Index _ | A | B | C | D | E | F | G | H | K | L | M | N | P | Q | R | S | T | U | V | W _ _initialized (nicheverse.VectorQuantizer attribute) A anndata_keys() (in module nicheverse) annotate_codebook() (in module nicheverse.annotate) annotate_codes() (in module nicheverse) annotate_niches() (in module nicheverse.annotate) AnnotationConfig (class in nicheverse.annotate) AnnotationResult (class in nicheverse.annotate) apply_lab_rules() (in module nicheverse.annotate) attach() (nicheverse.annotate.AnnotationResult method) attach_codes() (in module nicheverse) attach_codes_to_adata() (in module nicheverse) attach_labels() (in module nicheverse.annotate) B bernoulli_detection_bce() (in module nicheverse.losses) biorxiv_search() (in module nicheverse.annotate) BSQ (class in nicheverse.models) build_encoder() (in module nicheverse.models) build_quantizer() (in module nicheverse.models) C calibration (nicheverse.annotate.AnnotationResult attribute) calibration() (in module nicheverse.annotate) call_llm() (in module nicheverse.annotate) CELL_CODE (nicheverse.Keys attribute) CELL_EMBEDDING (nicheverse.Keys attribute) CellTypePrior (class in nicheverse.annotate) check_citations() (in module nicheverse.annotate) cluster_codes() (in module nicheverse.annotate) code_context() (in module nicheverse.annotate) code_dotplot() (in module nicheverse.annotate) code_evidence() (in module nicheverse) code_groundtruth_concordance() (in module nicheverse.annotate) code_usage (nicheverse.VectorQuantizer attribute) codebook_consistency() (in module nicheverse.losses) codebook_usage_pdf() (in module nicheverse.plotting) D dirichlet_multinomial_nll() (in module nicheverse.losses) E ema_cluster_size (nicheverse.VectorQuantizer attribute) ema_embed_sum (nicheverse.VectorQuantizer attribute) embedding (nicheverse.models.FSQ property) (nicheverse.VectorQuantizer attribute) encode() (nicheverse.HierarchicalVQVAE method) env_snapshot() (in module nicheverse) extra_repr() (nicheverse.VectorQuantizer method) F fit() (nicheverse.Trainer method) forward() (nicheverse.HierarchicalVQVAE method) (nicheverse.models.BSQ method) (nicheverse.models.FSQ method) (nicheverse.models.GroupedResidualVQ method) (nicheverse.models.LFQ method) (nicheverse.models.MoleculeSetEncoder method) (nicheverse.models.MoleculeSetVQVAE method) (nicheverse.models.ProductVQ method) (nicheverse.models.QINCoVQ method) (nicheverse.models.ResidualFSQ method) (nicheverse.models.ResidualMLP method) (nicheverse.models.ResidualVQ method) (nicheverse.models.RotVQ method) (nicheverse.models.SoftVQ method) (nicheverse.models.TransformerEncoder method) (nicheverse.VectorQuantizer method) from_anndata() (nicheverse.SpatialDataset class method) from_checkpoint() (nicheverse.HierarchicalVQVAE class method) from_dict() (nicheverse.annotate.ProjectContext class method) (nicheverse.ModelConfig class method) from_yaml() (nicheverse.annotate.ProjectContext class method) FSQ (class in nicheverse.models) fuse_codebooks (nicheverse.ModelConfig attribute) G gate() (in module nicheverse.annotate) gaussian_nll() (in module nicheverse.losses) graph_total_variation() (in module nicheverse.losses) GroupedResidualVQ (class in nicheverse.models) H HierarchicalVQVAE (class in nicheverse) holdout_key (nicheverse.TrainConfig attribute) K Keys (class in nicheverse) kind (nicheverse.annotate.AnnotationResult attribute) L label_map() (nicheverse.annotate.AnnotationResult method) labels_df (nicheverse.annotate.AnnotationResult attribute) laplacian_smoothness() (in module nicheverse.losses) LFQ (class in nicheverse.models) literature_for_markers() (in module nicheverse.annotate) load_checkpoint() (in module nicheverse) load_xenium_cohort() (in module nicheverse) load_xenium_run() (in module nicheverse) M mae_pretrain() (in module nicheverse) manifest_path (nicheverse.annotate.AnnotationResult attribute) marker_presence() (in module nicheverse.annotate) ModelConfig (class in nicheverse) module nicheverse.losses nicheverse.plotting MoleculeSetDataset (class in nicheverse.data) MoleculeSetEncoder (class in nicheverse.models) MoleculeSetVQVAE (class in nicheverse.models) N nb_nll() (in module nicheverse.losses) NEIGHBORHOOD_CODE (nicheverse.Keys attribute) NEIGHBORHOOD_EMBEDDING (nicheverse.Keys attribute) niche_evidence() (in module nicheverse.annotate) NICHE_SPATIAL_LOSSES (in module nicheverse.losses) NichePrior (class in nicheverse.annotate) nicheverse.losses module nicheverse.plotting module P per_sample_spatial_pdf() (in module nicheverse.plotting) poisson_nll() (in module nicheverse.losses) predict() (nicheverse.Trainer method) predict_codes() (in module nicheverse) ProductVQ (class in nicheverse.models) ProjectContext (class in nicheverse.annotate) pubmed_search() (in module nicheverse.annotate) Q QINCoVQ (class in nicheverse.models) R read_spatial() (in module nicheverse) read_xenium() (in module nicheverse) read_xenium_cohort() (in module nicheverse) records (nicheverse.annotate.AnnotationResult attribute) register_encoder() (in module nicheverse.models) register_quantizer() (in module nicheverse.models) ResidualFSQ (class in nicheverse.models) ResidualMLP (class in nicheverse.models) ResidualVQ (class in nicheverse.models) review_df (nicheverse.annotate.AnnotationResult attribute) RotVQ (class in nicheverse.models) S SAMPLE (nicheverse.Keys attribute) save_checkpoint() (in module nicheverse) score_code() (in module nicheverse.annotate) scorecard_df (nicheverse.annotate.AnnotationResult attribute) scorecard_table() (in module nicheverse.annotate) seed_everything() (in module nicheverse) sha256_array() (in module nicheverse) sha256_file() (in module nicheverse) SoftVQ (class in nicheverse.models) SPATIAL (nicheverse.Keys attribute) spatial_contrastive() (in module nicheverse.losses) spatial_loss_type (nicheverse.TrainConfig attribute) SPATIAL_LOSSES (in module nicheverse.losses) spatial_neighbors() (in module nicheverse) SpatialDataset (class in nicheverse) T to_dict() (nicheverse.annotate.ProjectContext method) (nicheverse.ModelConfig method) to_prompt_block() (nicheverse.annotate.ProjectContext method) to_yaml() (nicheverse.annotate.ProjectContext method) train_model() (in module nicheverse) TrainConfig (class in nicheverse) Trainer (class in nicheverse) training_loss_pdf() (in module nicheverse.plotting) transcript_context() (in module nicheverse.data) TransformerEncoder (class in nicheverse.models) U update_count (nicheverse.VectorQuantizer attribute) V validate_vocabulary() (in module nicheverse.annotate) VectorQuantizer (class in nicheverse) vq_distance (nicheverse.ModelConfig attribute) W write_env_snapshot() (in module nicheverse) write_evidence_bundle() (in module nicheverse.annotate) write_provenance_manifest() (in module nicheverse.annotate) write_template() (nicheverse.annotate.ProjectContext static method)