Index

_

__init__() (neurom.check.CheckResult method) (neurom.core.Neurite method) (neurom.core.Neuron method) (neurom.core.Population method) (neurom.core.Section method) (neurom.core.Soma method) (neurom.core.Tree method) (neurom.core._neuron.Neurite method) (neurom.core._neuron.Neuron method) (neurom.core._neuron.Section method) (neurom.core._soma.Soma method) (neurom.core._soma.SomaSimpleContour method) (neurom.core._soma.SomaSinglePoint method) (neurom.core._soma.SomaThreePoint method) (neurom.core.tree.Tree method) (neurom.fst.FstNeuron method)

A

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

area (neurom.core._neuron.Neurite attribute) (neurom.core.Neurite attribute) (neurom.core.Section attribute) (neurom.core._neuron.Section attribute) as_point() (in module neurom.core.point) average_points_dist() (in module neurom.morphmath) AXON (neurom.core.dataformat.POINT_TYPE attribute) axon (neurom.core.NeuriteType attribute) (neurom.NeuriteType attribute) (neurom.core.types.NeuriteType attribute)

B

BASAL_DENDRITE (neurom.core.dataformat.POINT_TYPE attribute) basal_dendrite (neurom.core.NeuriteType attribute) (neurom.NeuriteType attribute) (neurom.core.types.NeuriteType attribute)

branch_order() (in module neurom.fst.sectionfunc)

C

center (neurom.core._soma.Soma attribute) (neurom.core.Soma attribute) (neurom.core._soma.SomaSimpleContour attribute) (neurom.core._soma.SomaSinglePoint attribute) (neurom.core._soma.SomaThreePoint attribute) check_wrapper() (in module neurom.check) CheckResult (class in neurom.check) COLS (class in neurom.core.dataformat)

compare_two() (in module neurom.stats) count() (neurom.core.point.Point method) (neurom.io.hdf5.Section 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.morphmath)

draw() (in module neurom.viewer)

E

END_POINT (neurom.core.dataformat.POINT_TYPE attribute)

errs (neurom.stats.FitResults attribute)

F

figure_naming() (in module neurom.view.common) 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) FstNeuron (class in neurom.fst)

G

get() (in module neurom) (in module neurom.fst) get_color() (in module neurom.view.common) get_default() (in module neurom.view.view) get_figure() (in module neurom.view.common)

get_morph_files() (in module neurom.io.utils) get_test() (in module neurom.stats) get_type() (neurom.core._soma.SOMA_TYPE static method) get_version() (in module neurom.io.hdf5)

H

has_all_finite_radius_neurites() (in module neurom.check.structural_checks) has_all_monotonic_neurites() (in module neurom.check.neuron_checks) has_all_nonzero_neurite_radii() (in module neurom.check.neuron_checks) has_all_nonzero_section_lengths() (in module neurom.check.neuron_checks) has_all_nonzero_segment_lengths() (in module neurom.check.neuron_checks) has_apical_dendrite() (in module neurom.check.neuron_checks) has_axon() (in module neurom.check.neuron_checks) has_basal_dendrite() (in module neurom.check.neuron_checks) has_increasing_ids() (in module neurom.check.structural_checks)

has_no_fat_ends() (in module neurom.check.neuron_checks) has_no_flat_neurites() (in module neurom.check.neuron_checks) has_no_jumps() (in module neurom.check.neuron_checks) has_nonzero_soma_radius() (in module neurom.check.neuron_checks) has_sequential_ids() (in module neurom.check.structural_checks) has_soma_points() (in module neurom.check.structural_checks) has_valid_neurites() (in module neurom.check.structural_checks) has_valid_soma() (in module neurom.check.structural_checks)

