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 _ __call__() (spateo.tools.CCI_effects_modeling.distributions.Binomial_Variance method) (spateo.tools.CCI_effects_modeling.distributions.Log method) (spateo.tools.CCI_effects_modeling.distributions.Logit method) (spateo.tools.CCI_effects_modeling.distributions.Negative_Binomial_Variance method) (spateo.tools.CCI_effects_modeling.distributions.Power method) (spateo.tools.CCI_effects_modeling.distributions.Power_Variance method) (spateo.tools.CCI_effects_modeling.distributions.VarianceFunction method) __repr__() (spateo.tools.cluster.spagcn_utils.GraphConvolution method) (spateo.tools.Label method) (spateo.tools.labels.Label 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) _apply_layout() (spateo.plotting.static.networks.PlotNetwork method) _augment_labels() (in module spateo.segmentation.label) _blue() (in module spateo.plotting.static.utils) _cal_dis() (in module spateo.tools.spatially_variable_gene_ot) _cal_geodesic_distance() (in module spateo.tools.spatially_variable_gene_ot) _cal_wass_dis() (in module spateo.tools.spatially_variable_gene_ot) _cal_wass_dis_on_genes() (in module spateo.tools.spatially_variable_gene_ot) _cat (in module spateo.alignment.methods.morpho_sparse_utils) (in module spateo.alignment.methods.utils) _cellpose() (in module spateo.segmentation.external.cellpose) _check_cpos_in_multi_plot() (in module spateo.plotting.static.three_d_plot.align_plots) _check_index_in_adata() (in module spateo.plotting.static.three_d_plot.morphometrics_plots) _check_key_in_adata() (in module spateo.plotting.static.three_d_plot.morphometrics_plots) _choice (in module spateo.alignment.methods.utils) _chunk (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) _compute_all_wi() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) _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) _con_K() (in module spateo.tdr.morphometrics.morphofield.gaussian_process) _con_K_geodist() (in module spateo.tdr.morphometrics.morphofield.gaussian_process) _construct_arrow() (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.arrow_model) _construct_label_mask() (in module spateo.alignment.methods.morpho_sparse_utils) _construct_line() (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.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) _data (in module spateo.alignment.methods.utils) _deepcell() (in module spateo.segmentation.external.deepcell) _dendrogram_sig() (in module spateo.plotting.static.utils) _dense_to_sparse() (in module spateo.alignment.methods.morpho_sparse_utils) _dist() (in module spateo.alignment.methods.morpho_sparse_utils) (in module spateo.alignment.methods.utils) _dot (in module spateo.alignment.methods.morpho_sparse_utils) (in module spateo.alignment.methods.utils) _dotplot() (spateo.plotting.static.dotplot.Dotplot static method) _dstack (in module spateo.alignment.methods.utils) _embed_datashader_in_an_axis() (in module spateo.plotting.static.utils) _euclidean_distance() (in module spateo.tdr.models.models_backbone.backbone_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.morphometrics.morphofield_dg.differential_geometry) _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.three_dims_plotter) _get_extent() (in module spateo.plotting.static.utils) _get_mean_var() (in module spateo.preprocessing.transform) _getlink() (spateo.tools.CCI_effects_modeling.distributions.Distribution method) _gp_velocity() (in module spateo.tdr.morphometrics.morphofield.gaussian_process) _green() (in module spateo.plotting.static.utils) _hstack (in module spateo.alignment.methods.utils) _identity (in module spateo.alignment.methods.utils) _init_guess_beta2() (in module spateo.alignment.methods.morpho_sparse_utils) _init_guess_sigma2() (in module spateo.alignment.methods.morpho_sparse_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) _iteration() (in module spateo.alignment.utils) _kernel_functions() (spateo.tools.find_neighbors.Kernel method) _label_connected_components() (in module spateo.segmentation.label) _linalg (in module spateo.alignment.methods.utils) _mainplot() (spateo.plotting.static.dotplot.Dotplot method) _mask_cells_from_stain() (in module spateo.segmentation.icell) _mask_from_label_prior() (in module spateo.alignment.methods.utils) _mask_nuclei_from_stain() (in module spateo.segmentation.icell) _matplotlib_points() (in module spateo.plotting.static.utils) _merge_models() (in module spateo.alignment.deformation) _morphofield_sparsevfc() (in module spateo.tdr.morphometrics.morphofield.sparsevfc) _mul (in module spateo.alignment.methods.utils) _normalize_data() (in module spateo.preprocessing.normalize) _o3d2pv() (in module spateo.tdr.models.models_individual.mesh_methods) _pi (in module spateo.alignment.methods.utils) _pinv (in module spateo.alignment.methods.utils) _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) _power (in module spateo.alignment.methods.utils) _prod (in module spateo.alignment.methods.utils) _psi (in module spateo.alignment.methods.utils) _pv2o3d() (in module spateo.tdr.models.models_individual.mesh_methods) _rand_binary_array() (in module spateo.tools.labels) _randperm (in module spateo.alignment.methods.utils) _red() (in module spateo.plotting.static.utils) _repeat_interleave (in module spateo.alignment.methods.morpho_sparse_utils) _replace_labels() (in module spateo.segmentation.label) _roll (in module spateo.alignment.methods.utils) _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) _set_search_range() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) _set_up_model() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) _setlink() (spateo.tools.CCI_effects_modeling.distributions.Distribution method) _smooth_image() (spateo.preprocessing.auxseg.LiveWireSegmentation method) (spateo.tools.live_wire.LiveWireSegmentation method) (spateo.tools.LiveWireSegmentation method) _sort() (in module spateo.alignment.methods.morpho_sparse_utils) _SparseTensor() (in module spateo.alignment.methods.morpho_sparse_utils) _split (in module spateo.alignment.methods.morpho_sparse_utils) _stardist() (in module spateo.segmentation.external.stardist) _stardist_big() (in module spateo.segmentation.external.stardist) _streamlines_projection() (in module spateo.plotting.static.utils) _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) _topk (in module spateo.alignment.methods.utils) _unique (in module spateo.alignment.methods.utils) _unsqueeze (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) _update_var_groups() (spateo.plotting.static.dotplot.Dotplot method) _var (in module spateo.alignment.methods.utils) _vector_projection() (in module spateo.plotting.static.utils) _vstack (in module spateo.alignment.methods.utils) _watershed() (in module spateo.segmentation.label) _where (in module spateo.alignment.methods.morpho_sparse_utils) A A (class in spateo.tdr.interpolations.interpolation_deeplearn.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.morphometrics_plots) ADATA_AGG_TYPE (spateo.configuration.SpateoAdataKeyManager attribute) ADATA_DEFAULT_TYPE (spateo.configuration.SpateoAdataKeyManager attribute) adata_is_type() (spateo.configuration.SpateoAdataKeyManager method) adata_path (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) 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_dendrogram() (spateo.plotting.static.dotplot.Dotplot method) add_eh_boundary() (in module spateo.digitization.utils) add_ep_boundary() (in module spateo.digitization) (in module spateo.digitization.utils_old) add_gh_boundary() (in module spateo.digitization.utils) add_gp_boundary() (in module spateo.digitization) (in module spateo.digitization.utils_old) add_image_layer() (in module spateo.io.image_utils) add_interaction_effect_to_adata() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) add_legend() (in module spateo.plotting.static.three_d_plot.three_dims_plotter) add_model() (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.three_dims_plotter) add_outline() (in module spateo.plotting.static.three_d_plot.three_dims_plotter) add_pos_ratio_to_adata() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) add_sig_to_cell() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.allocate_cell) add_str_legend() (in module spateo.plotting.static.three_d_plot.three_dims_plotter) add_text() (in module spateo.plotting.static.three_d_plot.three_dims_plotter) adj_to_igraph() (in module spateo.tools.cluster.leiden) adj_to_knn() (in module spateo.tools.find_neighbors) 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_preprocess() (in module spateo.alignment) (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) align_slices_pca() (in module spateo.tools) (in module spateo.tools.coarse_align) AlignmentRefiner (class in spateo.segmentation.align) alpha_shape() (in module spateo.io) (in module spateo.io.bbs) (in module spateo.plotting.static.utils) alpha_shape_mesh() (in module spateo.tdr.models.models_individual.mesh_methods) Application (in module spateo.segmentation.external.deepcell) apply_threshold() (in module spateo.segmentation.utils) Approx_GPModel (class in spateo.tdr.interpolations.interpolation_gaussianprocess) (class in spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models) 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) assign_significance() (in module spateo.tools.CCI_effects_modeling.regression_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) axolotl() (in module spateo.sample_data) B B (class in spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn) BA_align() (in module spateo.alignment.methods) (in