster) prepare_data() (spateo.tools.ST_regression.spatial_regression.Base_Model method) preprocess_data() (spateo.tools.ST_regression.spatial_regression.Base_Model method) PreprocessingError PreprocessingWarning Principal_Curve() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.changes) procrustes() (in module spateo.tools) (in module spateo.tools.coarse_align) progress (in module spateo.segmentation.em) project() (spateo.tdr.NLPCA method) (spateo.tdr.widgets.NLPCA method) (spateo.tdr.widgets.tree.NLPCA method) pseudo_r2() (in module spateo.tools.ST_regression.generalized_lm) pv_mesh() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.reconstruction_methods) Q qc_regions() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.agg) quiver_autoscaler() (in module spateo.plotting.static.utils) R RE_GIT_DESCRIBE (in module spateo.get_version) RE_VERSION (in module spateo.get_version) read_10x() (in module spateo.io) (in module spateo.io.tenx) read_10x_as_anndata() (in module spateo.io) (in module spateo.io.tenx) read_10x_positions_as_dataframe() (in module spateo.io.tenx) read_bgi() (in module spateo.io) (in module spateo.io.bgi) read_bgi_agg() (in module spateo.io) (in module spateo.io.bgi) read_bgi_as_dataframe() (in module spateo.io.bgi) read_image() (in module spateo.io) (in module spateo.io.image) read_merfish() (in module spateo.io.merfish) read_merfish_as_anndata() (in module spateo.io.merfish) read_merfish_positions_as_dataframe() (in module spateo.io.merfish) read_model() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.io) read_nanostring() (in module spateo.io) (in module spateo.io.nanostring) read_nanostring_as_dataframe() (in module spateo.io.nanostring) read_seqfish() (in module spateo.io.seqfish) read_seqfish_meta_as_dataframe() (in module spateo.io.seqfish) read_seqscope() (in module spateo.io.seqscope) read_seqscope_as_anndata() (in module spateo.io.seqscope) read_seqscope_positions_as_dataframe() (in module spateo.io.seqscope) read_slideseq() (in module spateo.io) (in module spateo.io.slideseq) read_slideseq_as_dataframe() (in module spateo.io.slideseq) read_slideseq_beads_as_dataframe() (in module spateo.io.slideseq) read_starmap() (in module spateo.io.starmap) read_starmap_as_anndata() (in module spateo.io.starmap) read_starmap_positions_as_dataframe() (in module spateo.io.starmap) readData() (in module spateo.tools.roi) refine() (in module spateo.tools.cluster.spagcn_utils) refine_alignment() (in module spateo.segmentation) (in module spateo.segmentation.align) reg_lambda_opt (spateo.tools.ST_regression.generalized_lm.GLMCV attribute) release (spateo.get_version.Version attribute) remove_background() (in module spateo.preprocessing.image) remove_greater_than() (in module spateo.tools.find_neighbors) reorder_categories_after_dendrogram() (spateo.plotting.static.dotplot.Dotplot method) replace_labels() (in module spateo.segmentation.label) repmat() (in module spateo.tdr.widgets.tree) rescaling() (in module spateo.tools.utils) reset_parameters() (spateo.tools.cluster.spagcn_utils.GraphConvolution method) (spateo.tools.spatial_impute.impute_model.Encoder method) reset_rcParams() (in module spateo.configuration) rigid_transform_2D() (in module spateo.tools) (in module spateo.tools.three_dims_align) rigid_transform_3D() (in module spateo.tools) (in module spateo.tools.three_dims_align) RigidAlignmentRefiner (class in spateo.segmentation.align) rotate_model() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.model_utils) row_normalize() (in module spateo.tools.labels) run_bp() (in module spateo.segmentation.bp) run_em() (in module spateo.segmentation.em) run_GM_lag() (spateo.tools.Lagged_Model method), [1] (spateo.tools.ST_regression.Lagged_Model method) (spateo.tools.ST_regression.spatial_regression.Lagged_Model method) run_moran() (in module spateo.segmentation.moran) run_moran_and_mask_pixels() (in