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 | Y | Z _ __author__ (in module spateo.external.STAGATE_pyG) __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) __drop_feature() (in module spateo.external.CAST.model.aug) __email__ (in module spateo.external.STAGATE_pyG) __mask_edge() (in module spateo.external.CAST.model.aug) __name__ (spateo.alignment.methods.backend.Backend attribute) (spateo.alignment.methods.backend.NumpyBackend attribute) (spateo.alignment.methods.backend.TorchBackend attribute) (spateo.alignment.methods.backend_ot.Backend attribute) (spateo.alignment.methods.backend_ot.CupyBackend attribute) (spateo.alignment.methods.backend_ot.JaxBackend attribute) (spateo.alignment.methods.backend_ot.NumpyBackend attribute) (spateo.alignment.methods.backend_ot.TensorflowBackend attribute) (spateo.alignment.methods.backend_ot.TorchBackend attribute) (spateo.alignment.methods.NumpyBackend attribute) (spateo.alignment.methods.TorchBackend attribute) __optimizer (spateo.segmentation.align.AlignmentRefiner attribute) (spateo.segmentation.vi.NegativeBinomialMixture attribute) __post_init__() (spateo.external.CAST.CAST_Stack.reg_params method) (spateo.external.CAST.model.model_GCNII.Args method) (spateo.external.CAST.reg_params method) __random_aug() (in module spateo.external.CAST.model.aug) __repr__() (spateo.external.STAGATE_pyG.gat_conv.GATConv method) (spateo.tools.cluster.spagcn_utils.GraphConvolution method) (spateo.tools.Label method) (spateo.tools.labels.Label method) __str__() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (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) __type__ (spateo.alignment.methods.backend.Backend attribute) (spateo.alignment.methods.backend.NumpyBackend attribute) (spateo.alignment.methods.backend.TorchBackend attribute) (spateo.alignment.methods.backend_ot.Backend attribute) (spateo.alignment.methods.backend_ot.CupyBackend attribute) (spateo.alignment.methods.backend_ot.JaxBackend attribute) (spateo.alignment.methods.backend_ot.NumpyBackend attribute) (spateo.alignment.methods.backend_ot.TensorflowBackend attribute) (spateo.alignment.methods.backend_ot.TorchBackend attribute) (spateo.alignment.methods.NumpyBackend attribute) (spateo.alignment.methods.TorchBackend attribute) __type_list__ (spateo.alignment.methods.backend.Backend attribute) (spateo.alignment.methods.backend.NumpyBackend attribute) (spateo.alignment.methods.backend.TorchBackend attribute) (spateo.alignment.methods.backend_ot.Backend attribute) (spateo.alignment.methods.backend_ot.CupyBackend attribute) (spateo.alignment.methods.backend_ot.JaxBackend attribute) (spateo.alignment.methods.backend_ot.NumpyBackend attribute) (spateo.alignment.methods.backend_ot.TensorflowBackend attribute) (spateo.alignment.methods.backend_ot.TorchBackend attribute) (spateo.alignment.methods.NumpyBackend attribute) (spateo.alignment.methods.TorchBackend attribute) __version__ (in module spateo) (in module spateo.get_version) _agenerate_palette() (in module spateo.plotting.static.align) _align_preprocess() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _alpha (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) _apply_layout() (spateo.plotting.static.networks.PlotNetwork method) _augment_labels() (in module spateo.segmentation.label) _BACKEND_IMPLEMENTATIONS (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) _BACKENDS (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) _bench() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) _blue() (in module spateo.plotting.static.utils) _braycurtis_distance_backend() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _cached_inference() (spateo.external.MERFISHVI._module.VAE method) _cal_cosine_similarity() (in module spateo.alignment.methods.deprecated_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) _calculate_loss() (in module spateo.alignment.methods.mesh_correction_utils) _canberra_distance_backend() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _cat (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _cellpose() (in module spateo.segmentation.external.cellpose) _change_device() (spateo.alignment.methods.backend_ot.JaxBackend method) _chebyshev_distance_backend() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _check() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _check_args_backend() (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) _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.deprecated_utils) (in module spateo.alignment.methods.utils) _chunk (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _coarse_rigid_alignment() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _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) _compute_local_library_params() (spateo.external.MERFISHVI._module.VAE method) _compute_smallest_distance() (in module spateo.plotting.static.align) _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_kernel() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _construct_label_mask() (in module spateo.alignment.methods.deprecated_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) _convert_to_index_for_coo() (spateo.alignment.methods.backend_ot.TensorflowBackend method) _copy (in module spateo.alignment.methods.utils) _correlation_distance_backend() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _cos_similarity() (in module spateo.alignment.methods.deprecated_morpho_sparse_utils), [1] (in module spateo.alignment.methods.deprecated_utils) _cosine_distance_backend() (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _create_labels() (in module spateo.segmentation.simulation) _create_module() (spateo.external.MERFISHVI._model.MERFISHVI method) (spateo.external.MERFISHVI.MERFISHVI method) _create_spatial_adjacency() (in module spateo.segmentation.density) _data (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_utils) (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.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _detach() (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) _dist() (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) _dot (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _dotplot() (spateo.plotting.static.dotplot.Dotplot static method) _dstack (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _embed_datashader_in_an_axis() (in module spateo.plotting.static.utils) _euc_distance_backend() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _euclidean_distance() (in module spateo.tdr.models.models_backbone.backbone_utils) _expand_labels() (in module spateo.segmentation.label) _extract_contour_alpha_shape() (in module spateo.alignment.methods.mesh_correction_utils) _extract_contour_opencv() (in module spateo.alignment.methods.mesh_correction_utils) _extract_contours_from_mesh() (in module spateo.alignment.methods.mesh_correction_utils) _find_peaks() (in module spateo.segmentation.label) _from_numpy() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) _generate_labeling() (in module spateo.alignment.methods.mesh_correction_utils) _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_anneling_factor() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _get_array_values() (in module spateo.plotting.static.utils) _get_backend_instance() (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) _get_binary_values() (in module spateo.alignment.methods.mesh_correction_utils) _get_default_cmap() (in module spateo.plotting.static.three_d_plot.three_dims_plotter) _get_device() (spateo.alignment.methods.backend_ot.JaxBackend method) _get_extent() (in module spateo.plotting.static.utils) _get_generative_input() (spateo.external.MERFISHVI._module.VAE method) (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE method) _get_inference_input() (spateo.external.MERFISHVI._module.VAE method) (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE method) _get_mean_var() (in module spateo.preprocessing.transform) _get_optimal_R() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _get_parameters_from_pair() (in module spateo.alignment.methods.mesh_correction_utils) _get_reconstruction_loss_nonspatial() (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) _getBinary() (in module spateo.alignment.methods.mesh_correction_utils) _getlink() (spateo.tools.CCI_effects_modeling.distributions.Distribution method) _getUnaries() (in module spateo.alignment.methods.mesh_correction_utils) _gp_velocity() (in module spateo.tdr.morphometrics.morphofield.gaussian_process) _green() (in module spateo.plotting.static.utils) _guidance_pair_preprocess() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _hamming_distance_backend() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _hstack (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _identity (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _image (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) (spateo.tools.live_wire.LiveWireSegmentation attribute) (spateo.tools.LiveWireSegmentation attribute) _import_stdlib_logging() (in module spateo.external.lack) _init_guess_beta2() (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) _init_guess_sigma2() (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _init_probability_parameters() (in module spateo.alignment.methods.deprecated_utils) (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _initial_nb_params() (in module spateo.segmentation.icell) _initialize_variational_variables() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _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) _jaccard_distance_backend() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _kernel_functions() (spateo.tools.find_neighbors.Kernel method) _kl_distance_backend() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _label_connected_components() (in module spateo.segmentation.label) _label_distance_backend() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _linalg (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _link (spateo.tools.CCI_effects_modeling.distributions.Distribution attribute) _logging (in module spateo.external.lack) _mainplot() (spateo.plotting.static.dotplot.Dotplot method) _make_pairs() (in module spateo.alignment.methods.mesh_correction_utils) _mask_cells_from_stain() (in module spateo.segmentation.icell) _mask_nuclei_from_stain() (in module spateo.segmentation.icell) _matplotlib_points() (in module spateo.plotting.static.utils) _MERFISHVI_AVAILABLE (in module spateo.external) _merge_models() (in module spateo.alignment.deformation) _minkowski_distance_backend() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _model_summary_string (spateo.external.MERFISHVI._model.MERFISHVI attribute) (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.MERFISHVI attribute) (spateo.external.MERFISHVI.SpatialVI attribute) _module_cls (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.SpatialVI attribute) _module_kwargs (spateo.external.MERFISHVI._model.MERFISHVI attribute) (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.MERFISHVI attribute) (spateo.external.MERFISHVI.SpatialVI attribute) _morphofield_sparsevfc() (in module spateo.tdr.morphometrics.morphofield.sparsevfc) _mul (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _normalize_coords() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _normalize_data() (in module spateo.preprocessing.normalize) _normalize_exps() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _o3d2pv() (in module spateo.tdr.models.models_individual.mesh_methods) _original_import (in module spateo.external.lack) _pi (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _pinv (in module spateo.alignment.methods.deprecated_utils) (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) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _prod (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _psi (in module spateo.alignment.methods.deprecated_utils) (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.deprecated_utils) (in module spateo.alignment.methods.utils) _red() (in module spateo.plotting.static.utils) _register_backend_implementation() (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) _regular_inference() (spateo.external.MERFISHVI._module.VAE method) _repeat_interleave (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.utils) _replace_labels() (in module spateo.segmentation.label) _roll (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _sanitize_labels() (in module spateo.segmentation.external.stardist) _save_iter() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _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_contours() (in module spateo.alignment.methods.mesh_correction_utils) _smooth_image() (spateo.preprocessing.auxseg.LiveWireSegmentation method) (spateo.tools.live_wire.LiveWireSegmentation method) (spateo.tools.LiveWireSegmentation method) _sort() (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.utils) _SparseTensor() (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.utils) _split (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.