module spateo.alignment.methods.morpho) BA_align_sparse() (in module spateo.alignment.methods) (in module spateo.alignment.methods.morpho_sparse) BA_transform() (in module spateo.alignment) (in module spateo.alignment.transform) BA_transform_and_assignment() (in module spateo.alignment) (in module spateo.alignment.transform) backbone() (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.backbone_plots) backbone_scc() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_backbone) (in module spateo.tdr.models.models_backbone.backbone) ball_pivoting_mesh() (in module spateo.tdr.models.models_individual.mesh_methods) base (spateo.plotting.static.dotplot.CCDotplot attribute) bin_adata() (in module spateo.preprocessing.aggregate) (in module spateo.svg), [1], [2] (in module spateo.svg.utils) (in module spateo.tools.spatially_variable_gene_ot) bin_indices() (in module spateo.io.utils) bin_matrix() (in module spateo.io.utils) bin_scale_adata_get_distance() (in module spateo.svg), [1] (in module spateo.svg.get_svg) binary_morani_result() (in module spateo.segmentation.moran) binom_variance (in module spateo.tools.CCI_effects_modeling.distributions) Binomial (class in spateo.tools.CCI_effects_modeling.distributions) Binomial_Variance (class in spateo.tools.CCI_effects_modeling.distributions) BINS_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) boundary_gridding() (in module spateo.digitization) (in module spateo.digitization.boundary_old) BOUNDARY_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) bw (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) bw_fixed (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) C c_to_a_ratio_dis() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.prepare) cal_ami() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.evaluation) cal_cell_area() (in module spateo.segmentation.utils) cal_dist() (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) cal_dot() (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) cal_euclidean_distance() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) cal_f1score() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.evaluation) cal_geodesic_distance() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) cal_gro_wass_bs() (in module spateo.svg) (in module spateo.svg.get_svg_between_slice) cal_gw_dis_on_genes() (in module spateo.svg) (in module spateo.svg.get_svg_between_slice) cal_precision() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.evaluation) cal_rank_p() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) cal_wass_dis() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) cal_wass_dis_bs() (in module spateo.tools.spatially_variable_gene_ot) cal_wass_dis_for_genes() (in module spateo.svg) (in module spateo.svg.get_svg) cal_wass_dis_nobs() (in module spateo.svg) (in module spateo.svg.get_svg) cal_wass_dis_target_on_genes() (in module spateo.svg) (in module spateo.svg.get_svg) cal_wass_dist_bs() (in module spateo.svg) (in module spateo.svg.get_svg) calc_1nd_moment() (in module spateo.tools.utils) calc_distance() (in module spateo.alignment.methods.morpho_sparse_utils) calc_exp_dissimilarity() (in module spateo.alignment) (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) calc_op_field() (in module spateo.digitization) (in module spateo.digitization.utils_old) calc_P_related() (in module spateo.alignment.methods.morpho_sparse_utils) calcFactorQuantile() (in module spateo.preprocessing.normalize) calcFactorRLE() (in module spateo.preprocessing.normalize) calcFactorTMM() (in module spateo.preprocessing.normalize) calcFactorTMMwsp() (in module spateo.preprocessing.normalize) calcNormFactors() (in module spateo.preprocessing.normalize) calculate_adj_matrix() (in module spateo.tools.cluster.spagcn_utils) calculate_affinity() (in module spateo.tools.find_neighbors) calculate_distance() (in module spateo.tools.find_neighbors) calculate_distances_chunk() (in module spateo.tools.find_neighbors) calculate_eigenvector() (in module spateo.tdr.morphometrics.shape_similarity) calculate_group_pair_lr_pair() (in module spateo.tools.cci_two_cluster) calculate_leiden_partition() (in module spateo.tools.cluster.leiden) calculate_p() (in module spateo.tools.cluster.spagcn_utils) CCDotplot (class in spateo.plotting.static.dotplot) CCI_deg_detection() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) CCI_deg_detection_setup() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) cci_dir (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) Cell (class in spateo.segmentation.simulation_evaluation.allocate_cell) cell_area_dis() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.prepare) cell_directions() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield) (in module spateo.tdr.morphometrics.morphofield.sparsevfc) cell_marginals() (in module spateo.segmentation.bp) cell_type_interaction_fold_change() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) cell_type_specific_interactions() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) cellbin_morani() (in module spateo.tools) (in module spateo.tools.spatial_degs) cellbin_select() (in module spateo.plotting) (in module spateo.plotting.interactive) (in module spateo.plotting.interactive.agg) Cellpose (in module spateo.segmentation.external.cellpose) cellpose() (in module spateo.segmentation) (in module spateo.segmentation.external.cellpose) center_NMF() (in module spateo.alignment.methods.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) check_adata_is_type() (spateo.configuration.SpateoAdataKeyManager method) check_backend() (in module spateo.alignment.methods.utils) check_colornorm() (in module spateo.plotting.static.utils) check_exp() (in module spateo.alignment.methods.utils) check_spatial_coords() (in module spateo.alignment.methods.utils) 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.models_individual.mesh_utils) clear() (in module spateo.tools.roi) clip() (spateo.tools.CCI_effects_modeling.distributions.Binomial_Variance method) (spateo.tools.CCI_effects_modeling.distributions.Distribution method) (spateo.tools.CCI_effects_modeling.distributions.Gamma method) (spateo.tools.CCI_effects_modeling.distributions.Log method) (spateo.tools.CCI_effects_modeling.distributions.Logit method) (spateo.tools.CCI_effects_modeling.distributions.Negative_Binomial_Variance method) (spateo.tools.CCI_effects_modeling.distributions.NegativeBinomial method) (spateo.tools.CCI_effects_modeling.distributions.Poisson method) coarse_rigid_alignment() (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) coarse_rigid_alignment_debug() (in module spateo.alignment.methods.utils) 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_acceleration() (in module spateo.tdr.morphometrics.morphofield_dg.GPVectorField) (spateo.tdr.morphometrics.morphofield_dg.GPVectorField.GPVectorField method) compute_aicc_glm() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) compute_aicc_linear() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) compute_and_visualize_diagnostics() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) compute_betas() (in module spateo.tools.CCI_effects_modeling.regression_utils) compute_betas_local() (in module spateo.tools.CCI_effects_modeling.regression_utils) compute_coeff_significance() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) compute_corr_ci() (in module spateo.tools.utils) compute_curl() (in module spateo.tdr.morphometrics.morphofield_dg.GPVectorField) (spateo.tdr.morphometrics.morphofield_dg.GPVectorField.GPVectorField method) compute_curvature() (in module spateo.tdr.morphometrics.morphofield_dg.GPVectorField) (spateo.tdr.morphometrics.morphofield_dg.GPVectorField.GPVectorField method) compute_distances_and_connectivities() (in module spateo.tools.find_neighbors) compute_divergence() (in module spateo.tdr.morphometrics.morphofield_dg.GPVectorField) (spateo.tdr.morphometrics.morphofield_dg.GPVectorField.GPVectorField method) compute_gene_groups_p_val() (in module spateo.tools.gene_expression_variance) compute_jaccard_similarity_matrix() (in module spateo.tools.spatial_smooth) compute_pca_components() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) compute_sensitivity() (in module spateo.tdr.morphometrics.morphofield_dg.GPVectorField) 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_torsion() (in module spateo.tdr.morphometrics.morphofield_dg.GPVectorField) (spateo.tdr.morphometrics.morphofield_dg.GPVectorField.GPVectorField method) compute_variance_decomposition() (in module spateo.tools.gene_expression_variance) compute_velocity() (spateo.tdr.morphometrics.morphofield_dg.GPVectorField.GPVectorField method) con_K() (in module spateo.alignment.methods.morpho) (in module spateo.alignment.methods.morpho_sparse) 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) constant_var (in module spateo.tools.CCI_effects_modeling.distributions) construct_align_lines() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.line_model) construct_arrow() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.arrow_model) construct_arrows() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.arrow_model) construct_axis_line() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.line_model) construct_backbone() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_backbone) (in module spateo.tdr.models.models_backbone.backbone) construct_cells() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_individual) (in module spateo.tdr.models.models_individual.mesh) construct_field() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.morphofield_model) construct_field_streams() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.morphofield_model) construct_genesis() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.morphopath_model) construct_genesis_X() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.morphopath_model) construct_line() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.line_model) construct_lines() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.