module spateo.segmentation.moran) run_vi() (in module spateo.segmentation.vi) S safe_erode() (in module spateo.segmentation.utils) save() (spateo.tdr.DeepInterpolation method) (spateo.tdr.widgets.deep_interpolation.DeepInterpolation method) (spateo.tdr.widgets.DeepInterpolation method) save_draw() (in module spateo.tools.roi) save_fig() (in module spateo.plotting.static.utils) save_model() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.io) save_plotter() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plotter) save_return_show_fig_utils() (in module spateo.plotting.static.utils) scale() (in module spateo.preprocessing) (in module spateo.preprocessing.transform) scale_anndata() (in module spateo.preprocessing.transform) scale_array() (in module spateo.preprocessing.transform) scale_model() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.model_utils) scale_sparse() (in module spateo.preprocessing.transform) scale_to_01() (in module spateo.segmentation.utils) scale_to_255() (in module spateo.segmentation.utils) scatter_with_colorbar() (in module spateo.plotting.static.utils) scatter_with_legend() (in module spateo.plotting.static.utils) scatters() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.scatters) scc() (in module spateo.tools), [1] (in module spateo.tools.cluster) (in module spateo.tools.cluster.find_clusters) score() (spateo.tools.ST_regression.generalized_lm.GLM method) (spateo.tools.ST_regression.generalized_lm.GLMCV method) score_and_mask_pixels() (in module spateo.segmentation) (in module spateo.segmentation.icell) SCORES_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) sctransform() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) search_l() (in module spateo.tools.cluster.spagcn_utils) search_res() (in module spateo.tools.cluster.spagcn_utils) segment_bd_line() (in module spateo.digitization.utils) segment_densities() (in module spateo.segmentation) (in module spateo.segmentation.density) SegmentationError SegmentationWarning select_layer_data() (spateo.configuration.SpateoAdataKeyManager method) select_polygon() (in module spateo.plotting) (in module spateo.plotting.interactive) (in module spateo.plotting.interactive.agg) select_qc_regions() (in module spateo.segmentation) (in module spateo.segmentation.qc) SELECTION_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) sender_effect_on_all_receivers() (spateo.tools.ST_regression.spatial_regression.Base_Model method) sender_receiver_effect_volcanoplot() (spateo.tools.ST_regression.spatial_regression.Base_Model method) seqfish() (in module spateo.sample_data) seqscope() (in module spateo.sample_data) set_arrow_alpha() (in module spateo.plotting.static.utils) set_colorbar() (in module spateo.plotting.static.utils) set_domains() (in module spateo.digitization) (in module spateo.digitization.contour) set_figure_params() (in module spateo.configuration) set_l() (spateo.tools.cluster.spagcn_utils.SpaGCN method) set_layer_data() (spateo.configuration.SpateoAdataKeyManager method) set_pub_style() (in module spateo.configuration) set_pub_style_mpltex() (in module spateo.configuration) set_spine_linewidth() (in module spateo.plotting.static.utils) set_stream_line_alpha() (in module spateo.plotting.static.utils) set_uns_spatial_attribute() (spateo.configuration.SpateoAdataKeyManager method) shiftedColorMap() (in module spateo.configuration) simple_GC_DEC (class in spateo.tools.cluster.spagcn_utils) simple_GC_DEC_PyG (class in spateo.tools.cluster.spagcn_utils) SimplePPT_tree() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.changes) simulate_cells() (in module spateo.segmentation.simulation) SineLayer (class in spateo.tdr) (class in spateo.tdr.widgets) (class in spateo.tdr.widgets.interpolation_nn) single() (spateo.tools.Lagged_Model method), [1] (spateo.tools.ST_regression.Lagged_Model method) (spateo.tools.ST_regression.spatial_regression.Lagged_Model