Index A | B | C | D | E | F | G | H | I | L | M | N | P | R | S | T | U | W A all_trunks() (in module tmd.view.view) all_trunks3d() (in module tmd.view.view) apical (tmd.Neuron.Neuron.Neuron property) (tmd.Population.Population.Population property) apical_dendrite (tmd.Population.Population.Population property) append_neuron() (tmd.Population.Population.Population method) append_tree() (tmd.Neuron.Neuron.Neuron method) axon (tmd.Population.Population.Population property) B barcode() (in module tmd.view.plot) barcode_bin_centers() (in module tmd.Topology.analysis) barcode_enhanced() (in module tmd.view.plot) basal (tmd.Neuron.Neuron.Neuron property) (tmd.Population.Population.Population property) basal_dendrite (tmd.Population.Population.Population property) C closest_ph() (in module tmd.Topology.analysis) collapse() (in module tmd.Topology.analysis) convert_morphio_soma() (in module tmd.io.conversion) convert_morphio_trees() (in module tmd.io.conversion) copy_neuron() (tmd.Neuron.Neuron.Neuron method) copy_soma() (tmd.Soma.Soma.Soma method) copy_tree() (tmd.Tree.Tree.Tree method) D dendrites (tmd.Neuron.Neuron.Neuron property) (tmd.Population.Population.Population property) density_cloud() (in module tmd.view.view) diagram() (in module tmd.view.plot) diagram_enhanced() (in module tmd.view.plot) diameters (tmd.io.conversion.SectionData attribute) distance_horizontal() (in module tmd.Topology.analysis) distance_horizontal_unnormed() (in module tmd.Topology.analysis) distance_stepped() (in module tmd.Topology.analysis) E extract_connectivity_from_points() (in module tmd.Topology.methods) extract_ph() (in module tmd.Topology.methods) extract_ph_neuron() (in module tmd.Topology.methods) extract_simplified() (tmd.Tree.Tree.Tree method) F figure_naming() (in module tmd.view.common) find_apical_point_distance() (in module tmd.Topology.analysis) find_apical_point_distance_smoothed() (in module tmd.Topology.analysis) G get() (tmd.Topology.persistent_properties.NoProperty method) (tmd.Topology.persistent_properties.PersistentAngles method) (tmd.Topology.persistent_properties.PersistentMeanRadius method) (tmd.Topology.persistent_properties.PersistentProperty method) get_average_persistence_image() (in module tmd.Topology.analysis) get_bif_term() (tmd.Tree.Tree.Tree method) get_bifurcations() (in module tmd.Topology.statistics) (tmd.Tree.Tree.Tree method) get_bounding_box() (tmd.Neuron.Neuron.Neuron method) (tmd.Tree.Tree.Tree method) get_by_name() (tmd.Population.Population.Population method) get_center() (tmd.Soma.Soma.Soma method) get_color() (in module tmd.view.common) get_diameter() (tmd.Soma.Soma.Soma method) get_direction_between() (tmd.Tree.Tree.Tree method) get_figure() (in module tmd.view.common) get_image_add_data() (in module tmd.Topology.analysis) get_lengths() (in module tmd.Topology.statistics) get_lifetime() (in module tmd.Topology.methods) get_multifurcations() (tmd.Tree.Tree.Tree method) get_pca() (tmd.Tree.Tree.Tree method) get_persistence_diagram() (in module tmd.Topology.methods) get_ph_angles() (in module tmd.Topology.methods) get_ph_neuron() (in module tmd.Topology.methods) get_ph_radii() (in module tmd.Topology.methods) get_point_path_distances() (tmd.Tree.Tree.Tree method) get_point_projection() (tmd.Tree.Tree.Tree method) get_point_radial_distances() (tmd.Tree.Tree.Tree method) get_point_radial_distances_time() (tmd.Tree.Tree.Tree method) get_point_section_branch_orders() (tmd.Tree.Tree.Tree method) get_point_section_lengths() (tmd.Tree.Tree.Tree method) get_point_weighted_radial_distances() (tmd.Tree.Tree.Tree method) get_sections_2() (tmd.Tree.Tree.Tree method) get_sections_only_points() (tmd.Tree.Tree.Tree method) get_segments() (tmd.Tree.Tree.Tree method) get_terminations() (in module tmd.Topology.statistics) (tmd.Tree.Tree.Tree method) get_total_length() (in module tmd.Topology.statistics) get_trunk_length() (tmd.Tree.Tree.Tree method) get_type() (tmd.Tree.Tree.Tree method) H h5_data_to_lists() (in module tmd.io.h5) histogram_horizontal() (in module tmd.Topology.analysis) (in module tmd.view.plot) histogram_stepped() (in module tmd.Topology.analysis) (in module tmd.view.plot) histogram_stepped_population() (in module tmd.view.plot) I