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.models_individual) (in module spateo.tdr.models.models_individual.point_clouds) construct_surface() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_individual) (in module spateo.tdr.models.models_individual.mesh) construct_trajectory() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.morphopath_model) construct_trajectory_X() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.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) coords_key (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) copy_adata() (in module spateo.utils) cos_global_centroid_to_subspace() (in module spateo.tdr.morphometrics.shape_similarity) cosine_distance() (in module spateo.tdr.interpolations.interpolation_deeplearn.nn_losses) COUNT_COLUMN_MAPPING (in module spateo.io.bgi) covariate_keys (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) create_label_class() (in module spateo.tools) (in module spateo.tools.labels) create_line() (in module spateo.tdr.widgets.slice) create_model() (spateo.tdr.models.models_backbone.backbone_methods.NLPCA method) create_neighbor_offsets() (in module spateo.segmentation.bp) create_new_coordinate() (in module spateo.tools.utils) create_plotter() (in module spateo.plotting.static.three_d_plot.three_dims_plotter) create_polygon_object_nanostring() (in module spateo.plotting.static.geo) CRITICAL (spateo.external.lack.LoggerManager attribute) critical() (spateo.external.lack.Logger method) csv_path (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) 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.morphometrics_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.morphometrics_plots) custom_lig_path (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) custom_ligands (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) custom_pathways (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) custom_pathways_path (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) custom_rec_path (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) custom_receptors (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) custom_targets (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) 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.interpolations.interpolation_deeplearn) (class in spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation) deaxis_all() (in module spateo.plotting.static.utils) DEBUG (spateo.external.lack.LoggerManager attribute) debug() (spateo.external.lack.Logger method) deduplicate_kwargs() (in module spateo.plotting.static.utils) deep_intepretation() (in module spateo.tdr) (in module spateo.tdr.interpolations) (in module spateo.tdr.interpolations.interpolation_dl) deepcell() (in module spateo.segmentation) (in module spateo.segmentation.external.deepcell) DeepInterpolation (class in spateo.tdr.interpolations.interpolation_deeplearn) (class in spateo.tdr.interpolations.interpolation_deeplearn.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) define_effect_vf() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) define_sig_inputs() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) define_spateo_argparse() (in module spateo.tools) (in module spateo.tools.CCI_effects_modeling) (in module spateo.tools.CCI_effects_modeling.SWR) deformation() (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.align_plots) deg_effect_barplot() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) deg_effect_heatmap() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) 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) deriv() (spateo.tools.CCI_effects_modeling.distributions.Binomial_Variance method) (spateo.tools.CCI_effects_modeling.distributions.Link method) (spateo.tools.CCI_effects_modeling.distributions.Log method) (spateo.tools.CCI_effects_modeling.distributions.Logit method) (spateo.tools.CCI_effects_modeling.distributions.Negative_Binomial_Variance method) (spateo.tools.CCI_effects_modeling.distributions.Power method) (spateo.tools.CCI_effects_modeling.distributions.Power_Variance method) (spateo.tools.CCI_effects_modeling.distributions.VarianceFunction method) despline() (in module spateo.plotting.static.utils) despline_all() (in module spateo.plotting.static.utils) dev (spateo.get_version.Version attribute) deviance() (spateo.tools.CCI_effects_modeling.distributions.Binomial method) (spateo.tools.CCI_effects_modeling.distributions.Distribution method) (spateo.tools.CCI_effects_modeling.distributions.Gamma method) (spateo.tools.CCI_effects_modeling.distributions.Gaussian method) (spateo.tools.CCI_effects_modeling.distributions.NegativeBinomial method) (spateo.tools.CCI_effects_modeling.distributions.Poisson method) deviance_residuals() (spateo.tools.CCI_effects_modeling.distributions.Binomial method) (spateo.tools.CCI_effects_modeling.distributions.Distribution method) (spateo.tools.CCI_effects_modeling.distributions.Gamma method) (spateo.tools.CCI_effects_modeling.distributions.Gaussian method) (spateo.tools.CCI_effects_modeling.distributions.NegativeBinomial method) (spateo.tools.CCI_effects_modeling.distributions.Poisson method) digitize() (in module spateo.digitization) (in module spateo.digitization.grid) dist() (spateo.segmentation.vi.NegativeBinomialMixture method) dist_global_centroid_to_subspace() (in module spateo.tdr.morphometrics.shape_similarity) distance_knn_graph() (in module spateo.tools.cluster.leiden) DISTANCES_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) distr (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) Distribution (class in spateo.tools.CCI_effects_modeling.distributions) 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.morphometrics_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) downsampling() (in module spateo.alignment) (in module spateo.alignment.utils) (in module spateo.svg) (in module spateo.svg.get_svg) drag_mode() (in module spateo.tools.roi) draw_init() (in module spateo.tools.roi) draw_seg_grid() (in module spateo.digitization) (in module spateo.digitization.utils) (in module spateo.digitization.utils_old) drosophila() (in module spateo.sample_data) E ecp_silhouette() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) effect_distribution_density() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) effect_distribution_heatmap() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) effective_L2_error() (in module spateo.digitization) (in module spateo.digitization.utils) (in module spateo.digitization.utils_old) ElPiGraph_method() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_backbone) (in module spateo.tdr.models.models_backbone.backbone_methods) embedding_knn_graph() (in module spateo.tools.cluster.leiden) empty_cache() (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) enriched_interactions_barplot() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) enriched_tfs_barplot() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) EPS (in module spateo.configuration) error() (spateo.external.lack.Logger method) estimate() (spateo.plotting.static.utils.Loess method) euclidean_dist() (in module spateo.digitization) (in module spateo.digitization.utils) (in module spateo.digitization.utils_old) euclidean_distance() (in module spateo.tdr.widgets.slice) eval_permutation_test() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) Exact_GPModel (class in spateo.tdr.interpolations.interpolation_gaussianprocess) (class in spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models) EXCEPTION (spateo.external.lack.LoggerManager attribute) exception() (spateo.external.lack.Logger method) exclude_self (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) 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) (in module spateo.digitization.utils) (in module spateo.digitization.utils_old) EXTEND_WIDTH (in module spateo.tools.roi) extract_cluster_contours() (in module spateo.digitization), [1] (in module spateo.digitization.contour) extract_data_matrix (in module spateo.alignment.methods.utils) F factor_normalization() (in module spateo.preprocessing.normalize) fdr_correct() (in module spateo.tools.cci_fdr) feature() (in module spateo.plotting.static.three_d_plot.morphometrics_plots) field_contour_line() (in module spateo.digitization) (in module spateo.digitization.utils) (in module spateo.digitization.utils_old) field_contours() (in module spateo.digitization) (in module spateo.digitization.utils) (in module spateo.digitization.utils_old) fill (in module spateo.tools.roi) fill_contours() (spateo.preprocessing.auxseg.LiveWireSegmentation static method) fill_grid_label() (in module spateo.digitization) (in module spateo.digitization.utils) (in module spateo.digitization.utils_old) fill_mask_color() (in module spateo.tools.roi) filter_adata_by_pos_ratio() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) filter_adata_custom() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) filter_adata_spatial() (in module spateo.tools.utils) (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) 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.alignment.methods.utils) filter_genes() (in module spateo.preprocessing.filter) find_all_cluster_degs() (in