Index

_

__init__() (neurom.core.neuron.BaseSoma method) (neurom.core.neuron.Neuron method) (neurom.core.neuron.SomaSimpleContour method) (neurom.core.neuron.SomaSinglePoint method) (neurom.core.neuron.SomaThreePoint method) (neurom.core.tree.Tree method) (neurom.ezy.Neuron method) (neurom.ezy.Population method) (neurom.ezy.neuron.Neuron method) (neurom.ezy.population.Population method) (neurom.io.swc.SWCRawDataWrapper method)

A

add_child() (neurom.core.tree.Tree method) all (neurom.core.types.NeuriteType attribute) angle_3points() (in module neurom.analysis.morphmath) APICAL_DENDRITE (neurom.core.dataformat.POINT_TYPE attribute) apical_dendrite (neurom.core.types.NeuriteType attribute)

as_elements() (in module neurom.core.tree) as_point() (in module neurom.core.point) average_points_dist() (in module neurom.analysis.morphmath) AXON (neurom.core.dataformat.POINT_TYPE attribute) axon (neurom.core.types.NeuriteType attribute)

B

BASAL_DENDRITE (neurom.core.dataformat.POINT_TYPE attribute) basal_dendrite (neurom.core.types.NeuriteType attribute) BaseSoma (class in neurom.core.neuron)

bounding_box() (neurom.core.neuron.Neuron method) (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) branch_order() (in module neurom.analysis.morphtree)

C

center (neurom.core.neuron.BaseSoma attribute) (neurom.core.neuron.SomaSimpleContour attribute) (neurom.core.neuron.SomaSinglePoint attribute) (neurom.core.neuron.SomaThreePoint attribute) COLS (class in neurom.core.dataformat) compare_trees() (in module neurom.analysis.morphtree) compare_two() (in module neurom.stats)

copy() (neurom.core.neuron.Neuron method) (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) count() (neurom.core.point.Point method) (neurom.stats.FitResults method) CUSTOM (neurom.core.dataformat.POINT_TYPE attribute)

D

dendrogram() (in module neurom.view.view)

dist_point_line() (in module neurom.analysis.morphmath)

E

END_POINT (neurom.core.dataformat.POINT_TYPE attribute)

errs (neurom.stats.FitResults attribute)

F

figure_naming() (in module neurom.view.common) find_tree_type() (in module neurom.analysis.morphtree) fit() (in module neurom.stats)

fit_results_to_dict() (in module neurom.stats) FitResults (class in neurom.stats) FORK_POINT (neurom.core.dataformat.POINT_TYPE attribute)

G

get_bounding_box() (in module neurom.analysis.morphtree) get_children() (neurom.io.swc.SWCRawDataWrapper method) get_col() (neurom.io.swc.SWCRawDataWrapper method) get_color() (in module neurom.view.common) get_default() (in module neurom.view.view) get_end_points() (neurom.io.swc.SWCRawDataWrapper method) get_figure() (in module neurom.view.common) get_fork_points() (neurom.io.swc.SWCRawDataWrapper method) get_ids() (neurom.io.swc.SWCRawDataWrapper method) get_initial_neurite_segment_ids() (in module neurom.io.utils) get_local_bifurcation_angles() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_morph_files() (in module neurom.io.utils) get_n_neurites() (neurom.ezy.Neuron method) (neurom.ezy.Population method) (neurom.ezy.neuron.Neuron method) (neurom.ezy.population.Population method) get_n_sections() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_n_sections_per_neurite() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_parent() (neurom.io.swc.SWCRawDataWrapper method) get_point() (neurom.io.swc.SWCRawDataWrapper method) get_remote_bifurcation_angles() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method)

get_row() (neurom.io.swc.SWCRawDataWrapper method) get_section_lengths() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_section_path_distances() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_section_radial_distances() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_segment_lengths() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_soma_ids() (in module neurom.io.utils) get_soma_radius() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_soma_rows() (neurom.io.swc.SWCRawDataWrapper method) get_soma_surface_area() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_test() (in module neurom.stats) get_tree_type() (in module neurom.analysis.morphtree) get_trunk_origin_radii() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_trunk_section_lengths() (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) get_type() (neurom.core.neuron.SOMA_TYPE static method) get_version() (in module neurom.io.hdf5) GPFIRST (neurom.io.hdf5.H5 attribute) GPID (neurom.io.hdf5.H5 attribute) GTYPE (neurom.io.hdf5.H5 attribute)