I

i_chain2() (in module neurom.core.tree) ibifurcation_point() (neurom.core._neuron.Section method) (neurom.core.Section method) (neurom.core.Tree method) (neurom.core.tree.Tree method) ID (neurom.core.dataformat.COLS attribute) ids (neurom.io.hdf5.Section attribute) IDSequenceError iforking_point() (neurom.core._neuron.Section method) (neurom.core.Section method) (neurom.core.Tree method) (neurom.core.tree.Tree method) ileaf() (neurom.core._neuron.Section method) (neurom.core.Section method) (neurom.core.Tree method) (neurom.core.tree.Tree method) index() (neurom.core.point.Point method) (neurom.io.hdf5.Section method) (neurom.stats.FitResults method) interpolate_radius() (in module neurom.morphmath) INVALID (neurom.core._soma.SOMA_TYPE attribute) InvalidDrawModeError ipostorder() (neurom.core._neuron.Section method) (neurom.core.Section method) (neurom.core.Tree method) (neurom.core.tree.Tree method)

ipreorder() (neurom.core._neuron.Section method) (neurom.core.Section method) (neurom.core.Tree method) (neurom.core.tree.Tree method) is_bifurcation_point() (neurom.core._neuron.Section method) (neurom.core.Section method) (neurom.core.Tree method) (neurom.core.tree.Tree method) is_forking_point() (neurom.core._neuron.Section method) (neurom.core.Section method) (neurom.core.Tree method) (neurom.core.tree.Tree method) is_leaf() (neurom.core._neuron.Section method) (neurom.core.Section method) (neurom.core.Tree method) (neurom.core.tree.Tree method) is_root() (neurom.core._neuron.Section method) (neurom.core.Section method) (neurom.core.Tree method) (neurom.core.tree.Tree method) is_single_tree() (in module neurom.check.structural_checks) iter() (neurom.core._soma.Soma method) (neurom.core.Soma method) (neurom.core._soma.SomaSimpleContour method) (neurom.core._soma.SomaSinglePoint method) (neurom.core._soma.SomaThreePoint method) iter_neurites() (in module neurom) (in module neurom.core) iter_sections() (in module neurom) (in module neurom.core) (neurom.core.Neurite method) (neurom.core._neuron.Neurite method) iter_segments() (in module neurom.fst) iupstream() (neurom.core._neuron.Section method) (neurom.core.Section method) (neurom.core.Tree method) (neurom.core.tree.Tree method)

K

ks (neurom.stats.StatTests attribute)

L

length (neurom.core._neuron.Neurite attribute) (neurom.core.Neurite attribute) (neurom.core.Section attribute) (neurom.core._neuron.Section attribute) linear_interpolate() (in module neurom.morphmath) load_data() (in module neurom.io) (in module neurom.io.utils)

load_neuron() (in module neurom) (in module neurom.io) (in module neurom.io.utils) load_neurons() (in module neurom) (in module neurom.io) (in module neurom.io.utils)

M

make_soma() (in module neurom.core) (in module neurom.core._soma) map_segments() (in module neurom.fst.sectionfunc)

MissingParentError MultipleTrees

N

Neurite (class in neurom.core) (class in neurom.core._neuron) NEURITES (neurom.core.dataformat.POINT_TYPE attribute) NeuriteType (class in neurom) (class in neurom.core) (class in neurom.core.types) neurom (module) neurom.check (module) neurom.check.neuron_checks (module) neurom.check.structural_checks (module) neurom.core (module) neurom.core._neuron (module) neurom.core._soma (module) neurom.core.dataformat (module) neurom.core.point (module) neurom.core.tree (module) neurom.core.types (module) neurom.exceptions (module) neurom.fst (module) neurom.fst.sectionfunc (module)

neurom.io (module) neurom.io.hdf5 (module) neurom.io.swc (module) neurom.io.utils (module) neurom.morphmath (module) neurom.stats (module) neurom.view (module) neurom.view.common (module) neurom.view.view (module) neurom.viewer (module) NeuroMError Neuron (class in neurom.core) (class in neurom.core._neuron) neuron() (in module neurom.view.view) neuron3d() (in module neurom.view.view) no_missing_parents() (in module neurom.check.structural_checks) NotDrawableError ntype (neurom.io.hdf5.Section attribute)

O

ok() (in module neurom.check)

optimal_distribution() (in module neurom.stats)