module spateo.tools) (in module spateo.tools.cluster_degs) find_bw_for_n_neighbors() (in module spateo.tools.find_neighbors) 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_optimal_bw() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) find_optimal_n_umap_components() (in module spateo.tools.dimensionality_reduction) find_optimal_pca_components() (in module spateo.tools.dimensionality_reduction) 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) find_targets() (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector method) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector method) (spateo.tools.MuSIC_Molecule_Selector method) find_threshold_distance() (in module spateo.tools.find_neighbors) finish_progress() (spateo.external.lack.Logger method) fire_cmap (in module spateo.configuration) fit() (spateo.tdr.models.models_backbone.backbone_methods.NLPCA method) (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) (spateo.tools.MuSIC method) fit_intercept (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) fitted (in module spateo.tools.CCI_effects_modeling.distributions) fitted_cubed (in module spateo.tools.CCI_effects_modeling.distributions) fitted_squared (in module spateo.tools.CCI_effects_modeling.distributions) fix_mesh() (in module spateo.tdr.models.models_individual.mesh_utils) flatten() (in module spateo.tools.utils) FORMAT (spateo.external.lack.Logger attribute) format_boundary_line() (in module spateo.digitization) (in module spateo.digitization.utils_old) format_logging_message() (in module spateo.external.lack) forward() (spateo.segmentation.align.AlignmentRefiner method) (spateo.segmentation.vi.NegativeBinomialMixture method) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.A method) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.B method) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.h method) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.MainFlow method) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.SineLayer method) (spateo.tdr.interpolations.interpolation_gaussianprocess.Approx_GPModel method) (spateo.tdr.interpolations.interpolation_gaussianprocess.Exact_GPModel method) (spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models.Approx_GPModel method) (spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models.Exact_GPModel method) (spateo.tools.cluster.spagcn_utils.GraphConvolution method) (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) forward_with_intermediate() (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.SineLayer method) FOV_PARSER (in module spateo.io.nanostring) from_adata() (spateo.tdr.morphometrics.morphofield_dg.GPVectorField.GPVectorField method) G Gamma (class in spateo.tools.CCI_effects_modeling.distributions) Gaussian (class in spateo.tools.CCI_effects_modeling.distributions) gaussian_blur() (in module spateo.segmentation.utils) gen_cluster_image() (in module spateo.digitization), [1] (in module spateo.digitization.contour) gen_logger() (spateo.external.lack.LoggerManager static method) gen_new_layer_key() (spateo.configuration.SpateoAdataKeyManager method) gen_rotation_2d() (in module spateo.tools.utils) gene_expression_heatmap() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) generalized_procrustes_analysis() (in module spateo.alignment.methods) (in module spateo.alignment.methods.paste) generate_batch() (spateo.tdr.interpolations.interpolation_deeplearn.DataSampler method) (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DataSampler method) generate_edge_traces() (spateo.plotting.static.networks.PlotNetwork method) generate_edges() (in module spateo.tdr.models.models_migration) (in module spateo.tdr.models.models_migration.line_model) generate_figure() (spateo.plotting.static.networks.PlotNetwork method) generate_node_traces() (spateo.plotting.static.networks.PlotNetwork method) 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) 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_all_dependencies_version() (in module spateo.get_version) get_axes() (spateo.plotting.static.dotplot.Dotplot method) get_axes_from_area_and_ctoa() (in module spateo.segmentation.simulation_evaluation.allocate_cell) get_axes_from_area_and_ltos() (in module spateo.segmentation.simulation_evaluation.allocate_cell) get_bin_props() (in module spateo.io.utils) get_borderline() (in module spateo.digitization) (in module spateo.digitization.borderline) get_cell_pos() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.allocate_cell) get_cell_shape() (in module spateo.segmentation.utils) get_center() (in module spateo.segmentation.simulation_evaluation.allocate_cell) 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_data() (spateo.tdr.morphometrics.morphofield_dg.GPVectorField.GPVectorField method) get_effect_potential() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) get_eligible_rows() (in module spateo.tools.spatial_smooth) get_fb_dis() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.prepare) get_fb_dis_window() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.prepare) get_fisher_inverse() (in module spateo.tools.CCI_effects_modeling.regression_utils) get_genes_by_pos_ratio() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) get_genes_from_spatial_archetype() (in module spateo.tools) (in module spateo.tools.architype) get_highvar_genes() (in module spateo.tools.gene_expression_variance) get_highvar_genes_sparse() (in module spateo.tools.gene_expression_variance) get_Jacobian() (spateo.tdr.morphometrics.morphofield_dg.GPVectorField.GPVectorField method) get_label_props() (in module spateo.io.utils) get_labels_based_on_coords() (in module spateo.alignment) (in module spateo.alignment.utils) get_main_logger() (spateo.external.lack.LoggerManager method) 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_optimal_mapping_relationship() (in module spateo.alignment) (in module spateo.alignment.utils) get_optimal_R() (in module spateo.alignment.methods.utils) get_optimal_R_sparse() (in module spateo.alignment.methods.morpho_sparse_utils) get_P() (in module spateo.alignment.methods.morpho) get_P_chunk() (in module spateo.alignment.methods.morpho) (in module spateo.alignment.transform) get_P_sparse() (in module spateo.alignment.methods.morpho_sparse) get_params() (spateo.segmentation.align.AlignmentRefiner method) (spateo.segmentation.align.NonRigidAlignmentRefiner method) (spateo.segmentation.align.RigidAlignmentRefiner method) (spateo.segmentation.vi.NegativeBinomialMixture method) get_pathway_potential() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) get_points_props() (in module spateo.io.utils) get_predictors() (spateo.tools.CCI_effects_modeling.distributions.Distribution method) get_std_wasserstein() (in module spateo.svg) (in module spateo.svg.get_svg) get_temp_timer_logger() (spateo.external.lack.LoggerManager method) 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_wi() (in module spateo.tools.find_neighbors) get_X_Y_grid() (in module spateo.tdr.interpolations) (in module spateo.tdr.interpolations.utils) glasbey_dark_cmap (in module spateo.configuration) glasbey_white_cmap (in module spateo.configuration) 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_heatmap() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.glm) glm_test() (in module spateo.tools.glm) GM_lag_model() (in module spateo.tools) (in module spateo.tools.lisa) godsnot_102 (in module spateo.plotting.static.colorlabel) golden_section_search() (in module spateo.tools.CCI_effects_modeling.regression_utils) gp_interpolation() (in module spateo.tdr) (in module spateo.tdr.interpolations) (in module spateo.tdr.interpolations.interpolation_gp) gp_train() (in module spateo.tdr.interpolations.interpolation_gaussianprocess) (in module spateo.tdr.interpolations.interpolation_gaussianprocess.gp_train) GPVectorField (class in spateo.tdr.morphometrics.morphofield_dg.GPVectorField) GraphConvolution (class in spateo.tools.cluster.spagcn_utils) grid_borderline() (in module spateo.digitization) (in module spateo.digitization.borderline) grid_deformation() (in module spateo.alignment) (in module spateo.alignment.deformation) gridit() (in module spateo.digitization) (in module spateo.digitization.grid) group_key (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) group_subset (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) H h (class in spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn) has_uns_spatial_attribute() (spateo.configuration.SpateoAdataKeyManager method) high2low() (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation method) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation method) I identify_boundary() (in module spateo.digitization) (in module spateo.digitization.boundary_old) identity (class in spateo.tools.CCI_effects_modeling.distributions) image (spateo.preprocessing.auxseg.LiveWireSegmentation property) (spateo.tools.live_wire.LiveWireSegmentation property) (spateo.tools.LiveWireSegmentation property) img_segmentation() (in module spateo.tools.roi) Imputation_GPR (class in spateo.tdr.interpolations.interpolation_gp) 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) inference() (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR method) inferred_effect_direction() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) INFO (spateo.external.lack.LoggerManager attribute) info() (spateo.external.lack.Logger method) info_insert_adata() (spateo.external.lack.Logger method) info_insert_adata_obsm() (spateo.external.lack.Logger method) info_insert_adata_uns() (spateo.external.lack.Logger