method) SKM (in module spateo.configuration) slideseq() (in module spateo.sample_data) smooth_mesh() (in module spateo.tdr.models.mesh.mesh_utils) softplus() (in module spateo.tools.ST_regression.regression_utils) space() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.space) SpaGCN (class in spateo.tools.cluster.spagcn_utils) spagcn_pyg() (in module spateo.tools), [1] (in module spateo.tools.cluster) (in module spateo.tools.cluster.find_clusters) spagcn_vanilla() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.cluster_spagcn) sparse_mean_var_major_axis() (in module spateo.preprocessing.transform) sparse_mean_var_minor_axis() (in module spateo.preprocessing.transform) sparse_mean_variance_axis() (in module spateo.preprocessing.transform) spateo module spateo.configuration module spateo.cs module spateo.data_io module spateo.dd module spateo.digitization module spateo.digitization.borderline module spateo.digitization.contour module spateo.digitization.grid module spateo.digitization.utils module spateo.errors module spateo.get_version module spateo.io module spateo.io.bbs module spateo.io.bgi module spateo.io.image module spateo.io.image_utils module spateo.io.merfish module spateo.io.nanostring module spateo.io.seqfish module spateo.io.seqscope module spateo.io.slideseq module spateo.io.starmap module spateo.io.tenx module spateo.io.utils module spateo.logging module spateo.pl module spateo.plotting module spateo.plotting.interactive module spateo.plotting.interactive.agg module spateo.plotting.static module spateo.plotting.static.agg module spateo.plotting.static.align module spateo.plotting.static.bbs module spateo.plotting.static.colorlabel module spateo.plotting.static.contour module spateo.plotting.static.dotplot module spateo.plotting.static.geo module spateo.plotting.static.glm module spateo.plotting.static.interactions module spateo.plotting.static.lisa module spateo.plotting.static.polarity module spateo.plotting.static.position module spateo.plotting.static.scatters module spateo.plotting.static.space module spateo.plotting.static.three_d_plot module spateo.plotting.static.three_d_plot.morphogenesis_plots module spateo.plotting.static.three_d_plot.three_dims_plots module spateo.plotting.static.three_d_plot.three_dims_plotter module spateo.plotting.static.utils module spateo.pp module spateo.preprocessing module spateo.preprocessing.aggregate module spateo.preprocessing.auxseg module spateo.preprocessing.filter module spateo.preprocessing.image module spateo.preprocessing.normalize module spateo.preprocessing.transform module spateo.sample_data module spateo.segmentation module spateo.segmentation.align module spateo.segmentation.benchmark module spateo.segmentation.bp module spateo.segmentation.density module spateo.segmentation.em module spateo.segmentation.external module spateo.segmentation.external.cellpose module spateo.segmentation.external.deepcell module spateo.segmentation.external.stardist module spateo.segmentation.icell module spateo.segmentation.label module spateo.segmentation.moran module spateo.segmentation.qc module spateo.segmentation.simulation module spateo.segmentation.utils module spateo.segmentation.vi module spateo.tdr module spateo.tdr.models module spateo.tdr.models.mesh module spateo.tdr.models.mesh.mesh_model module spateo.tdr.models.mesh.mesh_utils module spateo.tdr.models.mesh.reconstruction_methods module spateo.tdr.models.morpho_models module spateo.tdr.models.morpho_models.arrow_model module spateo.tdr.models.morpho_models.line_model module spateo.tdr.models.morpho_models.morphofield_model module spateo.tdr.models.morpho_models.morphopath_model module spateo.tdr.models.morpho_models.uniform_model module spateo.tdr.models.pc module spateo.tdr.models.pc.pc_model module spateo.tdr.models.utilities module spateo.tdr.models.utilities.io module