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) _to_numpy() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) _topk (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _transform_points() (in module spateo.alignment.methods.mesh_correction_utils) _unique (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _unsqueeze (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _update_alpha() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _update_assignment_P() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _update_batch() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _update_gamma() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _update_nonrigid() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _update_parameter() (in module spateo.alignment.methods.mesh_correction_utils) _update_rigid() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _update_sigma2() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) _update_var_groups() (spateo.plotting.static.dotplot.Dotplot method) _var (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _vector_projection() (in module spateo.plotting.static.utils) _vstack (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) _watershed() (in module spateo.segmentation.label) _where (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.utils) _wrap_output() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) A A (class in spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.MainFlow attribute) abs() (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) 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 (spateo.plotting.static.dotplot.Dotplot attribute) (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.cluster._stagate.pySTAGATE attribute) (spateo.tools.cluster.pySTAGATE attribute) (spateo.tools.cluster_lasso.Lasso attribute) (spateo.tools.Lasso attribute) (spateo.tools.MuSIC attribute) (spateo.tools.pySTAGATE attribute) ADATA_AGG_TYPE (spateo.configuration.SpateoAdataKeyManager attribute) ADATA_DEFAULT_TYPE (spateo.configuration.SpateoAdataKeyManager attribute) adata_is_type() (spateo.configuration.SpateoAdataKeyManager method) adata_nonspatial (spateo.external.MERFISHVI._model.MERFISHVI attribute) (spateo.external.MERFISHVI.MERFISHVI attribute) 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_scale_bar() (in module spateo.external.CAST.visualize) add_self_loops (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) 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_GD() (in module spateo.external.CAST.CAST_Stack) affine_reg_params() (in module spateo.external.CAST.CAST_Stack) affine_trans_t() (in module spateo.external.CAST.CAST_Stack) 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.deprecated_utils) align_slices_pca() (in module spateo.tools) (in module spateo.tools.coarse_align) AlignmentRefiner (class in spateo.segmentation.align) allclose() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) allow_flip (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] alpha (spateo.plotting.static.dotplot.CCDotplot attribute) (spateo.tools.cluster.spagcn_utils.simple_GC_DEC attribute) alpha_basis (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) alpha_basis_bs (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) alpha_init() (in module spateo.external.CAST.CAST_Stack) 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) angle (spateo.segmentation.simulation_evaluation.allocate_cell.Cell attribute) anneal_rate (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] AnnTorchDataset (class in spateo.external.MERFISHVI.scvi_spatial_module) any() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) 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) arange() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) archetypes() (in module spateo.tools) (in module spateo.tools.architype) archetypes_genes() (in module spateo.tools) (in module spateo.tools.architype) are_axes_swapped (spateo.plotting.static.dotplot.Dotplot attribute) argmax() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) argmin() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) Args (class in spateo.external.CAST.model.model_GCNII) args_list (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) argsort() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) array_equal() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) arrowed_spines() (in module spateo.plotting.static.utils) assert_same_dtype_device() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) assign_significance() (in module spateo.tools.CCI_effects_modeling.regression_utils) assignment() (spateo.segmentation.vi.NegativeBinomialMixture method) atan2() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) att_dst (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) att_src (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) attention_heads (spateo.external.MERFISHVI._model.MERFISHVI attribute) (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.MERFISHVI attribute) (spateo.external.MERFISHVI.SpatialVI attribute) attention_params (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) attention_params_bs (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) attention_region (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) attentions (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) augment_labels() (in module spateo.segmentation) (in module spateo.segmentation.label) AUGMENTED_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) autoencoder_loss_traj (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) average_dist() (in module spateo.external.CAST.CAST_Projection) average_precision() (in module spateo.segmentation.benchmark) ax (spateo.plotting.static.dotplot.Dotplot attribute) ax_dict (spateo.plotting.static.dotplot.Dotplot attribute) axes (spateo.segmentation.simulation_evaluation.allocate_cell.Cell attribute) axolotl() (in module spateo.sample_data) B B (class in spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.MainFlow attribute) B_matrix() (in module spateo.external.CAST.CAST_Stack) BA_align() (in module spateo.alignment.methods.deprecated_morpho) BA_align_sparse() (in module spateo.alignment.methods.deprecated_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) Backend (class in spateo.alignment.methods.backend) (class in spateo.alignment.methods.backend_ot) ball_pivoting_mesh() (in module spateo.tdr.models.models_individual.mesh_methods) base (spateo.plotting.static.dotplot.CCDotplot attribute) (spateo.plotting.static.dotplot.Dotplot attribute) Batch_Data() (in module spateo.external.STAGATE_pyG) (in module spateo.external.STAGATE_pyG.utils) batch_representation (spateo.external.MERFISHVI._module.VAE attribute) batch_size (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] beta (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] 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 (spateo.tools.Label attribute) (spateo.tools.labels.Label attribute) BINS_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) bitsize() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) bleeding (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params 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) BSpline_GD() (in module spateo.external.CAST.CAST_Stack) BSpline_GD_preparation() (in module spateo.external.CAST.CAST_Stack) BSpline_GD_uv_ij_calculate() (in module spateo.external.CAST.CAST_Stack) BSpline_renew_coords() (in module spateo.external.CAST.CAST_Stack) buffer_path (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) button_pressed() (spateo.preprocessing.auxseg.LiveWireSegmentation method) bw (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.MuSIC attribute), [1] 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.deprecated_utils) cal_dot() (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_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_pSM() (spateo.tools.cluster._stagate.pySTAGATE method) (spateo.tools.cluster.pySTAGATE method) (spateo.tools.pySTAGATE method) cal_rank_p() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) Cal_Spatial_Net() (in module spateo.external.STAGATE_pyG) (in module spateo.external.STAGATE_pyG.utils) Cal_Spatial_Net_3D() (in module spateo.external.STAGATE_pyG) (in module spateo.external.STAGATE_pyG.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) (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) calc_exp_dissimilarity() (in module spateo.alignment) (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_utils) calc_expm1() (in module spateo.preprocessing.normalize) calc_mean_and_var() (in module spateo.preprocessing.normalize) calc_mean_and_var_dense() (in module spateo.preprocessing._fast_utils) calc_mean_and_var_sparse() (in module spateo.preprocessing._fast_utils) calc_op_field() (in module spateo.digitization) (in module spateo.digitization.utils_old) calc_P_related() (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) calc_probability() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) calc_stat_per_batch_dense() (in module spateo.preprocessing._fast_utils) calc_stat_per_batch_sparse() (in module spateo.preprocessing._fast_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_louvain_partition() (in module spateo.tools.cluster.leiden) calculate_p() (in module spateo.tools.cluster.spagcn_utils) CAST() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.find_clusters) CAST_MARK() (in module spateo.external.CAST) (in module spateo.external.CAST.main) CAST_PROJECT() (in module spateo.external.CAST) (in module spateo.external.CAST.main) CAST_STACK() (in module spateo.external.CAST) (in module spateo.external.CAST.main) CAST_STACK_rough() (in module spateo.external.CAST) (in module spateo.external.CAST.CAST_Stack) cat_key (spateo.plotting.static.dotplot.Dotplot attribute) categories_order (spateo.plotting.static.dotplot.Dotplot attribute) CCA_SSG (class in spateo.external.CAST.model.model_GCNII) 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_degs_model_interactions (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) 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) cdist_check() (in module spateo.external.CAST.CAST_Projection) cdist_hist() (in module spateo.external.CAST.CAST_Projection) 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_categories (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) 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_select() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) 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 (spateo.segmentation.simulation_evaluation.allocate_cell.Cell attribute) 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) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) check_colornorm() (in module spateo.plotting.static.utils) check_exp() (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) check_label_transfer() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) check_label_transfer_dict() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) check_obs() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) check_rep_layer() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) check_spatial_coords() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) choice() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) chunk() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) chunk_capacity (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] 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.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) clip() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (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) cmap (spateo.plotting.static.dotplot.Dotplot attribute) coarse_rigid_alignment() (in module spateo.alignment.methods.deprecated_utils), [1] coarse_rigid_alignment_debug() (in module spateo.alignment.methods.deprecated_utils) cof_db (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) 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) (spateo.segmentation.simulation_evaluation.allocate_cell.Cell attribute) color_index (in module spateo.tools.roi) color_label() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.colorlabel) color_legend_title (spateo.plotting.static.dotplot.Dotplot attribute) color_on (spateo.plotting.static.dotplot.Dotplot attribute) 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_pathway_effect (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) 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) (in module spateo.alignment.methods.deprecated_morpho) (in module spateo.alignment.methods.deprecated_morpho_sparse) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) con_K_geodist() (in module spateo.alignment.methods.deprecated_utils) con_K_graph() (in module spateo.alignment.methods.utils) concat (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) concatenate() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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 confusion_mat_plot() (in module spateo.external.CAST.CAST_Projection) 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_plain() (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_knn_graph() (in module spateo.alignment.methods.utils) 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 (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) contours() (in module spateo.plotting) (in module spateo.plotting.interactive) (in module spateo.plotting.interactive.agg) conv1 (spateo.external.STAGATE_pyG.STAGATE attribute) (spateo.external.STAGATE_pyG.STAGATE.STAGATE attribute) conv2 (spateo.external.STAGATE_pyG.STAGATE attribute) (spateo.external.STAGATE_pyG.STAGATE.STAGATE attribute) conv2d() (in module spateo.segmentation.utils) conv3 (spateo.external.STAGATE_pyG.STAGATE attribute) (spateo.external.STAGATE_pyG.STAGATE.STAGATE attribute) conv4 (spateo.external.STAGATE_pyG.STAGATE attribute) (spateo.external.STAGATE_pyG.STAGATE.STAGATE attribute) convs (spateo.external.CAST.model.model_GCNII.GCN attribute) (spateo.external.CAST.model.model_GCNII.GCNII attribute) coo_matrix() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) coords (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) coords2adjacentmat() (in module spateo.external.CAST) (in module spateo.external.CAST.