method) info_insert_adata_var() (spateo.external.lack.Logger method) init_adata_type() (spateo.configuration.SpateoAdataKeyManager method) init_best_params() (spateo.segmentation.vi.NegativeBinomialMixture method) init_betas_path (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) 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.interpolations.interpolation_deeplearn.interpolation_nn.SineLayer method) initial_predictions() (spateo.tools.CCI_effects_modeling.distributions.Binomial method) (spateo.tools.CCI_effects_modeling.distributions.Distribution method) inlier_from_NN() (in module spateo.alignment.methods.utils) inlier_from_NN_debug() (in module spateo.alignment.methods.utils) integrate() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) interaction_colors (in module spateo.plotting.static.colorlabel) 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() (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR method) intersect_lsts (in module spateo.alignment.methods.utils) inverse() (spateo.tools.CCI_effects_modeling.distributions.Link method) (spateo.tools.CCI_effects_modeling.distributions.Log method) (spateo.tools.CCI_effects_modeling.distributions.Logit method) (spateo.tools.CCI_effects_modeling.distributions.Power method) inverse_deriv() (spateo.tools.CCI_effects_modeling.distributions.Link method) (spateo.tools.CCI_effects_modeling.distributions.Log method) (spateo.tools.CCI_effects_modeling.distributions.Logit method) (spateo.tools.CCI_effects_modeling.distributions.Power method) inverse_power (class in spateo.tools.CCI_effects_modeling.distributions) 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) iwls() (in module spateo.tools.CCI_effects_modeling.regression_utils) J jaccard_index() (in module spateo.tools.find_neighbors) 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.morphometrics_plots) Jacobian_GP_gaussian_kernel() (in module spateo.tdr.morphometrics.morphofield_dg.GPVectorField) K Kernel (class in spateo.tools.find_neighbors) kernel (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) kernel_interpolation() (in module spateo.tdr) (in module spateo.tdr.interpolations) (in module spateo.tdr.interpolations.interpolation_sparseVFC) key_pressed() (spateo.preprocessing.auxseg.LiveWireSegmentation method) kl_distance() (in module spateo.alignment.methods.utils) kl_divergence_backend() (in module spateo.alignment.methods.utils) knee_threshold() (in module spateo.segmentation.utils) knn_to_adj() (in module spateo.tools.find_neighbors) L 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) 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) library_scaling_factors() (in module spateo.tools.CCI_effects_modeling.regression_utils) 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) Link (class in spateo.tools.CCI_effects_modeling.distributions) link (spateo.tools.CCI_effects_modeling.distributions.Distribution attribute) 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) lm (in module spateo.digitization) (in module spateo.svg), [1], [2] load() (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation method) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation method) load_and_process() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) local_dist() (in module spateo.tools.find_neighbors) local_fit() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) local_moran_i() (in module spateo.tools) (in module spateo.tools.lisa) Loess (class in spateo.plotting.static.utils) loess_reg() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) Log (class in spateo.tools.CCI_effects_modeling.distributions) 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() (spateo.tools.CCI_effects_modeling.distributions.Binomial method) (spateo.tools.CCI_effects_modeling.distributions.Distribution method) (spateo.tools.CCI_effects_modeling.distributions.Gamma method) (spateo.tools.CCI_effects_modeling.distributions.Gaussian method) (spateo.tools.CCI_effects_modeling.distributions.NegativeBinomial method) (spateo.tools.CCI_effects_modeling.distributions.Poisson method) log_time() (spateo.external.lack.Logger method) log_transform (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) Logger (class in spateo.external.lack) logger_manager (in module spateo.logging) LoggerManager (class in spateo.external.lack) logging_level (spateo.configuration.SpateoConfig property) logistic_objective() (in module spateo.tools.CCI_effects_modeling.regression_utils) Logit (class in spateo.tools.CCI_effects_modeling.distributions) loss() (spateo.segmentation.align.AlignmentRefiner method) loss_function() (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) low2high() (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation method) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation method) lrt() (in module spateo.tools.glm) ltos_ratio_dis() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.prepare) M mad() (in module spateo.tdr.interpolations.interpolation_deeplearn.nn_losses) mae() (in module spateo.tools.CCI_effects_modeling.regression_utils) main() (in module spateo.tools.roi) main_critical() (spateo.external.lack.LoggerManager method) main_debug() (spateo.external.lack.LoggerManager method) main_exception() (spateo.external.lack.LoggerManager method) main_finish_progress() (spateo.external.lack.LoggerManager method) main_info() (spateo.external.lack.LoggerManager method) main_info_insert_adata() (spateo.external.lack.LoggerManager method) main_info_insert_adata_layer() (spateo.external.lack.LoggerManager method) main_info_insert_adata_obs() (spateo.external.lack.LoggerManager method) main_info_insert_adata_obsm() (spateo.external.lack.LoggerManager method) main_info_insert_adata_uns() (spateo.external.lack.LoggerManager method) main_info_insert_adata_var() (spateo.external.lack.LoggerManager method) main_info_verbose_timeit() (spateo.external.lack.LoggerManager method) main_log_time() (spateo.external.lack.LoggerManager method) main_set_level() (spateo.external.lack.LoggerManager method) main_silence() (spateo.external.lack.LoggerManager method) main_tqdm() (spateo.external.lack.LoggerManager method) main_warning() (spateo.external.lack.LoggerManager method) MainFlow (class in spateo.tdr.interpolations.interpolation_deeplearn.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_backbone() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_backbone) (in module spateo.tdr.models.models_backbone.backbone_utils) map_new_cells() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) map_points_to_backbone() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_backbone) (in module spateo.tdr.models.models_backbone.backbone_utils) mapping_aligned_coords() (in module spateo.alignment) (in module spateo.alignment.utils) mapping_center_coords() (in module spateo.alignment) (in module spateo.alignment.utils) marching_cube_mesh() (in module spateo.tdr.models.models_individual.mesh_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) MAX (in module spateo.configuration) maxbw (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) 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) minbw (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) minimal_xticks() (in module spateo.plotting.static.utils) minimal_yticks() (in module spateo.plotting.static.utils) mod_type (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) model_eigenvector() (in module spateo.tdr.morphometrics.shape_similarity) model_morphology() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphology) module spateo spateo.align spateo.alignment spateo.alignment.deformation spateo.alignment.methods spateo.alignment.methods.morpho spateo.alignment.methods.morpho_sparse spateo.alignment.methods.morpho_sparse_utils spateo.alignment.methods.paste spateo.alignment.methods.utils spateo.alignment.morpho_alignment spateo.alignment.paste_alignment spateo.alignment.transform spateo.alignment.utils spateo.configuration spateo.cs spateo.data_io spateo.dd spateo.digitization spateo.digitization.borderline spateo.digitization.boundary_old spateo.digitization.contour spateo.digitization.grid spateo.digitization.utils spateo.digitization.utils_old spateo.errors spateo.external spateo.external.lack 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.dotplot spateo.plotting.static.geo spateo.plotting.static.glm spateo.plotting.static.interactions spateo.plotting.static.lisa spateo.plotting.static.networks 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.align_plots spateo.plotting.static.three_d_plot.backbone_plots spateo.plotting.static.three_d_plot.morphometrics_plots spateo.plotting.static.three_d_plot.pairwise_align_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.simulation_evaluation spateo.segmentation.simulation_evaluation.allocate_cell spateo.segmentation.simulation_evaluation.evaluation spateo.segmentation.simulation_evaluation.prepare spateo.segmentation.utils spateo.segmentation.vi spateo.svg spateo.svg.get_svg spateo.svg.get_svg_between_slice spateo.svg.utils spateo.tdr spateo.tdr.interpolations spateo.tdr.interpolations.interpolation_deeplearn spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn spateo.tdr.interpolations.interpolation_deeplearn.nn_losses spateo.tdr.interpolations.interpolation_dl spateo.tdr.interpolations.interpolation_gaussianprocess spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models spateo.tdr.interpolations.interpolation_gaussianprocess.gp_train spateo.tdr.interpolations.interpolation_gp spateo.tdr.interpolations.interpolation_sparseVFC