H

H5 (class in neurom.io.hdf5) has_all_finite_length_segments() (in module neurom.io.check) has_all_finite_radius_neurites() (in module neurom.io.check)

has_increasing_ids() (in module neurom.io.check) has_sequential_ids() (in module neurom.io.check) has_soma_points() (in module neurom.io.check)

I

i_branch_end_points() (in module neurom.core.tree) i_chain() (in module neurom.core.tree) i_chain2() (in module neurom.core.tree) i_neurites() (neurom.core.neuron.Neuron method) (neurom.ezy.Neuron method) (neurom.ezy.neuron.Neuron method) i_section_radial_dist() (in module neurom.analysis.morphtree) ibifurcation_point() (in module neurom.core.tree) ID (neurom.core.dataformat.COLS attribute) (neurom.io.swc.SWC attribute) IDSequenceError iforking_point() (in module neurom.core.tree) ileaf() (in module neurom.core.tree) imap_val() (in module neurom.core.tree) index() (neurom.core.point.Point method) (neurom.stats.FitResults method) interpolate_radius() (in module neurom.analysis.morphmath) INVALID (neurom.core.neuron.SOMA_TYPE attribute) ipostorder() (in module neurom.core.tree) ipreorder() (in module neurom.core.tree)

is_bifurcation_point() (in module neurom.core.tree) is_forking_point() (in module neurom.core.tree) is_leaf() (in module neurom.core.tree) is_neurite_segment() (in module neurom.io.check) is_root() (in module neurom.core.tree) is_single_tree() (in module neurom.io.check) isection() (in module neurom.core.tree) isegment() (in module neurom.core.tree) iter() (neurom.core.neuron.BaseSoma method) (neurom.core.neuron.SomaSimpleContour method) (neurom.core.neuron.SomaSinglePoint method) (neurom.core.neuron.SomaThreePoint method) iter_neurites() (in module neurom.core) (neurom.ezy.Population method) (neurom.ezy.population.Population method) iter_neurons() (neurom.ezy.Population method) (neurom.ezy.population.Population method) iter_row() (neurom.io.swc.SWCRawDataWrapper method) iter_somata() (neurom.ezy.Population method) (neurom.ezy.population.Population method) itriplet() (in module neurom.core.tree) iupstream() (in module neurom.core.tree)

K

ks (neurom.stats.StatTests attribute)

L

linear_interpolate() (in module neurom.analysis.morphmath) load_data() (in module neurom.io) (in module neurom.io.readers) load_neuron() (in module neurom.ezy) (in module neurom.io.utils) load_neurons() (in module neurom.io.utils)

load_population() (in module neurom.io.utils) load_trees() (in module neurom.io.utils) local_bifurcation_angle() (in module neurom.analysis.morphtree)

M

make_copy() (in module neurom.core.tree) make_neuron() (in module neurom.io.utils) make_soma() (in module neurom.core.neuron)

make_tree() (in module neurom.io.utils) MissingParentError MultipleTrees

N

n_bifurcations() (in module neurom.analysis.morphtree) n_sections() (in module neurom.analysis.morphtree) n_segments() (in module neurom.analysis.morphtree) n_terminations() (in module neurom.analysis.morphtree) NEURITES (neurom.core.dataformat.POINT_TYPE attribute) NeuriteType (class in neurom.core.types) neurom.analysis (module) neurom.analysis.morphmath (module) neurom.analysis.morphtree (module) neurom.core (module) neurom.core.dataformat (module) neurom.core.neuron (module) neurom.core.point (module) neurom.core.tree (module) neurom.core.types (module) neurom.exceptions (module) neurom.ezy (module)

neurom.ezy.neuron (module) neurom.ezy.population (module) neurom.io (module) neurom.io.check (module) neurom.io.hdf5 (module) neurom.io.readers (module) neurom.io.swc (module) neurom.io.utils (module) neurom.stats (module) neurom.view (module) neurom.view.common (module) neurom.view.view (module) NeuroMError Neuron (class in neurom.core.neuron) (class in neurom.ezy) (class in neurom.ezy.neuron) neuron() (in module neurom.view.view) neuron3d() (in module neurom.view.view) no_missing_parents() (in module neurom.io.check)

O

optimal_distribution() (in module neurom.stats)

