Index _ | A | C | D | E | F | G | I | L | M | N | P | R | S | T | V | X | Y | Z _ __add__() (tdm.tissue.Tissue method) __init__() (tdm.analysis.Analysis method) (tdm.dataset.Dataset method) (tdm.dataset.ExtrapolateNeighborsDataset method) (tdm.dataset.NeighborsDataset method) (tdm.dataset.PolynomialDataset method) (tdm.dataset.RestrictedNeighborsDataset method) (tdm.model.LogisticRegressionModel method) (tdm.model.Model method) (tdm.tissue.Tissue method) A all_image_numbers() (in module tdm.raw.breast_imc) (in module tdm.raw.breast_mibi) Analysis (class in tdm.analysis) C cell_a (tdm.analysis.Analysis property) cell_b (tdm.analysis.Analysis property) cell_c (tdm.analysis.Analysis property) cell_df() (tdm.tissue.Tissue method) CELL_TYPE_DEFINITIONS_CD4_CD8_B (in module tdm.raw.breast_mibi) cell_types (tdm.analysis.Analysis property) cell_types() (tdm.dataset.Dataset method) (tdm.model.Model method) (tdm.tissue.Tissue method) check_single_cell_df() (in module tdm.preprocess.single_cell_df) construct_dataset() (tdm.dataset.ExtrapolateNeighborsDataset method) (tdm.dataset.NeighborsDataset method) construct_features() (tdm.dataset.NeighborsDataset method) construct_features_from_counts() (tdm.dataset.Dataset method) (tdm.dataset.PolynomialDataset method) construct_observations() (tdm.dataset.NeighborsDataset method) construct_polynomial_features() (tdm.dataset.PolynomialDataset method) D Dataset (class in tdm.dataset) death_prob() (tdm.model.Model method) delta_cells() (tdm.model.Model method) download_breast_mibi_data() (in module tdm.raw.breast_mibi) dump() (tdm.analysis.Analysis method) E enforce_max_density (tdm.analysis.Analysis property) ExtrapolateNeighborsDataset (class in tdm.dataset) F fetch() (tdm.dataset.Dataset method) fetch_all() (tdm.dataset.Dataset method) fit() (tdm.model.LogisticRegressionModel method) (tdm.model.Model method) fit_summary() (in module tdm.plot.model.pval) G get_delta_cells_func() (tdm.model.Model method) get_include_mask() (tdm.dataset.RestrictedNeighborsDataset method) get_n_neighbors_by_xy() (tdm.dataset.NeighborsDataset method) get_parameter() (tdm.model.LogisticRegressionModel method) get_tissues_by_ids() (tdm.analysis.Analysis method) get_xys() (tdm.dataset.NeighborsDataset method) I img_id (tdm.tissue.Tissue property) intercept_idx() (tdm.dataset.PolynomialDataset method) is_dividing() (in module tdm.preprocess.ki67) L LLR_pval_per_cell_type() (in module tdm.plot.model.pval) load() (tdm.analysis.Analysis static method) LogisticRegressionModel (class in tdm.model) M Model (class in tdm.model) model (tdm.analysis.Analysis property) module tdm.raw.breast_imc tdm.raw.breast_mibi N n_cells() (tdm.dataset.Dataset method) (tdm.tissue.Tissue method) n_cells_df() (tdm.tissue.Tissue method) n_cells_list() (tdm.tissue.Tissue method) n_features() (tdm.dataset.Dataset method) n_neighbors() (tdm.dataset.NeighborsDataset method) n_obs() (tdm.dataset.Dataset method) nds (tdm.analysis.Analysis property) ndss (tdm.analysis.Analysis property) neighborhood_size (tdm.analysis.Analysis property) NeighborsDataset (class in tdm.dataset) P parameter_names() (tdm.model.LogisticRegressionModel method) (tdm.model.Model method) parameter_pvalues() (tdm.model.LogisticRegressionModel method) (tdm.model.Model method) parameter_stds() (tdm.model.LogisticRegressionModel method) (tdm.model.Model method) parameters() (tdm.model.LogisticRegressionModel method) (tdm.model.Model method) parameters_df() (tdm.model.Model method) pds (tdm.analysis.Analysis property) plot_calibration() (in module tdm.plot.model.calibration) plot_calibration_against_permuted_divisions() (in module tdm.plot.model.calibration) plot_divisions_per_image() (in module tdm.plot.preprocess.ki67) plot_fraction_of_dividing_cells() (in module tdm.plot.preprocess.ki67) plot_growth_rate() (in module tdm.plot.two_cells.phase_portrait) plot_marker_distributions() (in module tdm.plot.preprocess.ki67) plot_phase_portrait() (in module tdm.plot.two_cells.phase_portrait) PolynomialDataset (class in tdm.dataset) predict() (tdm.model.Model method) present_cell_types() (tdm.tissue.Tissue method) R read_clinical_df() (in module tdm.raw.breast_imc) (in module tdm.raw.breast_mibi) read_image_single_cell_df() (in module tdm.raw.breast_imc) read_single_cell_df() (in module tdm.raw.breast_imc) (in module tdm.raw.breast_mibi) reassign_ki67_cluster() (in module tdm.raw.breast_mibi) reset_maximal_density_enforcement() (tdm.model.Model method) RestrictedNeighborsDataset (class in tdm.dataset) rnds (tdm.analysis.Analysis property) run() (tdm.analysis.Analysis method) S sample_observations() (tdm.model.Model method) set_dataset() (tdm.dataset.Dataset method) set_death_prob() (tdm.model.Model method) set_maximal_density_enforcement() (tdm.model.Model method) set_maximal_density_enforcer() (tdm.analysis.Analysis method) set_parameter() (tdm.model.LogisticRegressionModel method) set_parameters() (tdm.model.LogisticRegressionModel method) subject_id (tdm.tissue.Tissue property) T tdm.raw.breast_imc module tdm.raw.breast_mibi module Tissue (class in tdm.tissue) tissue_dimensions() (tdm.tissue.Tissue method) tissue_states() (tdm.analysis.Analysis method) tissues (tdm.analysis.Analysis property) transform_ki67() (in module tdm.preprocess.ki67) V valid_cells() (tdm.dataset.NeighborsDataset method) X xlim (tdm.analysis.Analysis property) Y ylim (tdm.analysis.Analysis property) Z zlim (tdm.analysis.Analysis property)