spateo.tdr.interpolations.interpolation_vtk spateo.tdr.interpolations.utils spateo.tdr.models spateo.tdr.models.models_backbone spateo.tdr.models.models_backbone.backbone spateo.tdr.models.models_backbone.backbone_methods spateo.tdr.models.models_backbone.backbone_utils spateo.tdr.models.models_individual spateo.tdr.models.models_individual.mesh spateo.tdr.models.models_individual.mesh_methods spateo.tdr.models.models_individual.mesh_utils spateo.tdr.models.models_individual.point_clouds spateo.tdr.models.models_individual.voxel spateo.tdr.models.models_migration spateo.tdr.models.models_migration.arrow_model spateo.tdr.models.models_migration.line_model spateo.tdr.models.models_migration.morphofield_model spateo.tdr.models.models_migration.morphopath_model spateo.tdr.models.utilities spateo.tdr.models.utilities.io spateo.tdr.models.utilities.label_utils spateo.tdr.models.utilities.model_utils spateo.tdr.morphometrics spateo.tdr.morphometrics.gene_similarity spateo.tdr.morphometrics.morphofield spateo.tdr.morphometrics.morphofield.gaussian_process spateo.tdr.morphometrics.morphofield.sparsevfc spateo.tdr.morphometrics.morphofield.trajectory spateo.tdr.morphometrics.morphofield_dg spateo.tdr.morphometrics.morphofield_dg.differential_geometry spateo.tdr.morphometrics.morphofield_dg.GPVectorField spateo.tdr.morphometrics.morphology spateo.tdr.morphometrics.shape_similarity spateo.tdr.widgets spateo.tdr.widgets.clip spateo.tdr.widgets.pick spateo.tdr.widgets.slice spateo.tdr.widgets.utils spateo.tl spateo.tools spateo.tools.architype spateo.tools.CCI_effects_modeling spateo.tools.CCI_effects_modeling.distributions spateo.tools.CCI_effects_modeling.MuSIC spateo.tools.CCI_effects_modeling.MuSIC_downstream spateo.tools.CCI_effects_modeling.MuSIC_upstream spateo.tools.CCI_effects_modeling.regression_utils spateo.tools.CCI_effects_modeling.SWR 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.leiden spateo.tools.cluster.spagcn_utils spateo.tools.cluster.utils spateo.tools.cluster_degs spateo.tools.cluster_lasso spateo.tools.coarse_align spateo.tools.dimensionality_reduction spateo.tools.find_neighbors spateo.tools.gene_expression_variance spateo.tools.glm spateo.tools.labels spateo.tools.lisa spateo.tools.live_wire spateo.tools.roi spateo.tools.spatial_degs spateo.tools.spatial_smooth spateo.tools.spatially_variable_gene_ot 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) morpho_align() (in module spateo.alignment) (in module spateo.alignment.morpho_alignment) morpho_align_ref() (in module spateo.alignment) (in module spateo.alignment.morpho_alignment) morpho_align_sparse() (in module spateo.alignment) (in module spateo.alignment.morpho_alignment) morphofield_acceleration() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield_dg) (in module spateo.tdr.morphometrics.morphofield_dg.differential_geometry) morphofield_curl() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield_dg) (in module spateo.tdr.morphometrics.morphofield_dg.differential_geometry) morphofield_curvature() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield_dg) (in module spateo.tdr.morphometrics.morphofield_dg.differential_geometry) morphofield_divergence() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield_dg) (in module spateo.tdr.morphometrics.morphofield_dg.differential_geometry) morphofield_gp() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield) (in module spateo.tdr.morphometrics.morphofield.gaussian_process) morphofield_jacobian() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield_dg) (in module spateo.tdr.morphometrics.morphofield_dg.differential_geometry) morphofield_sparsevfc() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield) (in module spateo.tdr.morphometrics.morphofield.sparsevfc) morphofield_torsion() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield_dg) (in module spateo.tdr.morphometrics.morphofield_dg.differential_geometry) morphofield_velocity() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield_dg) (in module spateo.tdr.morphometrics.morphofield_dg.differential_geometry) morphopath() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphofield) (in module spateo.tdr.morphometrics.morphofield.trajectory) mouse_event() (in module spateo.tools.roi) mouse_moved() (spateo.preprocessing.auxseg.LiveWireSegmentation method) mousebrain() (in module spateo.sample_data) mpi_fit() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) mse() (in module spateo.tdr.interpolations.interpolation_deeplearn.nn_losses) (in module spateo.tools.CCI_effects_modeling.regression_utils) multi_models() (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.align_plots) 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) multicollinear_threshold (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) multicollinearity_check() (in module spateo.tools.CCI_effects_modeling.regression_utils) multitesting_correction() (in module spateo.tools.CCI_effects_modeling.regression_utils) MuSIC (class in spateo.tools) (class in spateo.tools.CCI_effects_modeling) (class in spateo.tools.CCI_effects_modeling.MuSIC) MuSIC_Interpreter (class in spateo.tools) (class in spateo.tools.CCI_effects_modeling) (class in spateo.tools.CCI_effects_modeling.MuSIC_downstream) MuSIC_Molecule_Selector (class in spateo.tools) (class in spateo.tools.CCI_effects_modeling) (class in spateo.tools.CCI_effects_modeling.MuSIC_upstream) muvar_to_lamtheta() (in module spateo.segmentation.em) N n_neighbors (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) n_neighbors_membrane_bound (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) n_neighbors_secreted (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) n_threads (spateo.configuration.SpateoConfig property) namespace_message() (spateo.external.lack.Logger method) namespaced() (spateo.external.lack.Logger method) namespaced_context() (spateo.external.lack.Logger method) nbinom_variance (in module spateo.tools.CCI_effects_modeling.distributions) nbn_em() (in module spateo.segmentation.em) nbn_pmf() (in module spateo.segmentation.em) Negative_Binomial_Variance (class in spateo.tools.CCI_effects_modeling.distributions) NegativeBinomial (class in spateo.tools.CCI_effects_modeling.distributions) NegativeBinomialMixture (class in spateo.segmentation.vi) neighbors() (in module spateo.tools) (in module spateo.tools.find_neighbors) niches() (in module spateo.tools) (in module spateo.tools.cell_communication) NLPCA (class in spateo.tdr.models.models_backbone.backbone_methods) NonRigidAlignmentRefiner (class in spateo.segmentation.align) normalize (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) normalize_adj() (in module spateo.tools.find_neighbors) normalize_array() (spateo.plotting.static.utils.Loess static method) normalize_coords() (in module spateo.alignment.methods.utils) (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR method) normalize_exps() (in module spateo.alignment.methods.utils) normalize_signaling (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) 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) nx_torch (in module spateo.alignment.methods.morpho_sparse_utils) (in module spateo.alignment.methods.utils) O on_hover() (spateo.plotting.static.networks.PlotNetwork method) ON_RTD (in module spateo.get_version) on_unhover() (spateo.plotting.static.networks.PlotNetwork method) 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.models.models_backbone.backbone_methods) output_diagnostics() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) output_path (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) output_plotter() (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 pairwise_iteration() (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.pairwise_align_plots) pairwise_mapping() (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.pairwise_align_plots) pairwise_shape_similarity() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.shape_similarity) parse() (spateo.get_version.Version static method) parse_instruction() (in module spateo.tools.utils) parse_stgwr_args() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) parser (in module spateo.tools.CCI_effects_modeling.SWR) partial_correlation_interactions() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) paste_align() (in module spateo.alignment) (in module spateo.alignment.paste_alignment) paste_align_ref() (in module spateo.alignment) (in module spateo.alignment.paste_alignment) paste_center_align() (in module spateo.alignment.methods) (in module spateo.alignment.methods.paste) paste_pairwise_align() (in module spateo.alignment.methods) (in module spateo.alignment.methods.paste) paste_transform() (in module spateo.alignment) (in module spateo.alignment.transform) pc_KDE() (in module spateo.tdr) (in module spateo.tdr.morphometrics) (in module spateo.tdr.morphometrics.morphology) pca() (in module spateo.tools.dimensionality_reduction) pca_align() (in module spateo.tools) (in module spateo.tools.coarse_align) pca_fit() (in module spateo.tools.dimensionality_reduction) PCA_project() (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) PCA_recover() (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) PCA_reduction() (in module spateo.alignment.methods) (in module spateo.alignment.methods.utils) 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) perform_dimensionality_reduction() (in module spateo.tools.dimensionality_reduction) permutation_test() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) permutation_testing() (in module