infinite_component() (tmd.Topology.persistent_properties.NoProperty method) (tmd.Topology.persistent_properties.PersistentAngles method) (tmd.Topology.persistent_properties.PersistentMeanRadius method) (tmd.Topology.persistent_properties.PersistentProperty method) is_equal() (tmd.Neuron.Neuron.Neuron method) (tmd.Soma.Soma.Soma method) (tmd.Tree.Tree.Tree method) is_same() (tmd.Neuron.Neuron.Neuron method) L load_file() (in module tmd.Topology.analysis) load_neuron() (in module tmd.io.io) load_neuron_from_morphio() (in module tmd.io.io) load_population() (in module tmd.io.io) LoadNeuronError M make_tree() (in module tmd.io.io) matching_munkress_modified() (in module tmd.Topology.analysis) module tmd tmd.io.conversion tmd.io.h5 tmd.io.io tmd.io.swc tmd.Neuron.Neuron tmd.Population.Population tmd.Soma.Soma tmd.Topology.analysis tmd.Topology.methods tmd.Topology.persistent_properties tmd.Topology.statistics tmd.Topology.transformations tmd.Tree.Tree tmd.view.common tmd.view.plot tmd.view.view move_to_point() (tmd.Tree.Tree.Tree method) N neurites (tmd.Neuron.Neuron.Neuron property) (tmd.Population.Population.Population property) Neuron (class in tmd.Neuron.Neuron) neuron() (in module tmd.view.view) neuron3d() (in module tmd.view.view) NoProperty (class in tmd.Topology.persistent_properties) nosify() (in module tmd.Topology.statistics) P parents (tmd.io.conversion.SectionData attribute) parents_children (tmd.Tree.Tree.Tree attribute) persistence_image() (in module tmd.view.plot) persistence_image_add() (in module tmd.view.plot) persistence_image_average() (in module tmd.view.plot) persistence_image_diff() (in module tmd.view.plot) PersistentAngles (class in tmd.Topology.persistent_properties) PersistentMeanRadius (class in tmd.Topology.persistent_properties) PersistentProperty (class in tmd.Topology.persistent_properties) plot_img_basic() (in module tmd.view.common) plot_labels() (in module tmd.view.common) plot_legend() (in module tmd.view.common) plot_limits() (in module tmd.view.common) plot_sphere() (in module tmd.view.common) plot_style() (in module tmd.view.common) plot_ticks() (in module tmd.view.common) plot_title() (in module tmd.view.common) points (tmd.io.conversion.SectionData attribute) polar_plot() (in module tmd.view.view) Population (class in tmd.Population.Population) population() (in module tmd.view.view) population3d() (in module tmd.view.view) R read_h5() (in module tmd.io.h5) read_swc() (in module tmd.io.swc) redefine_types() (in module tmd.io.io) remove_duplicate_points() (in module tmd.io.h5) rename() (tmd.Neuron.Neuron.Neuron method) rotate_xy() (tmd.Tree.Tree.Tree method) S save_plot() (in module tmd.view.common) section_type (tmd.io.conversion.SectionData attribute) SectionData (class in tmd.io.conversion) sections (tmd.Tree.Tree.Tree attribute) set_soma() (tmd.Neuron.Neuron.Neuron method) simplify() (tmd.Neuron.Neuron.Neuron method) size() (tmd.Neuron.Neuron.Neuron method) Soma (class in tmd.Soma.Soma) soma() (in module tmd.view.view) soma3d() (in module tmd.view.view) sort_ph() (in module tmd.Topology.analysis) start_length_diagram() (in module tmd.view.plot) swc_data_to_lists() (in module tmd.io.swc) swc_to_data() (in module tmd.io.swc) T tmd module tmd.io.conversion module tmd.io.h5 module tmd.io.io module tmd.io.swc module tmd.Neuron.Neuron module tmd.Population.Population module tmd.Soma.Soma module tmd.Topology.analysis module tmd.Topology.methods module tmd.Topology.persistent_properties module tmd.Topology.statistics module tmd.Topology.transformations module tmd.Tree.Tree module tmd.view.common module tmd.view.plot module tmd.view.view module tmd_scale() (in module tmd.Topology.transformations) transform_ph_from_length() (in module tmd.Topology.statistics) transform_ph_to_length() (in module tmd.Topology.statistics) Tree (class in tmd.Tree.Tree) tree() (in module tmd.view.view) tree3d() (in module tmd.view.view) tree_barcode_colors() (in module tmd.view.view) tree_full_persistence_colors() (in module tmd.view.view) tree_to_property_barcode() (in module tmd.Topology.methods) trunk() (in module tmd.view.view) trunk3d() (in module tmd.view.view) U undefined (tmd.Population.Population.Population property) W write_ph() (in module tmd.Topology.methods)