P

P (neurom.core.dataformat.COLS attribute) params (neurom.stats.FitResults attribute) path_distance() (in module neurom.morphmath) path_fraction_point() (in module neurom.morphmath) pca() (in module neurom.morphmath) pid (neurom.io.hdf5.Section 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.morphmath) point_dist2() (in module neurom.morphmath) POINT_TYPE (class in neurom.core.dataformat) points (neurom.core._neuron.Neurite attribute) (neurom.core.Neurite attribute) (neurom.core.Soma attribute) (neurom.core._soma.Soma attribute) (neurom.core._soma.SomaSimpleContour attribute) (neurom.core._soma.SomaSinglePoint attribute) (neurom.core._soma.SomaThreePoint attribute) (neurom.fst.FstNeuron attribute) polygon_diameter() (in module neurom.morphmath) Population (class in neurom.core) principal_direction_extent() (in module neurom.morphmath)

R

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

RawDataError read() (in module neurom.io.hdf5) (in module neurom.io.swc)

S

save_plot() (in module neurom.view.common) scalar_projection() (in module neurom.morphmath) scalar_stats() (in module neurom.stats) Section (class in neurom.core) (class in neurom.core._neuron) (class in neurom.io.hdf5) section_area() (in module neurom.fst.sectionfunc) section_fun() (in module neurom.fst.sectionfunc) section_length() (in module neurom.morphmath) section_meander_angles() (in module neurom.fst.sectionfunc) section_path_length() (in module neurom.fst.sectionfunc) section_radial_distance() (in module neurom.fst.sectionfunc) section_tortuosity() (in module neurom.fst.sectionfunc) section_volume() (in module neurom.fst.sectionfunc) segment_area() (in module neurom.morphmath) segment_length() (in module neurom.morphmath) segment_length2() (in module neurom.morphmath) segment_radial_dist() (in module neurom.morphmath) segment_radius() (in module neurom.morphmath) segment_taper_rate() (in module neurom.morphmath)

segment_volume() (in module neurom.morphmath) segment_x_coordinate() (in module neurom.morphmath) segment_y_coordinate() (in module neurom.morphmath) segment_z_coordinate() (in module neurom.morphmath) SimpleContour (neurom.core._soma.SOMA_TYPE attribute) SinglePoint (neurom.core._soma.SOMA_TYPE attribute) Soma (class in neurom.core) (class in neurom.core._soma) SOMA (neurom.core.dataformat.POINT_TYPE attribute) soma (neurom.core.NeuriteType attribute) (neurom.NeuriteType attribute) (neurom.core.types.NeuriteType attribute) soma() (in module neurom.view.view) soma3d() (in module neurom.view.view) SOMA_TYPE (class in neurom.core._soma) SomaError SomaSimpleContour (class in neurom.core._soma) SomaSinglePoint (class in neurom.core._soma) SomaThreePoint (class in neurom.core._soma) sphere_area() (in module neurom.morphmath) StatTests (class in neurom.stats)

T

t (neurom.core.point.Point attribute) taper_rate() (in module neurom.morphmath) ThreePoint (neurom.core._soma.SOMA_TYPE attribute) total_score() (in module neurom.stats) transform() (neurom.core._neuron.Neurite method) (neurom.core.Neurite method) (neurom.fst.FstNeuron method) Tree (class in neurom.core) (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) ttest (neurom.stats.StatTests attribute) TYPE (neurom.core.dataformat.COLS attribute) type (neurom.stats.FitResults attribute)

U

UNDEFINED (neurom.core.dataformat.POINT_TYPE attribute)

undefined (neurom.core.NeuriteType attribute) (neurom.NeuriteType attribute) (neurom.core.types.NeuriteType attribute)

V

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

ViewerError volume (neurom.core._neuron.Neurite attribute) (neurom.core.Neurite attribute) (neurom.core.Section attribute) (neurom.core._neuron.Section attribute)

W

wilcoxon (neurom.stats.StatTests attribute)

X

X (neurom.core.dataformat.COLS attribute)

x (neurom.core.point.Point attribute)

Y

Y (neurom.core.dataformat.COLS attribute)

y (neurom.core.point.Point attribute)

Z

Z (neurom.core.dataformat.COLS attribute)

z (neurom.core.point.Point attribute)