spateo.tools.CCI_effects_modeling.regression_utils) pi_heatmap() (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.pairwise_align_plots) plot_cell_signaling() (in module spateo.plotting.static.space) 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_expression_3D() (in module spateo.plotting.static.three_d_plot.three_dims_plots) plot_interaction_effect_3D() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) plot_multiple_genes_3D() (in module spateo.plotting.static.three_d_plot.three_dims_plots) plot_multiple_interaction_effects_3D() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) plot_network() (in module spateo.plotting.static.networks) plot_polygon() (in module spateo.plotting.static.utils) plot_tf_effect_3D() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) plot_variance_decomposition() (in module spateo.tools.gene_expression_variance) plot_vectors() (in module spateo.plotting.static.utils) PlotNetwork (class in spateo.plotting.static.networks) PlottingError PlottingWarning Poisson (class in spateo.tools.CCI_effects_modeling.distributions) poisson_mesh() (in module spateo.tdr.models.models_individual.mesh_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) Power (class in spateo.tools.CCI_effects_modeling.distributions) Power_Variance (class in spateo.tools.CCI_effects_modeling.distributions) predict() (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation method) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation method) (spateo.tools.CCI_effects_modeling.distributions.Distribution method) (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) (spateo.tools.cluster.spagcn_utils.SpaGCN method) (spateo.tools.MuSIC method) predict_and_save() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC 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) PreprocessingError PreprocessingWarning PrinCurve_method() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_backbone) (in module spateo.tdr.models.models_backbone.backbone_methods) procrustes() (in module spateo.tools) (in module spateo.tools.coarse_align) progress (in module spateo.segmentation.em) progress_logger() (spateo.external.lack.LoggerManager method) project() (spateo.tdr.models.models_backbone.backbone_methods.NLPCA method) project_and_calculate_distance() (in module spateo.tools.utils) pv_mesh() (in module spateo.tdr.models.models_individual.mesh_methods) Q qc_regions() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.agg) quick_plot_3D_celltypes() (in module spateo.plotting.static.three_d_plot.three_dims_plots) quiver_autoscaler() (in module spateo.plotting.static.utils) R r_squared_threshold (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) 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) release (spateo.get_version.Version attribute) remove_background() (in module spateo.preprocessing.image) remove_kwargs() (in module spateo.utils) reorder_categories_after_dendrogram() (spateo.plotting.static.dotplot.Dotplot method) replace_col_with_collagens() (in module spateo.tools.CCI_effects_modeling.MuSIC_downstream) replace_hla_with_hlas() (in module spateo.tools.CCI_effects_modeling.MuSIC_downstream) replace_labels() (in module spateo.segmentation.label) report_progress() (spateo.external.lack.Logger method) request_report_hook() (spateo.external.lack.Logger method) rescaling() (in module spateo.tools.utils) reset_parameters() (spateo.tools.cluster.spagcn_utils.GraphConvolution method) reset_rcParams() (in module spateo.configuration) return_intercepts() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) return_outputs() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) rigid_transform() (in module spateo.tdr.models.models_individual.mesh_methods) 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) rough_subspace() (in module spateo.tdr.morphometrics.shape_similarity) row_normalize() (in module spateo.tools.labels) run_bp() (in module spateo.segmentation.bp) run_em() (in module spateo.segmentation.em) run_moran() (in module spateo.segmentation.moran) run_moran_and_mask_pixels() (in module spateo.segmentation.moran) run_permutation_test() (in module spateo.tools.CCI_effects_modeling.regression_utils) run_subsample() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) run_vi() (in module spateo.segmentation.vi) S safe_erode() (in module spateo.segmentation.utils) sample_from_eligible_neighbors() (in module spateo.tools.spatial_smooth) save() (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation method) (spateo.tdr.interpolations.interpolation_deeplearn.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.static.three_d_plot.three_dims_plotter) save_results() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) 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() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) 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_and_mask_pixels() (in module spateo.segmentation) (in module spateo.segmentation.icell) SCORES_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) search_l() (in module spateo.tools.cluster.spagcn_utils) search_res() (in module spateo.tools.cluster.spagcn_utils) second_deriv() (spateo.tools.CCI_effects_modeling.distributions.Link method) (spateo.tools.CCI_effects_modeling.distributions.Log method) (spateo.tools.CCI_effects_modeling.distributions.Logit method) (spateo.tools.CCI_effects_modeling.distributions.Power method) segment_bd_line() (in module spateo.digitization) (in module spateo.digitization.utils) (in module spateo.digitization.utils_old) segment_densities() (in module spateo.segmentation) (in module spateo.segmentation.density) SegmentationError SegmentationWarning select_area() (in module spateo.segmentation.simulation_evaluation.allocate_cell) select_ctoa() (in module spateo.segmentation.simulation_evaluation.allocate_cell) 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) seqfish() (in module spateo.sample_data) seqscope() (in module spateo.sample_data) set_arrow_alpha() (in module spateo.plotting.static.utils) set_center() (spateo.segmentation.simulation_evaluation.allocate_cell.Cell method) set_colorbar() (in module spateo.plotting.static.utils) set_domains() (in module spateo.digitization), [1] (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_logger_level() (in module spateo.external.lack) set_main_logger_namespace() (spateo.external.lack.LoggerManager 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) setLevel() (spateo.external.lack.Logger method) setup_downstream() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) shape_align_preprocess() (in module spateo.alignment.methods.utils) shift_cells() (in module spateo.segmentation.simulation_evaluation.allocate_cell) shiftedColorMap() (in module spateo.configuration) shuffle_adata() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) (in module spateo.tools.spatially_variable_gene_ot) silence_logger() (in module spateo.external.lack) simple_GC_DEC (class in spateo.tools.cluster.spagcn_utils) SimplePPT_method() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_backbone) (in module spateo.tdr.models.models_backbone.backbone_methods) simulate_cell_and_sig() (in module spateo.segmentation.simulation_evaluation) (in module spateo.segmentation.simulation_evaluation.allocate_cell) simulate_cells() (in module spateo.segmentation.simulation) SineLayer (class in spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn) SKM (in module spateo.configuration) (in module spateo.digitization) slideseq() (in module spateo.sample_data) smooth (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) smooth() (in module spateo.tools.spatial_smooth) smooth_mesh() (in module spateo.tdr.models.models_individual.mesh_utils) smooth_process_column() (in module spateo.tools.spatial_smooth) smoothing() (in module spateo.svg) (in module spateo.svg.get_svg) smoothing_and_sampling() (in module spateo.svg) (in module spateo.svg.get_svg) softplus() (in module spateo.tools.CCI_effects_modeling.regression_utils) sort_nodes_of_curve() (in module spateo.tdr.models.models_backbone.backbone_utils) space() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.space) space_polygons() (in module spateo.plotting.static.geo) 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_add_pseudocount() (in module spateo.tools.CCI_effects_modeling.regression_utils) sparse_dot() (in module spateo.tools.CCI_effects_modeling.regression_utils) sparse_element_by_element() (in module spateo.tools.CCI_effects_modeling.regression_utils) sparse_matrix_median() (in module spateo.tools.spatial_smooth) 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) sparse_minmax_scale() (in module spateo.tools.CCI_effects_modeling.regression_utils) spateo module spateo.align module spateo.alignment module spateo.alignment.deformation module spateo.alignment.methods module spateo.alignment.methods.morpho module spateo.alignment.methods.morpho_sparse module spateo.alignment.methods.morpho_sparse_utils module spateo.alignment.methods.paste module spateo.alignment.methods.utils module spateo.alignment.morpho_alignment module spateo.alignment.paste_alignment module spateo.alignment.transform module spateo.alignment.utils module spateo.configuration module spateo.cs module spateo.data_io module spateo.dd module spateo.digitization module spateo.digitization.borderline module spateo.digitization.boundary_old module spateo.digitization.contour module spateo.digitization.grid module spateo.digitization.utils module spateo.digitization.utils_old module spateo.errors module spateo.external module spateo.external.lack 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.