Index Symbols | A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W Symbols |project| module A add_bounding_box() (seg_visualization method) add_fit() (seg_visualization method) add_model() (seg_visualization method) adjustLength() (ImageIO method) analyze_protein_membrane_min_distance() (ColabSegData method) annotation (ColabSegNapariWidget property) append() (ColabSegNapariWidget method) asdict() (ColabSegNapariWidget method) B backup_step_to_previous() (ColabSegData method) (JupyterFramework method) boot_gui() (JupyterFramework method) byte_order (ImageIO attribute) C calculate_and_plot_distances_proteins() (JupyterFramework method) calculate_and_plot_sphere_radii() (JupyterFramework method) calculate_normals() (ColabSegData method) changed (ColabSegNapariWidget attribute) checkFile() (ImageIO method) clear() (ColabSegNapariWidget method) close() (ColabSegNapariWidget method) (NapariManager method) cluster_checkbox() (seg_visualization method) colabseg.utilities module ColabSegData (class in colabseg) ColabSegNapariWidget (class in colabseg.napari_integration) compile_xyz_string() (ColabSegData method) compute_normal() (Ellipsoid method) (Sphere method) convert_tomo() (ColabSegData method) count() (ColabSegNapariWidget method) create_sphere_points() (in module colabseg.utilities) crop_fit() (JupyterFramework method) crop_fit_around_membrane() (ColabSegData method) Cylinder (class in colabseg.parametrization) D dbscan_clustering() (ColabSegData method) dbscan_recluster() (JupyterFramework method) delete_cluster() (ColabSegData method) (JupyterFramework method) delete_fit() (ColabSegData method) (JupyterFramework method) delete_model() (seg_visualization method) delete_multiple_clusters() (ColabSegData method) delete_multiple_fits() (ColabSegData method) delete_normals() (ColabSegData method) (JupyterFramework method) delete_protein_position() (ColabSegData method) E eigenvalue_outlier_removal() (ColabSegData method) Ellipsoid (class in colabseg.parametrization) em (ImageIO attribute) emByteOrderTab (ImageIO attribute) emByteOrderTabInv (ImageIO attribute) emDataTypeTab (ImageIO attribute) emDataTypeTabInv (ImageIO attribute) emDefaultHeader (ImageIO attribute) emDefaultShape (ImageIO attribute) emHeaderFields (ImageIO attribute) enabled (ColabSegNapariWidget property) execute_delete_protein_positions() (JupyterFramework method) execute_load_protein_position() (JupyterFramework method) export_data() (ColabSegNapariWidget method) (NapariManager method) extend() (ColabSegNapariWidget method) extract_slice() (ColabSegData method) F fileFormats (ImageIO attribute) fit() (Cylinder class method) (Ellipsoid class method) (Parametrization method) (Sphere class method) fit_cylinder() (JupyterFramework method) fit_ellipsoid() (JupyterFramework method) fit_idx_conv() (JupyterFramework method) fit_parametrization() (JupyterFramework method) fit_rbf() (JupyterFramework method) fit_sphere() (JupyterFramework method) fix() (ImageIO method) fixHeader() (ImageIO method) flip_normals() (ColabSegData method) (JupyterFramework method) from_callable() (ColabSegNapariWidget class method) from_signature() (ColabSegNapariWidget class method) G generate_tensor_voting_gui (class in colabseg.tensorvoting_wrapper) get_and_plot_normals() (JupyterFramework method) get_fit_normals() (JupyterFramework method) get_lamina_rotation_matrix() (ColabSegData method) get_selected_sphere_radii() (ColabSegData method) getFromEMHeader() (ImageIO method) getPixelsize() (ImageIO method) getTiltAngle() (ImageIO method) gui_elements_cluster_analysis() (JupyterFramework method) gui_elements_loading() (JupyterFramework method) H height (ColabSegNapariWidget property) hide() (ColabSegNapariWidget method) highlight_cluster() (seg_visualization method) highlight_clusters() (JupyterFramework method) (seg_visualization method) highlight_clusters_size() (JupyterFramework method) highlight_fits() (JupyterFramework method) (seg_visualization method) I ImageIO (class in colabseg) index() (ColabSegNapariWidget method) insert() (ColabSegNapariWidget method) interpolate_membrane_closed_surface() (ColabSegData method) interpolate_membrane_rbf() (ColabSegData method) J JupyterFramework (class in colabseg.segmentation_gui) L label (ColabSegNapariWidget property) label_changed (ColabSegNapariWidget attribute) labels (ColabSegNapariWidget property) layout (ColabSegNapariWidget property) load_all_models() (seg_visualization method) load_all_models_fit() (seg_visualization method) load_all_models_from_file() (seg_visualization method) load_data() (ColabSegNapariWidget method) load_from_point_cloud() (JupyterFramework method) load_from_stl_file() (JupyterFramework method) load_hdf() (ColabSegData method) load_model_from_file() (seg_visualization method) load_mrc_file() (JupyterFramework method) load_normal_positions() (seg_visualization method) load_pickle() (ColabSegData class method) (JupyterFramework method) load_point_cloud() (ColabSegData