spateo.tdr.models.utilities.label_utils module spateo.tdr.models.utilities.model_utils module spateo.tdr.models.voxel module spateo.tdr.models.voxel.voxel_model module spateo.tdr.widgets module spateo.tdr.widgets.changes module spateo.tdr.widgets.clip module spateo.tdr.widgets.deep_interpolation module spateo.tdr.widgets.interpolation_nn module spateo.tdr.widgets.interpolations module spateo.tdr.widgets.morphogenesis module spateo.tdr.widgets.morphology module spateo.tdr.widgets.nn_losses module spateo.tdr.widgets.pick module spateo.tdr.widgets.slice module spateo.tdr.widgets.tree module spateo.tdr.widgets.utils module spateo.tdr.widgets.vtk_interpolate module spateo.tl module spateo.tools module spateo.tools.architype module spateo.tools.cci_fdr module spateo.tools.cci_two_cluster module spateo.tools.cell_communication module spateo.tools.cluster module spateo.tools.cluster.cluster_spagcn module spateo.tools.cluster.find_clusters module spateo.tools.cluster.spagcn_utils module spateo.tools.cluster.utils module spateo.tools.cluster_degs module spateo.tools.cluster_lasso module spateo.tools.coarse_align module spateo.tools.find_neighbors module spateo.tools.gene_expression_variance module spateo.tools.glm module spateo.tools.labels module spateo.tools.lisa module spateo.tools.live_wire module spateo.tools.paste module spateo.tools.roi module spateo.tools.spatial_degs module spateo.tools.spatial_impute module spateo.tools.spatial_impute.impute module spateo.tools.spatial_impute.impute_model module spateo.tools.spatial_impute.run_impute module spateo.tools.spatial_regression_interpretation module spateo.tools.ST_regression module spateo.tools.ST_regression.generalized_lm module spateo.tools.ST_regression.regression_utils module spateo.tools.ST_regression.spatial_regression module spateo.tools.three_dims_align module spateo.tools.utils module spateo.utils module spateo.warnings module spateo_theme() (in module spateo.configuration) SpateoAdataKeyManager (class in spateo.configuration) SpateoConfig (class in spateo.configuration) spatial_adj_dyn() (in module spateo.tools.cluster.utils) spatial_domains() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.contour) SPLICED_LAYER_KEY (spateo.configuration.SpateoAdataKeyManager attribute) split_model() (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.model_utils) sqdist() (in module spateo.tdr.widgets.tree) STAIN_LAYER_KEY (spateo.configuration.SpateoAdataKeyManager attribute) stardist() (in module spateo.segmentation) (in module spateo.segmentation.external.stardist) StarDist2D (in module spateo.segmentation.external.stardist) starmap() (in module spateo.sample_data) STGNN (class in spateo.tools), [1] (class in spateo.tools.spatial_impute) (class in spateo.tools.spatial_impute.impute) stitch_images() (in module spateo.io.nanostring) style() (spateo.plotting.static.dotplot.Dotplot method) sub_adata (spateo.tools.cluster_lasso.Lasso attribute) (spateo.tools.Lasso attribute) subset_best_samples() (in module spateo.tdr.widgets.deep_interpolation) swap_axes() (spateo.plotting.static.dotplot.Dotplot method) T target_distribution() (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) three_d_animate() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plots) three_d_multi_plot() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plots) three_d_pick() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.pick) three_d_plot() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.three_dims_plots) three_d_slice() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.slice) to_dense_matrix (in module spateo.tools.cluster.find_clusters) (in module spateo.tools.cluster.utils) (in module spateo.tools.paste) top_n_degs() (in module spateo.tools) (in module spateo.tools.cluster_degs) torsion() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.three_d_plot) (in module