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.networks 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.align_plots module spateo.plotting.static.three_d_plot.backbone_plots module spateo.plotting.static.three_d_plot.morphometrics_plots module spateo.plotting.static.three_d_plot.pairwise_align_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.simulation_evaluation module spateo.segmentation.simulation_evaluation.allocate_cell module spateo.segmentation.simulation_evaluation.evaluation module spateo.segmentation.simulation_evaluation.prepare module spateo.segmentation.utils module spateo.segmentation.vi module spateo.svg module spateo.svg.get_svg module spateo.svg.get_svg_between_slice module spateo.svg.utils module spateo.tdr module spateo.tdr.interpolations module spateo.tdr.interpolations.interpolation_deeplearn module spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation module spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn module spateo.tdr.interpolations.interpolation_deeplearn.nn_losses module spateo.tdr.interpolations.interpolation_dl module spateo.tdr.interpolations.interpolation_gaussianprocess module spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models module spateo.tdr.interpolations.interpolation_gaussianprocess.gp_train module spateo.tdr.interpolations.interpolation_gp module spateo.tdr.interpolations.interpolation_sparseVFC module spateo.tdr.interpolations.interpolation_vtk module spateo.tdr.interpolations.utils module spateo.tdr.models module spateo.tdr.models.models_backbone module spateo.tdr.models.models_backbone.backbone module spateo.tdr.models.models_backbone.backbone_methods module spateo.tdr.models.models_backbone.backbone_utils module spateo.tdr.models.models_individual module spateo.tdr.models.models_individual.mesh module spateo.tdr.models.models_individual.mesh_methods module spateo.tdr.models.models_individual.mesh_utils module spateo.tdr.models.models_individual.point_clouds module spateo.tdr.models.models_individual.voxel module spateo.tdr.models.models_migration module spateo.tdr.models.models_migration.arrow_model module spateo.tdr.models.models_migration.line_model module spateo.tdr.models.models_migration.morphofield_model module spateo.tdr.models.models_migration.morphopath_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.morphometrics module spateo.tdr.morphometrics.gene_similarity module spateo.tdr.morphometrics.morphofield module spateo.tdr.morphometrics.morphofield.gaussian_process module spateo.tdr.morphometrics.morphofield.sparsevfc module spateo.tdr.morphometrics.morphofield.trajectory module spateo.tdr.morphometrics.morphofield_dg module spateo.tdr.morphometrics.morphofield_dg.differential_geometry module spateo.tdr.morphometrics.morphofield_dg.GPVectorField module spateo.tdr.morphometrics.morphology module spateo.tdr.morphometrics.shape_similarity module spateo.tdr.widgets module spateo.tdr.widgets.clip module spateo.tdr.widgets.pick module spateo.tdr.widgets.slice module spateo.tdr.widgets.utils module spateo.tl module spateo.tools module spateo.tools.architype module spateo.tools.CCI_effects_modeling module spateo.tools.CCI_effects_modeling.distributions module spateo.tools.CCI_effects_modeling.MuSIC module spateo.tools.CCI_effects_modeling.MuSIC_downstream module spateo.tools.CCI_effects_modeling.MuSIC_upstream module spateo.tools.CCI_effects_modeling.regression_utils module spateo.tools.CCI_effects_modeling.SWR 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.leiden 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.dimensionality_reduction 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.roi module spateo.tools.spatial_degs module spateo.tools.spatial_smooth module spateo.tools.spatially_variable_gene_ot 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() (in module spateo.tools.cluster.utils) species (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) SPLICED_LAYER_KEY (spateo.configuration.SpateoAdataKeyManager attribute) split_model() (in module spateo.tdr.models.utilities) (in module spateo.tdr.models.utilities.model_utils) sqrt (class in spateo.tools.CCI_effects_modeling.distributions) 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) 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) subsample_neighbors_dense() (in module spateo.tools.spatial_smooth) subsample_neighbors_sparse() (in module spateo.tools.spatial_smooth) subset_best_samples() (in module spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation) subspace_surface_fitting() (in module spateo.tdr.morphometrics.shape_similarity) suggested_link (spateo.tools.CCI_effects_modeling.distributions.Binomial attribute) (spateo.tools.CCI_effects_modeling.distributions.Gamma attribute) (spateo.tools.CCI_effects_modeling.distributions.Gaussian attribute) (spateo.tools.CCI_effects_modeling.distributions.NegativeBinomial attribute) (spateo.tools.CCI_effects_modeling.distributions.Poisson attribute) svg_iden_reg() (in module spateo.svg) (in module spateo.svg.get_svg) swap_axes() (spateo.plotting.static.dotplot.Dotplot method) T target_distribution() (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) target_expr_threshold (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) targets_path (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute) (spateo.tools.MuSIC_Molecule_Selector attribute) 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.alignment.methods.utils) (in module spateo.tools.cluster.find_clusters) (in module spateo.tools.cluster.utils) top_n_degs() (in module spateo.tools) (in module spateo.tools.cluster_degs) top_target_barplot() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) 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.morphometrics_plots) total_counts_key (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) total_counts_threshold (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) train() (spateo.segmentation.align.AlignmentRefiner method) (spateo.segmentation.vi.NegativeBinomialMixture method) (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation method) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation method) (spateo.tools.cluster.spagcn_utils.SpaGCN method) 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) truncated_SVD_with_center() (in module spateo.tools.dimensionality_reduction) U umap_conn_indices_dist_embedding() (in module spateo.tools.dimensionality_reduction) uniform_larger_pc() (in module spateo.tdr.models.models_individual.mesh_utils) uniform_mesh() (in module spateo.tdr.models.models_individual.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_backbone() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_backbone) (in module spateo.tdr.models.models_backbone.backbone) update_dict() (in module spateo.tools.utils) use_expression_neighbors (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) V valid (spateo.tools.CCI_effects_modeling.distributions.Poisson attribute) valid_links (spateo.tools.CCI_effects_modeling.distributions.Binomial attribute) (spateo.tools.CCI_effects_modeling.distributions.Gamma attribute) (spateo.tools.CCI_effects_modeling.distributions.Gaussian attribute) (spateo.tools.CCI_effects_modeling.distributions.NegativeBinomial attribute) (spateo.tools.CCI_effects_modeling.distributions.Poisson attribute) variance (spateo.tools.CCI_effects_modeling.distributions.Binomial attribute) (spateo.tools.CCI_effects_modeling.distributions.Gamma attribute) (spateo.tools.CCI_effects_modeling.distributions.Gaussian attribute) (spateo.tools.CCI_effects_modeling.distributions.NegativeBinomial attribute) (spateo.tools.CCI_effects_modeling.distributions.Poisson attribute) VarianceFunction (class in spateo.tools.CCI_effects_modeling.distributions) 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_3D_increasing_direction_gradient() (in module spateo.plotting.static.three_d_plot.three_dims_plots) visualize_effect_specificity() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) visualize_effect_vf_3D() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) visualize_intercellular_network() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) visualize_neighborhood() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) visualize_overlap_between_interacting_components_3D() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) voxel_data() (in module spateo.alignment.methods.utils) voxelize_mesh() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_individual) (in module spateo.tdr.models.models_individual.voxel) voxelize_pc() (in module spateo.tdr) (in module spateo.tdr.models) (in module spateo.tdr.models.models_individual) (in module spateo.tdr.models.models_individual.voxel) vtk_interpolation() (in module spateo.tdr) (in module spateo.tdr.interpolations) (in module spateo.tdr.interpolations.interpolation_vtk) W wald_test() (in module spateo.tools.CCI_effects_modeling.regression_utils) warning() (spateo.external.lack.Logger method) watershed() (in module spateo.segmentation) (in module spateo.segmentation.label) weighted_binary_crossentropy() (in module spateo.tools.CCI_effects_modeling.regression_utils) weighted_cosine_distance() (in module spateo.tdr.interpolations.interpolation_deeplearn.nn_losses) weighted_mad() (in module spateo.tdr.interpolations.interpolation_deeplearn.nn_losses) weighted_mean() (in module spateo.tdr.interpolations.interpolation_deeplearn.nn_losses) weighted_mse() (in module spateo.tdr.interpolations.interpolation_deeplearn.nn_losses) weights() (spateo.tools.CCI_effects_modeling.distributions.Distribution 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)