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) coords_minus_mean() (in module spateo.external.CAST.CAST_Stack) coords_minus_min() (in module spateo.external.CAST.CAST_Stack) coords_minus_min_t() (in module spateo.external.CAST.CAST_Stack) copy() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) copy_adata() (in module spateo.utils) corr_dist() (in module spateo.external.CAST) (in module spateo.external.CAST.CAST_Stack) corr_heat() (in module spateo.external.CAST.CAST_Stack) cos_global_centroid_to_subspace() (in module spateo.tdr.morphometrics.shape_similarity) cosine_distance() (in module spateo.tdr.interpolations.interpolation_deeplearn.nn_losses) cosine_IDW() (in module spateo.external.CAST.CAST_Projection) COUNT_COLUMN_MAPPING (in module spateo.io.bgi) counts (spateo.tools.Label attribute) (spateo.tools.labels.Label attribute) covar_module (spateo.tdr.interpolations.interpolation_gaussianprocess.Approx_GPModel attribute) (spateo.tdr.interpolations.interpolation_gaussianprocess.Exact_GPModel attribute) (spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models.Approx_GPModel attribute) (spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models.Exact_GPModel attribute) covariate_keys (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) cp_type (in module spateo.alignment.methods.backend_ot) 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) ct_vec (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) cumsum() (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) CupyBackend (class in spateo.alignment.methods.backend_ot) 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) current_path_plot (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) current_point (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) 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 d_list (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) darkblue_cmap (in module spateo.configuration) darkgreen_cmap (in module spateo.configuration) darkpurple_cmap (in module spateo.configuration) darkred_cmap (in module spateo.configuration) data (spateo.tdr.morphometrics.morphofield_dg.GPVectorField.GPVectorField attribute) (spateo.tools.cluster._stagate.pySTAGATE attribute) (spateo.tools.cluster.pySTAGATE attribute) (spateo.tools.pySTAGATE attribute) data() (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) data_dim (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) data_sampler (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) dataframe_to_filled_labels() (in module spateo.io.bgi) dataframe_to_labels() (in module spateo.io.bgi) dataname (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.model.model_GCNII.Args attribute) (spateo.external.CAST.reg_params attribute) 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) decoder (spateo.external.MERFISHVI._module.LDVAE attribute) (spateo.external.MERFISHVI._module.VAE attribute) 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) degree (spateo.plotting.static.utils.Loess attribute) delaunay() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.bbs) delaunay_dgl() (in module spateo.external.CAST.CAST_Mark) delta (spateo.plotting.static.dotplot.CCDotplot attribute) delta_cell_cal() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) delta_exp_cal() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) delta_exp_sigplot() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) delta_exp_statistics() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) dendrogram() (in module spateo.plotting.static.utils) denormalize_y() (spateo.plotting.static.utils.Loess method) dense (spateo.tools.Label attribute) (spateo.tools.labels.Label attribute) der (spateo.external.CAST.model.model_GCNII.Args attribute) 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) design_matrix (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) despline() (in module spateo.plotting.static.utils) despline_all() (in module spateo.plotting.static.utils) detach() (spateo.alignment.methods.backend_ot.Backend method) detect_highly_variable_genes() (in module spateo.external.CAST) (in module spateo.external.CAST.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) device (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.model.model_GCNII.Args attribute) (spateo.external.CAST.reg_params attribute) (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) (spateo.tools.cluster._stagate.pySTAGATE attribute) (spateo.tools.cluster.pySTAGATE attribute) (spateo.tools.pySTAGATE attribute) device_type() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) dfr (spateo.external.CAST.model.model_GCNII.Args attribute) diag() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) diff_sending_or_receiving (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) diff_step (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) digitize() (in module spateo.digitization) (in module spateo.digitization.grid) digitize_general() (in module spateo.digitization) (in module spateo.digitization.utils) DISABLE_CUPY_KEY (in module spateo.alignment.methods.backend_ot) DISABLE_JAX_KEY (in module spateo.alignment.methods.backend_ot) DISABLE_TF_KEY (in module spateo.alignment.methods.backend_ot) DISABLE_TORCH_KEY (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) discrete_optimization_step() (spateo.alignment.Mesh_correction method) (spateo.alignment.methods.Mesh_correction method) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction method) disp (spateo.tools.CCI_effects_modeling.distributions.Negative_Binomial_Variance attribute) dispersion (spateo.external.MERFISHVI._module.VAE attribute) displacement (spateo.segmentation.align.NonRigidAlignmentRefiner attribute) dissimilarity (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] dist() (spateo.segmentation.vi.NegativeBinomialMixture method) dist_global_centroid_to_subspace() (in module spateo.tdr.morphometrics.shape_similarity) dist_penalty1 (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) dist_penalty2 (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) distance_knn_graph() (in module spateo.tools.cluster.leiden) DISTANCES_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) distr (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute), [1] (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) dJ_dt_cal() (in module spateo.external.CAST.CAST_Stack) dJ_dtheta_cal() (in module spateo.external.CAST.CAST_Stack) domain_heat_eqn_solver() (in module spateo.digitization.utils) dot() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) dot_color_df (spateo.plotting.static.dotplot.Dotplot attribute) dot_edge_color (spateo.plotting.static.dotplot.Dotplot attribute) dot_edge_lw (spateo.plotting.static.dotplot.Dotplot attribute) dot_max (spateo.plotting.static.dotplot.Dotplot attribute) dot_min (spateo.plotting.static.dotplot.Dotplot attribute) dot_size_df (spateo.plotting.static.dotplot.Dotplot attribute) 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) downstream_model_ligand_design_matrix (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) downstream_model_receptor_design_matrix (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) downstream_model_target_design_matrix (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) drag_mode() (in module spateo.tools.roi) draw_init() (in module spateo.tools.roi) draw_sample() (spateo.alignment.methods.sampling.TRNET method) draw_seg_grid() (in module spateo.digitization) (in module spateo.digitization.utils) (in module spateo.digitization.utils_old) drop_feature() (in module spateo.external.CAST.model.aug) dropout (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) drosophila() (in module spateo.sample_data) dsplot() (in module spateo.external.CAST) (in module spateo.external.CAST.visualize) dstack() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) dtype (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] dtype_device() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) E ecp_silhouette() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.utils) edge_index (spateo.external.MERFISHVI._model.MERFISHVI attribute) (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.MERFISHVI attribute) (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE attribute) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE attribute) (spateo.external.MERFISHVI.SpatialVI attribute) edges (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) (spateo.tools.live_wire.LiveWireSegmentation attribute) (spateo.tools.LiveWireSegmentation attribute) 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) eigh() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) einsum() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) eliminate_zeros() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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.deprecated_utils) (in module spateo.alignment.methods.utils) encode_covariates (spateo.external.MERFISHVI._module.VAE attribute) Encoder (class in spateo.external.CAST.model.model_GCNII) encoder_dim (spateo.external.CAST.model.model_GCNII.Args attribute) enforce_positivity (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.MainFlow attribute) 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) epochs (spateo.external.CAST.model.model_GCNII.Args attribute) 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) evaluation_project() (in module spateo.external.CAST.CAST_Projection) 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) exp() (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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) extra_payload_autotune (spateo.external.MERFISHVI._module.VAE attribute) extract_cluster_contours() (in module spateo.digitization), [1] (in module spateo.digitization.contour) extract_contours() (spateo.alignment.Mesh_correction method) (spateo.alignment.methods.Mesh_correction method) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction method) extract_coords_exp() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) extract_data_matrix (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) eye() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) F f (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.A attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.B attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.h attribute) factor_normalization() (in module spateo.preprocessing.normalize) fastpd_iter (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] fdr_correct() (in module spateo.tools.cci_fdr) feature() (in module spateo.plotting.static.three_d_plot.morphometrics_plots) feature_distance (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) feature_names (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) FFD_Bspline_apply_t() (in module spateo.external.CAST.CAST_Stack) 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) fig (spateo.plotting.static.dotplot.Dotplot attribute) fig_title (spateo.plotting.static.dotplot.Dotplot attribute) 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) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) filter_genes() (in module spateo.preprocessing.filter) filter_target_threshold (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) filter_targets (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) 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) fit_points (spateo.tdr.models.models_backbone.backbone_methods.NLPCA 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) flip() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) floor() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) 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.external.CAST.model.model_GCNII.CCA_SSG method) (spateo.external.CAST.model.model_GCNII.Encoder method) (spateo.external.CAST.model.model_GCNII.GCN method) (spateo.external.CAST.model.model_GCNII.GCNII method) (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialEncoder method) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE method) (spateo.external.STAGATE_pyG.gat_conv.GATConv method) (spateo.external.STAGATE_pyG.STAGATE method) (spateo.external.STAGATE_pyG.STAGATE.STAGATE method) (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) from_numpy() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) full() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) G G (spateo.plotting.static.networks.PlotNetwork attribute) (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) (spateo.tools.live_wire.LiveWireSegmentation attribute) (spateo.tools.LiveWireSegmentation attribute) Gamma (class in spateo.tools.CCI_effects_modeling.distributions) gamma_a (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) gamma_b (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) gat (spateo.external.MERFISHVI.scvi_spatial_module.SpatialEncoder attribute) GATConv (class in spateo.external.STAGATE_pyG.gat_conv) Gaussian (class in spateo.tools.CCI_effects_modeling.distributions) gaussian_blur() (in module spateo.segmentation.utils) gc (spateo.tools.cluster.spagcn_utils.simple_GC_DEC attribute) GCN (class in spateo.external.CAST.model.model_GCNII) GCNII (class in spateo.external.CAST.model.model_GCNII) 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) gene_likelihood (spateo.external.MERFISHVI._module.VAE attribute) 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_label_transfer_dict() (in module spateo.alignment) (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) generate_label_transfer_prior() (in module spateo.alignment) (in module spateo.alignment.utils) generate_labels() (spateo.alignment.Mesh_correction method) (spateo.alignment.methods.Mesh_correction method) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction 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) generative() (spateo.external.MERFISHVI._module.VAE method) (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) generative_nonspatial() (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) generative_spatial() (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) genes (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] 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_available_backend_implementations() (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) 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_backend() (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) get_backend_list() (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) 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_dxy_ffd() (in module spateo.external.CAST.CAST_Stack) 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_embedding() (spateo.external.CAST.model.model_GCNII.CCA_SSG method) 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_fused_representation() (spateo.external.MERFISHVI._model.MERFISHVI method) (spateo.external.MERFISHVI.MERFISHVI method) (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) 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_H() (in module spateo.plotting.static.align) 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_kernel() (in module spateo.alignment.methods.deprecated_utils) get_label_props() (in module spateo.io.utils) get_labels_based_on_coords() (in module spateo.alignment) (in module spateo.alignment.utils) get_latent_representation() (spateo.external.MERFISHVI._model.MERFISHVI method) (spateo.external.MERFISHVI.MERFISHVI method) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE method) get_latent_representation_by_modality() (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) get_loadings() (spateo.external.MERFISHVI._module.LDVAE method) (spateo.external.MERFISHVI._module.VAE method) get_main_logger() (spateo.external.lack.LoggerManager method) get_mapper() (in module spateo.tools.utils) get_merfishvi_requirements() (in module spateo.external) get_min_max() (in module spateo.plotting.static.align) get_min_range() (spateo.plotting.static.utils.Loess static method) get_neighborhood_rad() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) get_nonspatial_specific_features() (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE 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.deprecated_utils) get_optimal_R_sparse() (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) get_P() (in module spateo.alignment.methods.deprecated_morpho) (in module spateo.alignment.methods.deprecated_utils) get_P_chunk() (in module spateo.alignment.methods.deprecated_morpho) (in module spateo.alignment.transform) get_P_core() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) get_P_sparse() (in module spateo.alignment.methods.deprecated_morpho_sparse) (in module spateo.alignment.methods.deprecated_utils) 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_range() (in module spateo.external.CAST.CAST_Stack) get_rep() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) get_spatial_representation() (spateo.external.MERFISHVI._model.MERFISHVI method) (spateo.external.MERFISHVI.MERFISHVI method) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE 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) gpu (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.model.model_GCNII.Args attribute) (spateo.external.CAST.reg_params attribute) GPVectorField (class in spateo.tdr.morphometrics.morphofield_dg.GPVectorField) graph (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) graph_knn (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) GraphConvolution (class in spateo.tools.cluster.spagcn_utils) grid (spateo.plotting.static.dotplot.Dotplot attribute) 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) grn (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) group_extra_size (spateo.plotting.static.dotplot.Dotplot attribute) 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_pca() (in module spateo.alignment) (in module spateo.alignment.utils) group_shift() (in module spateo.external.CAST.CAST_Projection) group_subset (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) groups (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) guidance_effect (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] guidance_pair (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] guidance_pair_preprocess() (in module spateo.alignment.methods.deprecated_utils) guidance_weight (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] H h (class in spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.MainFlow attribute) Harmony_integration() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) has_uns_spatial_attribute() (spateo.configuration.SpateoAdataKeyManager method) has_var_groups (spateo.plotting.static.dotplot.Dotplot attribute) heads (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) hidden_dims (spateo.tools.cluster._stagate.pySTAGATE attribute) (spateo.tools.cluster.pySTAGATE attribute) (spateo.tools.pySTAGATE attribute) hidden_layers (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.A attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.B attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.h attribute) high2low() (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation method) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation method) history (spateo.segmentation.align.AlignmentRefiner attribute) hstack() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) hv_cutoff() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) I ICP() (in module spateo.alignment.methods.mesh_correction_utils) identify_boundary() (in module spateo.digitization) (in module spateo.digitization.boundary_old) identity (class in spateo.tools.CCI_effects_modeling.distributions) ids (spateo.tools.Label attribute) (spateo.tools.labels.Label attribute) IDW() (in module spateo.external.CAST.CAST_Projection) ifrigid (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) image (spateo.preprocessing.auxseg.LiveWireSegmentation property) (spateo.tools.live_wire.LiveWireSegmentation property) (spateo.tools.LiveWireSegmentation property) img_segmentation() (in module spateo.tools.roi) img_size_bs (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) 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_channels (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) in_concave_hull() (in module spateo.io.utils) in_convex_hull() (in module spateo.io.utils) in_features (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.SineLayer attribute) (spateo.tools.cluster.spagcn_utils.GraphConvolution attribute) in_hull() (in module spateo.tools.utils) inference() (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE method) (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR method) inference_nonspatial() (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) inference_spatial() (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE 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) info_keys (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) 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_field (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] init_layer (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] init_mean_variance() (spateo.segmentation.vi.NegativeBinomialMixture method) init_params_ (spateo.external.MERFISHVI._model.MERFISHVI attribute) (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.MERFISHVI attribute) (spateo.external.MERFISHVI.SpatialVI attribute) init_rotation (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) init_scaling (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) init_transform (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) init_translation (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) 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.deprecated_utils) (in module spateo.alignment.methods.utils) inlier_from_NN_debug() (in module spateo.alignment.methods.deprecated_utils) input_network_dim (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) 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) intermediate_layer_model (spateo.tdr.models.models_backbone.backbone_methods.NLPCA attribute) interpolate() (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR method) intersect_lsts (in module spateo.alignment.methods) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) inv() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) 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_pos_dict (spateo.plotting.static.networks.PlotNetwork attribute) 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_first (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.SineLayer attribute) is_floating_point() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) 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) is_merfishvi_available() (in module spateo.external) isfinite() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) isinf() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) isnan() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) issparse() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) iter_key_added (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] iterations (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) iterations_bs (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) iwls() (in module spateo.tools.CCI_effects_modeling.regression_utils) J J_cal() (in module spateo.external.CAST.CAST_Stack) 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) jax_new_version (spateo.alignment.methods.backend_ot.JaxBackend attribute) jax_type (in module spateo.alignment.methods.backend_ot) JaxBackend (class in spateo.alignment.methods.backend_ot) K K (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] k (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) kappa (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) Kernel (class in spateo.tools.find_neighbors) kernel (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.find_neighbors.Kernel attribute) (spateo.tools.MuSIC attribute), [1] kernel_bandwidth (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) kernel_interpolation() (in module spateo.tdr) (in module spateo.tdr.interpolations) (in module spateo.tdr.interpolations.interpolation_sparseVFC) kernel_type (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] key_added (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] key_pressed() (spateo.preprocessing.auxseg.LiveWireSegmentation method) keys (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) kl_distance() (in module spateo.alignment.methods.deprecated_utils) kl_div() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) kl_divergence_backend() (in module spateo.alignment.methods.deprecated_utils) kmeans_clustering() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.find_clusters) kmeans_plot_multiple() (in module spateo.external.CAST) (in module spateo.external.CAST.visualize) knee_threshold() (in module spateo.segmentation.utils) knn_to_adj() (in module spateo.tools.find_neighbors) kwargs (spateo.plotting.static.dotplot.Dotplot attribute) L l (spateo.tools.cluster.spagcn_utils.SpaGCN attribute) l_encoder (spateo.external.MERFISHVI._module.LDVAE attribute) (spateo.external.MERFISHVI._module.VAE attribute) Label (class in spateo.tools) (class in spateo.tools.labels) label_connected_components() (in module spateo.segmentation) (in module spateo.segmentation.label) label_num (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] label_overlap() (in module spateo.segmentation.utils) label_transfer_dict (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] 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) lambd (spateo.external.CAST.model.model_GCNII.Args attribute) lambdaVF (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] lamtheta_to_muvar() (in module spateo.segmentation.em) lamtheta_to_r() (in module spateo.segmentation.em) largest_dot (spateo.plotting.static.dotplot.CCDotplot attribute) (spateo.plotting.static.dotplot.Dotplot attribute) Lasso (class in spateo.tools) (class in spateo.tools.cluster_lasso) latent_distribution (spateo.external.MERFISHVI._module.VAE attribute) latent_mean_key (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.SpatialVI attribute) latent_var_key (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.SpatialVI attribute) layer (spateo.external.CAST.model.model_GCNII.Encoder attribute) layer1 (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.A attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.B attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.h attribute) layout (spateo.plotting.static.networks.PlotNetwork attribute) LDVAE (class in spateo.external.MERFISHVI._module) legend() (spateo.plotting.static.dotplot.Dotplot method) legends_width (spateo.plotting.static.dotplot.Dotplot attribute) lhsclassic() (in module spateo.alignment.methods.sampling) library_scaling_factors() (in module spateo.tools.CCI_effects_modeling.regression_utils) ligand_for_downstream (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) ligands (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) ligands_expr (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) ligands_expr_nonlag (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) ligrec() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.interactions) lin_dst (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) lin_src (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) line_ls (in module spateo.tools.roi) line_mode() (in module spateo.tools.roi) linear (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.SineLayer attribute) LineDDA() (spateo.preprocessing.auxseg.LiveWireSegmentation static method) Link (class in spateo.tools.CCI_effects_modeling.distributions) link (spateo.tools.CCI_effects_modeling.distributions.Binomial attribute) (spateo.tools.CCI_effects_modeling.distributions.Distribution 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) link_plot() (in module spateo.external.CAST) (in module spateo.external.CAST.visualize) link_plot_3d() (in module spateo.external.CAST.CAST_Projection) linspace() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) lisa() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.lisa) lisa_geo_df() (in module spateo.tools) (in module spateo.tools.lisa) lisa_quantiles() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.lisa) live_wire() (in module spateo.tools) (in module spateo.tools.live_wire) LiveWireSegmentation (class in spateo.preprocessing.auxseg) (class in spateo.tools) (class in spateo.tools.live_wire) 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) loader (spateo.tools.cluster._stagate.pySTAGATE attribute) (spateo.tools.cluster.pySTAGATE attribute) (spateo.tools.pySTAGATE attribute) 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) log() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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_nb_positive() (in module spateo.external.MERFISHVI.multimodal_spatial_vae) log_normal() (in module spateo.external.MERFISHVI.multimodal_spatial_vae) log_poisson() (in module spateo.external.MERFISHVI.multimodal_spatial_vae) log_time() (spateo.external.lack.Logger method) log_transform (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute), [1] (spateo.tools.MuSIC_Molecule_Selector attribute) log_variational (spateo.external.MERFISHVI._module.VAE attribute) log_zinb_positive() (in module spateo.external.MERFISHVI.multimodal_spatial_vae) Logger (class in spateo.external.lack) logger (in module spateo.external.MERFISHVI._model) (in module spateo.external.MERFISHVI._module) (in module spateo.external.MERFISHVI.multimodal_spatial_vae) (in module spateo.external.MERFISHVI.scvi_spatial_module) (spateo.external.lack.Logger attribute) (spateo.plotting.static.dotplot.Dotplot attribute) (spateo.plotting.static.networks.PlotNetwork attribute) (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) (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) 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) logsumexp() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) loss() (spateo.external.MERFISHVI._module.VAE method) (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE method) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE method) (spateo.segmentation.align.AlignmentRefiner method) loss_function (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) loss_function() (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) loss_traj (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) low2high() (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation method) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation method) lr (spateo.tools.cluster._stagate.pySTAGATE attribute) (spateo.tools.cluster.pySTAGATE attribute) (spateo.tools.pySTAGATE attribute) lr1 (spateo.external.CAST.model.model_GCNII.Args attribute) lr_db (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) lr_pairs (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) 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) marginal_ll() (spateo.external.MERFISHVI._module.VAE method) MARKERS_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) mask_cells_from_stain() (in module spateo.segmentation) (in module spateo.segmentation.icell) mask_edge() (in module spateo.external.CAST.model.aug) 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) matmul() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) MAX (in module spateo.configuration) max() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) max_id (spateo.tools.Label attribute) (spateo.tools.labels.Label attribute) max_iter (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] max_minus_value() (in module spateo.external.CAST.CAST_Stack) max_minus_value_t() (in module spateo.external.CAST.CAST_Stack) max_num_categories (spateo.plotting.static.dotplot.Dotplot attribute) max_rotation_angle (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] max_scaling (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] max_translation_scale (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] maxbw (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.MuSIC attribute), [1] maximum() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) mclose_mopen() (in module spateo.segmentation.utils) mclust_py() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.find_clusters) mclust_R() (in module spateo.external.STAGATE_pyG) (in module spateo.external.STAGATE_pyG.utils) mean() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) mean_encoder (spateo.external.MERFISHVI.scvi_spatial_module.SpatialEncoder attribute) mean_module (spateo.tdr.interpolations.interpolation_gaussianprocess.Approx_GPModel attribute) (spateo.tdr.interpolations.interpolation_gaussianprocess.Exact_GPModel attribute) (spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models.Approx_GPModel attribute) (spateo.tdr.interpolations.interpolation_gaussianprocess.gp_models.Exact_GPModel attribute) mean_q (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) mean_r (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) median() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) median_blur() (in module spateo.segmentation.utils) merfish() (in module spateo.sample_data) MERFISHVI (class in spateo.external.MERFISHVI) (class in spateo.external.MERFISHVI._model) 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) mesh (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] Mesh_correction (class in spateo.alignment) (class in spateo.alignment.methods) (class in spateo.alignment.methods.morpho_mesh_correction) mesh_plot() (in module spateo.external.CAST.CAST_Stack) mesh_trans_list (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) mesh_weight (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) meshgrid() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) meshsize (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) message() (spateo.external.STAGATE_pyG.gat_conv.GATConv method) method (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) min() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) min_figure_height (spateo.plotting.static.dotplot.Dotplot attribute) min_qr2 (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) min_rotation_angle (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) min_scaling (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) min_translation_scale (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) minbw (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.MuSIC attribute), [1] minimal_xticks() (in module spateo.plotting.static.utils) minimal_yticks() (in module spateo.plotting.static.utils) minimum() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) minn (spateo.plotting.static.dotplot.CCDotplot attribute) mirror_t (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) mod_type (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute), [1] (spateo.tools.MuSIC_Molecule_Selector attribute) modality_weights (spateo.external.MERFISHVI._model.MERFISHVI attribute) (spateo.external.MERFISHVI.MERFISHVI attribute) (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE attribute) model (spateo.tdr.models.models_backbone.backbone_methods.NLPCA attribute) (spateo.tools.cluster._stagate.pySTAGATE attribute) (spateo.tools.cluster.pySTAGATE attribute) (spateo.tools.pySTAGATE 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.backend spateo.alignment.methods.backend_ot spateo.alignment.methods.deprecated_morpho spateo.alignment.methods.deprecated_morpho_sparse spateo.alignment.methods.deprecated_morpho_sparse_utils spateo.alignment.methods.deprecated_utils spateo.alignment.methods.mesh_correction_utils spateo.alignment.methods.morpho_class spateo.alignment.methods.morpho_mesh_correction spateo.alignment.methods.paste spateo.alignment.methods.sampling 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.CAST spateo.external.CAST.CAST_Mark spateo.external.CAST.CAST_Projection spateo.external.CAST.CAST_Stack spateo.external.CAST.main spateo.external.CAST.model spateo.external.CAST.model.aug spateo.external.CAST.model.model_GCNII spateo.external.CAST.utils spateo.external.CAST.visualize spateo.external.lack spateo.external.MERFISHVI spateo.external.MERFISHVI._model spateo.external.MERFISHVI._module spateo.external.MERFISHVI.multimodal_spatial_vae spateo.external.MERFISHVI.scvi_spatial_module spateo.external.STAGATE_pyG spateo.external.STAGATE_pyG.gat_conv spateo.external.STAGATE_pyG.STAGATE spateo.external.STAGATE_pyG.Train_STAGATE spateo.external.STAGATE_pyG.utils spateo.get_version spateo.io spateo.io.bbs spateo.io.bgi spateo.io.image spateo.io.image_utils spateo.io.merfish spateo.io.nanostring spateo.io.seqfish spateo.io.seqscope spateo.io.slideseq spateo.io.starmap spateo.io.tenx spateo.io.utils spateo.logging spateo.pl spateo.plotting spateo.plotting.interactive spateo.plotting.interactive.agg spateo.plotting.static spateo.plotting.static.agg spateo.plotting.static.align spateo.plotting.static.bbs spateo.plotting.static.colorlabel spateo.plotting.static.contour spateo.plotting.static.dotplot spateo.plotting.static.geo spateo.plotting.static.glm spateo.plotting.static.interactions spateo.plotting.static.lisa spateo.plotting.static.