P

P (neurom.core.dataformat.COLS attribute) (neurom.io.swc.SWC attribute) params (neurom.stats.FitResults attribute) partition() (in module neurom.analysis.morphtree) path_distance() (in module neurom.analysis.morphmath) path_fraction_point() (in module neurom.analysis.morphmath) path_length() (in module neurom.analysis.morphtree) pca() (in module neurom.analysis.morphmath) PD (neurom.io.hdf5.H5 attribute) plot_labels() (in module neurom.view.common) plot_legend() (in module neurom.view.common) plot_limits() (in module neurom.view.common) plot_sphere() (in module neurom.view.common) plot_style() (in module neurom.view.common)

plot_ticks() (in module neurom.view.common) plot_title() (in module neurom.view.common) Point (class in neurom.core.point) point_dist() (in module neurom.analysis.morphmath) point_dist2() (in module neurom.analysis.morphmath) POINT_TYPE (class in neurom.core.dataformat) polygon_diameter() (in module neurom.analysis.morphmath) Population (class in neurom.ezy) (class in neurom.ezy.population) principal_direction_extent() (in module neurom.analysis.morphmath) (in module neurom.analysis.morphtree) PX (neurom.io.hdf5.H5 attribute) PY (neurom.io.hdf5.H5 attribute) PZ (neurom.io.hdf5.H5 attribute)

R

R (neurom.core.dataformat.COLS attribute) r (neurom.core.point.Point attribute) R (neurom.io.swc.SWC attribute)

read() (neurom.io.hdf5.H5 static method) (neurom.io.swc.SWC static method) remove_duplicate_points() (neurom.io.hdf5.H5 static method)

S

save_plot() (in module neurom.view.common) scalar_projection() (in module neurom.analysis.morphmath) scalar_stats() (in module neurom.stats) section_length() (in module neurom.analysis.morphmath) segment_area() (in module neurom.analysis.morphmath) segment_length() (in module neurom.analysis.morphmath) segment_length2() (in module neurom.analysis.morphmath) segment_radial_dist() (in module neurom.analysis.morphmath) segment_radius() (in module neurom.analysis.morphmath) segment_taper_rate() (in module neurom.analysis.morphmath) segment_volume() (in module neurom.analysis.morphmath) segment_x_coordinate() (in module neurom.analysis.morphmath) segment_y_coordinate() (in module neurom.analysis.morphmath) segment_z_coordinate() (in module neurom.analysis.morphmath) set_tree_type() (in module neurom.analysis.morphtree)

SimpleContour (neurom.core.neuron.SOMA_TYPE attribute) SinglePoint (neurom.core.neuron.SOMA_TYPE attribute) SOMA (neurom.core.dataformat.POINT_TYPE attribute) soma (neurom.core.types.NeuriteType attribute) soma() (in module neurom.view.view) soma3d() (in module neurom.view.view) SOMA_TYPE (class in neurom.core.neuron) SomaError SomaSimpleContour (class in neurom.core.neuron) SomaSinglePoint (class in neurom.core.neuron) SomaThreePoint (class in neurom.core.neuron) sphere_area() (in module neurom.analysis.morphmath) StatTests (class in neurom.stats) SWC (class in neurom.io.swc) SWCRawDataWrapper (class in neurom.io.swc)

T

t (neurom.core.point.Point attribute) taper_rate() (in module neurom.analysis.morphmath) ThreePoint (neurom.core.neuron.SOMA_TYPE attribute) total_score() (in module neurom.stats) Tree (class in neurom.core.tree) tree() (in module neurom.view.view) tree3d() (in module neurom.view.view) tree_type_checker() (in module neurom.core.types)

trunk_origin_azimuth() (in module neurom.analysis.morphtree) trunk_origin_direction() (in module neurom.analysis.morphtree) trunk_origin_elevation() (in module neurom.analysis.morphtree) trunk_origin_radius() (in module neurom.analysis.morphtree) trunk_section_length() (in module neurom.analysis.morphtree) ttest (neurom.stats.StatTests attribute) TYPE (neurom.core.dataformat.COLS attribute) (neurom.io.swc.SWC attribute) type (neurom.stats.FitResults attribute)

U

UNDEFINED (neurom.core.dataformat.POINT_TYPE attribute) undefined (neurom.core.types.NeuriteType attribute)

unpack_data() (neurom.io.hdf5.H5 static method)

V

val_iter() (in module neurom.core.tree) vector() (in module neurom.analysis.morphmath)

vector_projection() (in module neurom.analysis.morphmath)

W

wilcoxon (neurom.stats.StatTests attribute)

X

X (neurom.core.dataformat.COLS attribute) x (neurom.core.point.Point attribute)

X (neurom.io.swc.SWC attribute)

Y

Y (neurom.core.dataformat.COLS attribute) y (neurom.core.point.Point attribute)

Y (neurom.io.swc.SWC attribute)

Z

Z (neurom.core.dataformat.COLS attribute) z (neurom.core.point.Point attribute)

Z (neurom.io.swc.SWC attribute)