spateo.plotting.static.three_d_plot.morphogenesis_plots) train() (spateo.segmentation.align.AlignmentRefiner method) (spateo.segmentation.vi.NegativeBinomialMixture method) (spateo.tdr.DeepInterpolation method) (spateo.tdr.widgets.deep_interpolation.DeepInterpolation method) (spateo.tdr.widgets.DeepInterpolation method) (spateo.tools.cluster.spagcn_utils.SpaGCN method) (spateo.tools.spatial_impute.impute.Trainer method) train_STGNN() (spateo.tools.spatial_impute.impute.STGNN method) (spateo.tools.spatial_impute.STGNN method) (spateo.tools.STGNN method), [1] Trainer (class in spateo.tools.spatial_impute.impute) transcriptomic_connectivity() (in module spateo.tools.find_neighbors) transform() (spateo.segmentation.align.AlignmentRefiner static method) (spateo.segmentation.align.NonRigidAlignmentRefiner static method) (spateo.segmentation.align.RigidAlignmentRefiner static method) translate_model() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.model_utils) tricubic() (in module spateo.plotting.static.utils) type_coupling() (spateo.tools.ST_regression.spatial_regression.Base_Model method) U uniform_larger_pc() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.mesh_utils) uniform_mesh() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.mesh) (in module spateo.tdr.models.mesh.mesh_utils) UNS_PP_KEY (spateo.configuration.SpateoAdataKeyManager attribute) UNS_SPATIAL_ALIGNMENT_KEY (spateo.configuration.SpateoAdataKeyManager attribute) UNS_SPATIAL_BINSIZE_KEY (spateo.configuration.SpateoAdataKeyManager attribute) UNS_SPATIAL_KEY (spateo.configuration.SpateoAdataKeyManager attribute) UNS_SPATIAL_QC_KEY (spateo.configuration.SpateoAdataKeyManager attribute) UNS_SPATIAL_SCALE_KEY (spateo.configuration.SpateoAdataKeyManager attribute) UNS_SPATIAL_SCALE_UNIT_KEY (spateo.configuration.SpateoAdataKeyManager attribute) UNS_SPATIAL_SEGMENTATION_KEY (spateo.configuration.SpateoAdataKeyManager attribute) UNSPLICED_LAYER_KEY (spateo.configuration.SpateoAdataKeyManager attribute) update_dict() (in module spateo.tools.utils) V vega_10 (in module spateo.plotting.static.colorlabel) vega_10_scanpy (in module spateo.plotting.static.colorlabel) vega_20 (in module spateo.plotting.static.colorlabel) vega_20_scanpy (in module spateo.plotting.static.colorlabel) Version (class in spateo.get_version) VERSIONS (in module spateo.io.bgi) (in module spateo.io.nanostring) (in module spateo.io.slideseq) (in module spateo.io.tenx) vi_plot() (spateo.tools.cluster_lasso.Lasso method) (spateo.tools.Lasso method) visualize_params() (spateo.tools.ST_regression.spatial_regression.Base_Model method) voxelize_mesh() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.voxel) (in module spateo.tdr.models.voxel.voxel_model) voxelize_pc() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.voxel) (in module spateo.tdr.models.voxel.voxel_model) W wald_test() (in module spateo.tools.ST_regression.regression_utils) watershed() (in module spateo.segmentation) (in module spateo.segmentation.label) weighted_cosine_distance() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.nn_losses) weighted_expr_neighbors_graph() (in module spateo.tools) (in module spateo.tools.find_neighbors) weighted_mad() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.nn_losses) weighted_mean() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.nn_losses) weighted_mse() (in module spateo.tdr) (in module spateo.tdr.widgets) (in module spateo.tdr.widgets.nn_losses) weighted_spatial_graph() (in module spateo.tools) (in module spateo.tools.find_neighbors) weights_init() (spateo.tools.spatial_impute.impute_model.Discriminator method) wrap_to_plotter() (in module spateo.plotting.static.three_d_plot.three_dims_plots) X X_LAYER (spateo.configuration.SpateoAdataKeyManager attribute) Z zebrafish_256 (in module spateo.configuration) zebrafish_colors (in module spateo.configuration) zeileis_28 (in module spateo.plotting.static.colorlabel)