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._fast_utils 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._stagate 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_correlation 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_apply_transformation() (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_transformation() (in module spateo.alignment) (in module spateo.alignment.morpho_alignment) Morpho_pairwise (class in spateo.alignment.methods) (class in spateo.alignment.methods.morpho_class) 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_processing (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] multi_slices() (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) MultiModalSpatialVAE (class in spateo.external.MERFISHVI.multimodal_spatial_vae) multiply() (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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 (spateo.segmentation.vi.NegativeBinomialMixture attribute) N (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) n (spateo.tools.CCI_effects_modeling.distributions.Binomial attribute) (spateo.tools.CCI_effects_modeling.distributions.Binomial_Variance attribute) n_batch (spateo.external.MERFISHVI._module.VAE attribute) n_dim (spateo.alignment.methods.sampling.TRNET attribute) n_dims (spateo.alignment.methods.sampling.TRNET attribute) n_features (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) n_labels (spateo.external.MERFISHVI._module.VAE attribute) n_latent (spateo.external.MERFISHVI._module.VAE attribute) n_layers (spateo.external.CAST.model.model_GCNII.Args attribute) (spateo.external.CAST.model.model_GCNII.GCN attribute) (spateo.external.CAST.model.model_GCNII.GCNII attribute) n_neighbors (spateo.external.MERFISHVI._model.MERFISHVI attribute) (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.MERFISHVI attribute) (spateo.external.MERFISHVI.SpatialVI attribute) (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_nodes (spateo.alignment.methods.sampling.TRNET attribute), [1] n_samples (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) n_samples_subsampled (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) n_samples_subset (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) n_slices (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) n_spatial (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE attribute) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialEncoder attribute) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE attribute) n_threads (spateo.configuration.SpateoConfig property) name (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.A attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.B attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.h attribute) namespace (spateo.external.lack.Logger attribute) namespace_message() (spateo.external.lack.Logger method) namespaced() (spateo.external.lack.Logger method) namespaced_context() (spateo.external.lack.Logger method) nan_to_num() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend 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) nearest_neighbors_idx() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) Negative_Binomial_Variance (class in spateo.tools.CCI_effects_modeling.distributions) negative_slope (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) NegativeBinomial (class in spateo.tools.CCI_effects_modeling.distributions) NegativeBinomialMixture (class in spateo.segmentation.vi) neighboring_unsampled (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) neighbors() (in module spateo.tools) (in module spateo.tools.find_neighbors) net (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.A attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.B attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.h attribute) nhid (spateo.tools.cluster.spagcn_utils.simple_GC_DEC attribute) niches() (in module spateo.tools) (in module spateo.tools.cell_communication) NLPCA (class in spateo.tdr.models.models_backbone.backbone_methods) nn_init (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] nn_init_top_K (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] nn_init_weight (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] no_cell_type_markers (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) non_zero_center_scale() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) nonrigid_start_iter (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) NonRigidAlignmentRefiner (class in spateo.segmentation.align) nonspatial_encoder (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE attribute) norm() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) normalization_factor (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) normalize (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute), [1] (spateo.tools.MuSIC_Molecule_Selector attribute) normalize_adj() (in module spateo.tools.find_neighbors) normalize_array() (spateo.plotting.static.utils.Loess static method) normalize_c (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] normalize_coords() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR method) normalize_exps() (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) normalize_g (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] normalize_mesh_spatial_coordinates() (spateo.alignment.Mesh_correction method) (spateo.alignment.methods.Mesh_correction method) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction method) normalize_signaling (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) normalize_spatial (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) normalize_total() (in module spateo.preprocessing) (in module spateo.preprocessing.normalize) normalize_x() (spateo.plotting.static.utils.Loess method) normalized_onehot (spateo.tools.Label attribute) (spateo.tools.labels.Label attribute) num (in module spateo.tools.roi) num_colorbar_ticks (spateo.plotting.static.dotplot.Dotplot attribute) num_epoch (spateo.tools.cluster._stagate.pySTAGATE attribute) (spateo.tools.cluster.pySTAGATE attribute) (spateo.tools.pySTAGATE attribute) num_labels (spateo.tools.Label attribute) (spateo.tools.labels.Label attribute) num_samples (spateo.tools.Label attribute) (spateo.tools.labels.Label attribute) num_size_legend_dots (spateo.plotting.static.dotplot.Dotplot attribute) NumpyBackend (class in spateo.alignment.methods) (class in spateo.alignment.methods.backend) (class in spateo.alignment.methods.backend_ot) nx (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) nx_torch (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) O omega_0 (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.SineLayer attribute) on_hover() (spateo.plotting.static.networks.PlotNetwork method) ON_RTD (in module spateo.get_version) on_unhover() (spateo.plotting.static.networks.PlotNetwork method) onehot (spateo.tools.Label attribute) (spateo.tools.labels.Label attribute) ones() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) optimal_bw (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) optimization_animation() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.align) optimizer (spateo.tools.cluster._stagate.pySTAGATE attribute) (spateo.tools.cluster.pySTAGATE attribute) (spateo.tools.pySTAGATE attribute) 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) out_channels (spateo.external.STAGATE_pyG.gat_conv.GATConv attribute) out_features (spateo.tools.cluster.spagcn_utils.GraphConvolution attribute) outer() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) outlayer (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.A attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.B attribute) (spateo.tdr.interpolations.interpolation_deeplearn.interpolation_nn.h attribute) output_diagnostics() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) output_network_dim (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) 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) overlay_slices_2d() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.align) P PaddingRate_bs (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) 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_iteration_panel() (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) (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) partial_robust_level (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] 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) path (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) path_list (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) path_plot_list (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) pathway_for_downstream (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) 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_reduction (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) 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_correction() (spateo.alignment.Mesh_correction method) (spateo.alignment.methods.Mesh_correction method) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction method) 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) physical_dist_priority_project() (in module spateo.external.CAST.CAST_Projection) pi() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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_deformation_grid() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.align) plot_dendrogram() (in module spateo.plotting.static.utils) plot_expression_3D() (in module spateo.plotting.static.three_d_plot.three_dims_plots) plot_group_extra (spateo.plotting.static.dotplot.Dotplot attribute) 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_mid() (in module spateo.external.CAST) (in module spateo.external.CAST.CAST_Stack) (in module spateo.external.CAST.visualize) plot_mid_v2() (in module spateo.external.CAST) (in module spateo.external.CAST.visualize) 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) plot_x_padding (spateo.plotting.static.dotplot.Dotplot attribute) plot_y_padding (spateo.plotting.static.dotplot.Dotplot attribute) PlotNetwork (class in spateo.plotting.static.networks) PlottingError PlottingWarning point_list (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) point_plot_list (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) 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 (spateo.tools.CCI_effects_modeling.distributions.Power attribute) (spateo.tools.CCI_effects_modeling.distributions.Power_Variance attribute) power() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) Power_Variance (class in spateo.tools.CCI_effects_modeling.distributions) pre_compute_dist (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] 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) predicted() (spateo.tools.cluster._stagate.pySTAGATE method) (spateo.tools.cluster.pySTAGATE method) (spateo.tools.pySTAGATE method) prelocate() (in module spateo.external.CAST.CAST_Stack) prelocate_loss_plot() (in module spateo.external.CAST.CAST_Stack) 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) preprocess_fast() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) PreprocessingError PreprocessingWarning previous_timestamp (spateo.external.lack.Logger attribute) 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) probability_parameters (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] probability_type (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] process_edges() (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE method) process_in_batches() (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE method) procrustes() (in module spateo.tools) (in module spateo.tools.coarse_align) prod() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) progress (in module spateo.segmentation.em) progress_logger() (spateo.external.lack.LoggerManager method) project() (spateo.tdr.models.models_backbone.backbone_methods.NLPCA method) pv_mesh() (in module spateo.tdr.models.models_individual.mesh_methods) pySTAGATE (class in spateo.tools) (class in spateo.tools.cluster) (class in spateo.tools.cluster._stagate) Q qc_regions() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.agg) qr() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) 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) r_tf_db (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) rand() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) randn() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) random_aug() (in module spateo.external.CAST.model.aug) random_sample() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) randperm() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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) receiver_ct_for_downstream (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) receptor_for_downstream (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) receptors (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) receptors_expr (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) reference (spateo.segmentation.align.AlignmentRefiner attribute) refine() (in module spateo.tools.cluster.spagcn_utils) refine_alignment() (in module spateo.segmentation) (in module spateo.segmentation.align) reg_params (class in spateo.external.CAST) (class in spateo.external.CAST.CAST_Stack) reg_total_t() (in module spateo.external.CAST.CAST_Stack) region_detect() (in module spateo.external.CAST) (in module spateo.external.CAST.CAST_Stack) register_result() (in module spateo.external.CAST.CAST_Stack) release (spateo.get_version.Version attribute) relu (spateo.external.CAST.model.model_GCNII.Encoder attribute) (spateo.external.CAST.model.model_GCNII.GCN attribute) (spateo.external.CAST.model.model_GCNII.GCNII attribute) remove_all_files_in_directory() (in module spateo.alignment.morpho_alignment) remove_background() (in module spateo.preprocessing.image) remove_kwargs() (in module spateo.utils) reorder_categories_after_dendrogram() (spateo.plotting.static.dotplot.Dotplot