method) load_protein_position() (ColabSegData method) load_protein_positions() (seg_visualization method) load_raw_image() (JupyterFramework method) load_state_hdf() (JupyterFramework method) load_stl_file() (ColabSegData method) load_tomogram() (ColabSegData method) load_viz() (JupyterFramework method) lstsq_sphere_fitting() (in module colabseg.utilities) M machineByteOrder (ImageIO attribute) make_plot_array() (in module colabseg.utilities) make_xyz_string() (seg_visualization static method) make_xyz_string_protein() (seg_visualization static method) margins (ColabSegNapariWidget property) max_height (ColabSegNapariWidget property) max_width (ColabSegNapariWidget property) merge_clusters() (ColabSegData method) (JupyterFramework method) min_height (ColabSegNapariWidget property) min_width (ColabSegNapariWidget property) module |project| colabseg.utilities mrc (ImageIO attribute) mrcDataTypeTab (ImageIO attribute) mrcDataTypeTabInv (ImageIO attribute) mrcDefaultHeader (ImageIO attribute) mrcDefaultPixel (ImageIO attribute) mrcDefaultShape (ImageIO attribute) N NapariManager (class in colabseg.napari_integration) native (ColabSegNapariWidget property) native_parent_changed (ColabSegNapariWidget attribute) NO_VALUE (ColabSegNapariWidget attribute) O options (ColabSegNapariWidget property) orientation (ColabSegNapariWidget property) outlier_removal() (JupyterFramework method) P param_kind (ColabSegNapariWidget property) Parametrization (class in colabseg.parametrization) parent (ColabSegNapariWidget property) parent_changed (ColabSegNapariWidget property) parseMRCHeader() (ImageIO method) pixelsize (ImageIO property) plain_fit_and_rotate_lamina() (ColabSegData method) plane_fit() (in module colabseg.utilities) plot_cluster_size() (JupyterFramework method) points_per_sampling() (Cylinder method) (Ellipsoid method) (Sphere method) pop() (ColabSegNapariWidget method) putInEMHeader() (ImageIO method) R R_2vect() (in module colabseg.utilities) raw (ImageIO attribute) read() (ImageIO method) read_mrc() (ColabSegData method) readData() (ImageIO method) readEM() (ImageIO method) readEMHeader() (ImageIO method) readHeader() (ImageIO method) readMRC() (ImageIO method) readMRCHeader() (ImageIO method) readRaw() (ImageIO method) readRawHeader() (ImageIO method) reload_gui() (JupyterFramework method) reload_original_values() (ColabSegData method) reload_previous_step() (ColabSegData method) remove() (ColabSegNapariWidget method) remove_eigenvalue_outliers() (JupyterFramework method) removeAll() (seg_visualization method) render() (ColabSegNapariWidget method) reset_choices() (ColabSegNapariWidget method) reset_input() (JupyterFramework method) reset_optimal_default_values() (generate_tensor_voting_gui method) reverse() (ColabSegNapariWidget method) root_native_widget (ColabSegNapariWidget property) rotate_back() (JupyterFramework method) rotate_flat() (JupyterFramework method) run() (NapariManager method) run_tv_code() (generate_tensor_voting_gui method) S sample() (Cylinder method) (Ellipsoid method) (Parametrization method) (Sphere method) sample_fit() (JupyterFramework method) save_clusters_mrc() (JupyterFramework method) save_clusters_txt() (JupyterFramework method) save_distance_file() (JupyterFramework method) save_distance_plot() (JupyterFramework method) save_downcloud_txt() (JupyterFramework method) save_hdf() (ColabSegData method) save_normals_file() (JupyterFramework method) save_pickle() (ColabSegData method) (JupyterFramework method) save_radii_file() (JupyterFramework method) save_radii_plot() (JupyterFramework method) save_state_hdf() (JupyterFramework method) save_values_txt() (ColabSegData static method) seg_visualization (class in colabseg.py3dmol_controls) setData() (ImageIO method) setFileFormat() (ImageIO method) setTiltAngle() (ImageIO method) show() (ColabSegNapariWidget method) shown() (ColabSegNapariWidget method) Sphere (class in colabseg.parametrization) split_clusters() (ColabSegData method) (JupyterFramework method) statistical_outlier_removal() (ColabSegData method) T tiltAngle (ImageIO property) tooltip (ColabSegNapariWidget property) trim_cluster_egdes_cluster() (ColabSegData method) trim_cluster_egdes_fit() (ColabSegData method) trim_top_bottom() (JupyterFramework method) U undo_step() (JupyterFramework method) update() (ColabSegNapariWidget method) update_downsampling() (JupyterFramework method) update_highlight_clusters() (seg_visualization method) update_highlight_fits() (seg_visualization method) V view_update() (seg_visualization method) view_zoomto() (seg_visualization method) visible (ColabSegNapariWidget property) W widget_type (ColabSegNapariWidget property) width (ColabSegNapariWidget property) write() (ImageIO method) write_output_mrc() (ColabSegData method) write_txt() (ColabSegData static method) write_xyz() (ColabSegData static method) writeData() (ImageIO method) writeEM() (ImageIO method) writeMRC() (ImageIO method) writeRaw() (ImageIO method)