method) rep_field (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] rep_layer (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] repeat() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend 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_hook_percent_state (spateo.external.lack.Logger attribute) report_progress() (spateo.external.lack.Logger method) request_report_hook() (spateo.external.lack.Logger method) rescale_coords() (in module spateo.external.CAST.CAST_Stack) rescaling() (in module spateo.tools.utils) reset_parameters() (spateo.tools.cluster.spagcn_utils.GraphConvolution method) reset_rcParams() (in module spateo.configuration) reshape() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) return_intercepts() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) return_mapping (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) 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) rigid_transformation() (in module spateo.alignment) (in module spateo.alignment.utils) RigidAlignmentRefiner (class in spateo.segmentation.align) rng_ (spateo.alignment.methods.backend.Backend attribute) (spateo.alignment.methods.backend.NumpyBackend attribute) (spateo.alignment.methods.backend.TorchBackend attribute) (spateo.alignment.methods.backend_ot.Backend attribute) (spateo.alignment.methods.backend_ot.CupyBackend attribute) (spateo.alignment.methods.backend_ot.JaxBackend attribute) (spateo.alignment.methods.backend_ot.NumpyBackend attribute) (spateo.alignment.methods.backend_ot.TensorflowBackend attribute) (spateo.alignment.methods.backend_ot.TorchBackend attribute) (spateo.alignment.methods.NumpyBackend attribute) (spateo.alignment.methods.TorchBackend attribute) roll() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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) rst (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) run() (spateo.alignment.methods.morpho_class.Morpho_pairwise method) (spateo.alignment.methods.Morpho_pairwise method) (spateo.alignment.methods.sampling.TRNET method) run_bp() (in module spateo.segmentation.bp) run_discrete_optimization() (spateo.alignment.Mesh_correction method) (spateo.alignment.methods.Mesh_correction method) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction method) 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_n_pause() (spateo.alignment.methods.sampling.TRNET method) 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) runOnce() (spateo.alignment.methods.sampling.TRNET method) S safe_erode() (in module spateo.segmentation.utils) sample() (in module spateo.alignment.methods.sampling) (spateo.external.MERFISHVI._module.VAE method) sample_by_kmeans() (in module spateo.alignment.methods.sampling) sample_by_velocity() (in module spateo.alignment.methods.sampling) sample_from_eligible_neighbors() (in module spateo.tools.spatial_smooth) sample_names (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) sampleA (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] sampleB (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] save() (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation method) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation method) save_concrete_iter (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] 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) save_subsampling (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) scale (spateo.segmentation.vi.NegativeBinomialMixture attribute) 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) searchsorted() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) 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) seed (spateo.alignment.methods.sampling.TRNET attribute), [1] seed() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend 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_hvf_seurat() (in module spateo.preprocessing) (in module spateo.preprocessing.normalize) select_hvf_seurat_single() (in module spateo.preprocessing.normalize) select_layer_data() (spateo.configuration.SpateoAdataKeyManager method) select_polygon() (in module spateo.plotting) (in module spateo.plotting.interactive) (in module spateo.plotting.interactive.agg) select_qc_regions() (in module spateo.segmentation) (in module spateo.segmentation.qc) SELECTION_SUFFIX (spateo.configuration.SpateoAdataKeyManager attribute) sender_ct_for_downstream (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) separate_mean (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) separate_scale (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise 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_gradients() (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) set_init_parameters() (spateo.alignment.Mesh_correction method) (spateo.alignment.methods.Mesh_correction method) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction method) 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) set_up (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) setLevel() (spateo.external.lack.Logger method) setup_anndata() (spateo.external.MERFISHVI._model.SpatialVI class method) (spateo.external.MERFISHVI.SpatialVI class method) setup_downstream() (spateo.tools.CCI_effects_modeling.MuSIC method) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC method) (spateo.tools.MuSIC method) setup_nonspatial_anndata() (spateo.external.MERFISHVI._model.MERFISHVI class method) (spateo.external.MERFISHVI.MERFISHVI class method) setup_spatial_graph() (spateo.external.MERFISHVI._model.SpatialVI method) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE method) (spateo.external.MERFISHVI.SpatialVI method) shift_cells() (in module spateo.segmentation.simulation_evaluation.allocate_cell) shiftedColorMap() (in module spateo.configuration) show_colorbar (spateo.plotting.static.dotplot.Dotplot attribute) show_size_legend (spateo.plotting.static.dotplot.Dotplot attribute) shuffle_adata() (in module spateo.svg), [1], [2] (in module spateo.svg.utils) (in module spateo.tools.spatially_variable_gene_ot) sigma2_end (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) sigma2_init_scale (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] sign() (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) 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) size_exponent (spateo.plotting.static.dotplot.Dotplot attribute) size_title (spateo.plotting.static.dotplot.Dotplot attribute) SKM (in module spateo.configuration) (in module spateo.digitization) slices (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) slices_2d() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.align) slices_spatial (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) slideseq() (in module spateo.sample_data) smallest_dot (spateo.plotting.static.dotplot.Dotplot attribute) smooth (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute), [1] (spateo.tools.MuSIC_Molecule_Selector attribute) smooth() (in module spateo.tools) (in module spateo.tools.cluster) (in module spateo.tools.cluster.find_clusters) (in module spateo.tools.spatial_smooth) smooth_image (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) (spateo.tools.live_wire.LiveWireSegmentation attribute) (spateo.tools.LiveWireSegmentation attribute) 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) smoothing_factor (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) softplus() (in module spateo.tools.CCI_effects_modeling.regression_utils) solve() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) solve_RT_by_correspondence() (in module spateo.alignment) (in module spateo.alignment.methods) (in module spateo.alignment.methods.mesh_correction_utils) (in module spateo.alignment.methods.utils) (in module spateo.alignment.utils) sort() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) sort2() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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) space_project() (in module spateo.external.CAST.CAST_Projection) 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_calculation_mode (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] 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_mask() (in module spateo.external.CAST.CAST_Projection) 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) sparse_tensor_to_scipy() (in module spateo.alignment.methods.utils) sparse_top_k (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] spateo module spateo.align module spateo.alignment module spateo.alignment.deformation module spateo.alignment.methods module spateo.alignment.methods.backend module spateo.alignment.methods.backend_ot module spateo.alignment.methods.deprecated_morpho module spateo.alignment.methods.deprecated_morpho_sparse module spateo.alignment.methods.deprecated_morpho_sparse_utils module spateo.alignment.methods.deprecated_utils module spateo.alignment.methods.mesh_correction_utils module spateo.alignment.methods.morpho_class module spateo.alignment.methods.morpho_mesh_correction module spateo.alignment.methods.paste module spateo.alignment.methods.sampling 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.CAST module spateo.external.CAST.CAST_Mark module spateo.external.CAST.CAST_Projection module spateo.external.CAST.CAST_Stack module spateo.external.CAST.main module spateo.external.CAST.model module spateo.external.CAST.model.aug module spateo.external.CAST.model.model_GCNII module spateo.external.CAST.utils module spateo.external.CAST.visualize module spateo.external.lack module spateo.external.MERFISHVI module spateo.external.MERFISHVI._model module spateo.external.MERFISHVI._module module spateo.external.MERFISHVI.multimodal_spatial_vae module spateo.external.MERFISHVI.scvi_spatial_module module spateo.external.STAGATE_pyG module spateo.external.STAGATE_pyG.gat_conv module spateo.external.STAGATE_pyG.STAGATE module spateo.external.STAGATE_pyG.Train_STAGATE module spateo.external.STAGATE_pyG.utils module spateo.get_version module spateo.io module spateo.io.bbs module spateo.io.bgi module spateo.io.image module spateo.io.image_utils module spateo.io.merfish module spateo.io.nanostring module spateo.io.seqfish module spateo.io.seqscope module spateo.io.slideseq module spateo.io.starmap module spateo.io.tenx module spateo.io.utils module spateo.logging module spateo.pl module spateo.plotting module spateo.plotting.interactive module spateo.plotting.interactive.agg module spateo.plotting.static module spateo.plotting.static.agg module spateo.plotting.static.align module spateo.plotting.static.bbs module spateo.plotting.static.colorlabel module spateo.plotting.static.contour module spateo.plotting.static.dotplot module spateo.plotting.static.geo module spateo.plotting.static.glm module spateo.plotting.static.interactions module spateo.plotting.static.lisa module spateo.plotting.static.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._fast_utils 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._stagate 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_correlation 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) spatial_bv_local_moran() (in module spateo.tools) (in module spateo.tools.spatial_correlation) spatial_bv_moran_obs_genes() (in module spateo.tools) (in module spateo.tools.spatial_correlation) spatial_domains() (in module spateo.plotting) (in module spateo.plotting.static) (in module spateo.plotting.static.contour) spatial_encoder (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE attribute) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE attribute) spatial_graph_type (spateo.external.MERFISHVI._model.MERFISHVI attribute) (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.MERFISHVI attribute) (spateo.external.MERFISHVI.SpatialVI attribute) spatial_key (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) (spateo.alignment.methods.Morpho_pairwise attribute), [1] spatial_kl_weight (spateo.external.MERFISHVI._model.MERFISHVI attribute) (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.MERFISHVI attribute) (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE attribute) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialVAE attribute) (spateo.external.MERFISHVI.SpatialVI attribute) SpatialEncoder (class in spateo.external.MERFISHVI.scvi_spatial_module) SpatialVAE (class in spateo.external.MERFISHVI.scvi_spatial_module) SpatialVI (class in spateo.external.MERFISHVI) (class in spateo.external.MERFISHVI._model) species (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute), [1] (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) split_slice() (in module spateo.alignment) (in module spateo.alignment.utils) sqrt (class in spateo.tools.CCI_effects_modeling.distributions) sqrt() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) sqrtm() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) squeeze() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) src_points (spateo.segmentation.align.NonRigidAlignmentRefiner attribute) stability_factor (spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation.DeepInterpolation attribute) (spateo.tdr.interpolations.interpolation_deeplearn.DeepInterpolation attribute) stack() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) STAGATE (class in spateo.external.STAGATE_pyG) (class in spateo.external.STAGATE_pyG.STAGATE) STAIN_LAYER_KEY (spateo.configuration.SpateoAdataKeyManager attribute) standardize() (in module spateo.external.CAST.model.model_GCNII) stardist() (in module spateo.segmentation) (in module spateo.segmentation.external.stardist) StarDist2D (in module spateo.segmentation.external.stardist) starmap() (in module spateo.sample_data) Stats_Spatial_Net() (in module spateo.external.STAGATE_pyG) (in module spateo.external.STAGATE_pyG.utils) std() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) stitch_images() (in module spateo.io.nanostring) str_type_error (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) style() (spateo.plotting.static.dotplot.Dotplot method) sub_adata (spateo.tools.cluster_lasso.Lasso attribute) (spateo.tools.Lasso attribute) sub_data_extract() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) sub_node_sum() (in module spateo.external.CAST) (in module spateo.external.CAST.utils) subsample_neighbors_dense() (in module spateo.tools.spatial_smooth) subsample_neighbors_sparse() (in module spateo.tools.spatial_smooth) subsample_slices (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) subsampled (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) subsampled_sample_names (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) subset (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) subset_best_samples() (in module spateo.tdr.interpolations.interpolation_deeplearn.deep_interpolation) subset_indices (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) subset_sample_names (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) 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) sum() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) summarize_interaction_effects() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) summarize_tf_effects() (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter method) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter method) (spateo.tools.MuSIC_Interpreter method) svg_iden_reg() (in module spateo.svg) (in module spateo.svg.get_svg) SVI_mode (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] swap_axes() (spateo.plotting.static.dotplot.Dotplot method) T take_along_axis() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) target_distribution() (spateo.tools.cluster.spagcn_utils.simple_GC_DEC method) target_expr_threshold (spateo.tools.CCI_effects_modeling.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC_Molecule_Selector attribute) (spateo.tools.CCI_effects_modeling.MuSIC_upstream.MuSIC_Molecule_Selector attribute) (spateo.tools.MuSIC attribute), [1] (spateo.tools.MuSIC_Molecule_Selector attribute) target_for_downstream (spateo.tools.CCI_effects_modeling.MuSIC_downstream.MuSIC_Interpreter attribute) (spateo.tools.CCI_effects_modeling.MuSIC_Interpreter attribute) (spateo.tools.MuSIC_Interpreter attribute) target_points (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) targets (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) targets_expr (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC 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) temp_timer_logger (spateo.external.lack.LoggerManager attribute) TensorflowBackend (class in spateo.alignment.methods.backend_ot) tf_tf_db (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) tf_type (in module spateo.alignment.methods.backend_ot) theta_r1 (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) theta_r2 (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) theta_renew() (in module spateo.external.CAST.CAST_Stack) 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) threshold_gradient_image (spateo.preprocessing.auxseg.LiveWireSegmentation attribute) (spateo.tools.live_wire.LiveWireSegmentation attribute) (spateo.tools.LiveWireSegmentation attribute) tile() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) time_passed (spateo.external.lack.Logger attribute) to_align (spateo.segmentation.align.AlignmentRefiner attribute) to_dense_matrix (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) (in module spateo.tools.cluster.find_clusters) (in module spateo.tools.cluster.utils) to_numpy() (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) tocsr() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) todense() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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) topk() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) torch_Bspline() (in module spateo.external.CAST.CAST_Stack) torch_like_split() (in module spateo.alignment.methods.deprecated_morpho_sparse_utils) (in module spateo.alignment.methods.deprecated_utils) (in module spateo.alignment.methods.utils) torch_type (in module spateo.alignment.methods.backend) (in module spateo.alignment.methods.backend_ot) TorchBackend (class in spateo.alignment.methods) (class in spateo.alignment.methods.backend) (class in spateo.alignment.methods.backend_ot) 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) tps_deformation() (in module spateo.alignment) (in module spateo.alignment.utils) trace() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) 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._stagate.pySTAGATE method) (spateo.tools.cluster.pySTAGATE method) (spateo.tools.cluster.spagcn_utils.SpaGCN method) (spateo.tools.pySTAGATE method) train_seq() (in module spateo.external.CAST.CAST_Mark) train_STAGATE() (in module spateo.external.STAGATE_pyG) (in module spateo.external.STAGATE_pyG.Train_STAGATE) train_x (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) train_y (spateo.tdr.interpolations.interpolation_gp.Imputation_GPR attribute) Transfer_pytorch_Data() (in module spateo.external.STAGATE_pyG) (in module spateo.external.STAGATE_pyG.utils) transform() (spateo.segmentation.align.AlignmentRefiner static method) (spateo.segmentation.align.NonRigidAlignmentRefiner static method) (spateo.segmentation.align.RigidAlignmentRefiner static method) transform_by_min_max() (in module spateo.plotting.static.align) transform_H() (in module spateo.plotting.static.align) 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) translation_params (spateo.external.CAST.CAST_Stack.reg_params attribute) (spateo.external.CAST.reg_params attribute) transpose() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) tricubic() (in module spateo.plotting.static.utils) trn() (in module spateo.alignment.methods.sampling) TRNET (class in spateo.alignment.methods.sampling) 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) unique() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) 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) unsqueeze() (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) unsupported_if_adata_minified() (in module spateo.external.MERFISHVI.multimodal_spatial_vae) (in module spateo.external.MERFISHVI.scvi_spatial_module) update_alpha() (in module spateo.alignment.methods.deprecated_utils) update_assignment_P() (in module spateo.alignment.methods.deprecated_utils) 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) update_gamma() (in module spateo.alignment.methods.deprecated_utils) update_nonrigid() (in module spateo.alignment.methods.deprecated_utils) update_R (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) update_rigid() (in module spateo.alignment.methods.deprecated_utils) update_sigma2() (in module spateo.alignment.methods.deprecated_utils) update_Sp() (in module spateo.alignment.methods.deprecated_utils) use_batch_norm (spateo.external.MERFISHVI._module.LDVAE attribute) use_chunk (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] use_encoder (spateo.external.CAST.model.model_GCNII.Args attribute) (spateo.external.CAST.model.model_GCNII.GCN attribute) (spateo.external.CAST.model.model_GCNII.GCNII attribute) use_expression_neighbors (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) use_hvg (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute) (spateo.alignment.methods.Morpho_pairwise attribute) use_observed_lib_size (spateo.external.MERFISHVI._module.VAE attribute) use_size_factor_key (spateo.external.MERFISHVI._module.VAE attribute) use_spatial (spateo.external.MERFISHVI._model.SpatialVI attribute) (spateo.external.MERFISHVI.SpatialVI attribute) V VAE (class in spateo.external.MERFISHVI._module) ValFunction (spateo.alignment.methods.backend.TorchBackend attribute) (spateo.alignment.methods.backend_ot.TorchBackend attribute) (spateo.alignment.methods.TorchBackend attribute) 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) var_encoder (spateo.external.MERFISHVI.scvi_spatial_module.SpatialEncoder attribute) var_eps (spateo.external.MERFISHVI.multimodal_spatial_vae.MultiModalSpatialVAE attribute) (spateo.external.MERFISHVI.scvi_spatial_module.SpatialEncoder attribute) var_group_labels (spateo.plotting.static.dotplot.Dotplot attribute) var_group_positions (spateo.plotting.static.dotplot.Dotplot attribute) var_group_rotation (spateo.plotting.static.dotplot.Dotplot attribute) var_names (spateo.plotting.static.dotplot.Dotplot attribute) var_names_idx_order (spateo.plotting.static.dotplot.Dotplot attribute) variance (spateo.tools.CCI_effects_modeling.distributions.Binomial attribute) (spateo.tools.CCI_effects_modeling.distributions.Distribution 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) vboundnorm (spateo.plotting.static.dotplot.Dotplot attribute) vecfld_key_added (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.Morpho_pairwise attribute), [1] 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) verbose (spateo.alignment.Mesh_correction attribute) (spateo.alignment.methods.Mesh_correction attribute) (spateo.alignment.methods.morpho_class.Morpho_pairwise attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute) (spateo.alignment.methods.Morpho_pairwise attribute), [1] (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.Label attribute) (spateo.tools.labels.Label attribute) (spateo.tools.MuSIC attribute) 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_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.deprecated_utils) (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) vstack() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) vtk_interpolation() (in module spateo.tdr) (in module spateo.tdr.interpolations) (in module spateo.tdr.interpolations.interpolation_vtk) W W (spateo.alignment.methods.sampling.TRNET attribute), [1] 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) wd1 (spateo.external.CAST.model.model_GCNII.Args attribute) weight (spateo.segmentation.align.AlignmentRefiner attribute) (spateo.tools.cluster.spagcn_utils.GraphConvolution attribute) weight_decay (spateo.tools.cluster._stagate.pySTAGATE attribute) (spateo.tools.cluster.pySTAGATE attribute) (spateo.tools.pySTAGATE attribute) 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) where() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) wrap_to_plotter() (in module spateo.plotting.static.three_d_plot.three_dims_plots) wspace (spateo.plotting.static.dotplot.Dotplot attribute) X X (spateo.alignment.methods.sampling.TRNET attribute), [1] x (spateo.segmentation.vi.NegativeBinomialMixture attribute) X (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) x_chunk (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) X_df (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) X_LAYER (spateo.configuration.SpateoAdataKeyManager attribute) Y y (spateo.tools.CCI_effects_modeling.MuSIC attribute) (spateo.tools.CCI_effects_modeling.MuSIC.MuSIC attribute) (spateo.tools.MuSIC attribute) Z z_encoder (spateo.external.MERFISHVI._module.LDVAE attribute) (spateo.external.MERFISHVI._module.VAE attribute) z_heights (spateo.alignment.Mesh_correction attribute), [1] (spateo.alignment.methods.Mesh_correction attribute), [1] (spateo.alignment.methods.morpho_mesh_correction.Mesh_correction attribute), [1] zebrafish_256 (in module spateo.configuration) zebrafish_colors (in module spateo.configuration) zeileis_28 (in module spateo.plotting.static.colorlabel) zero_inflated (spateo.segmentation.vi.NegativeBinomialMixture attribute) zero_pad() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) zeros() (spateo.alignment.methods.backend.Backend method) (spateo.alignment.methods.backend.NumpyBackend method) (spateo.alignment.methods.backend.TorchBackend method) (spateo.alignment.methods.backend_ot.Backend method) (spateo.alignment.methods.backend_ot.CupyBackend method) (spateo.alignment.methods.backend_ot.JaxBackend method) (spateo.alignment.methods.backend_ot.NumpyBackend method) (spateo.alignment.methods.backend_ot.TensorflowBackend method) (spateo.alignment.methods.backend_ot.TorchBackend method) (spateo.alignment.methods.NumpyBackend method) (spateo.alignment.methods.TorchBackend method) zinb_test() (in module spateo.tools.glm)
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