NeuroM
v1.4.11
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NeuroM morphology definitions
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Index
_
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
_
__init__() (neurom.check.CheckResult method)
(neurom.core._neuron.Neurite method)
(neurom.core._neuron.Neuron method)
(neurom.core._neuron.Section method)
(neurom.core._soma.Soma method)
(neurom.core._soma.SomaCylinders method)
(neurom.core._soma.SomaNeuromorphoThreePointCylinders method)
(neurom.core._soma.SomaSimpleContour method)
(neurom.core._soma.SomaSinglePoint method)
(neurom.core.tree.Tree method)
(neurom.io.utils.NeuronLoader method)
A
add_child() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
all (neurom.core.types.NeuriteType attribute)
angle_3points() (in module neurom.morphmath)
angle_between_vectors() (in module neurom.morphmath)
APICAL_DENDRITE (neurom.core.dataformat.POINT_TYPE attribute)
apical_dendrite (neurom.core.types.NeuriteType attribute)
area (neurom.core._neuron.Neurite 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.types.NeuriteType attribute)
axon_filter() (in module neurom.core.types)
B
BASAL_DENDRITE (neurom.core.dataformat.POINT_TYPE attribute)
basal_dendrite (neurom.core.types.NeuriteType attribute)
branch_order() (in module neurom.fst.sectionfunc)
C
center (neurom.core._soma.Soma attribute)
(neurom.core._soma.SomaCylinders attribute)
(neurom.core._soma.SomaNeuromorphoThreePointCylinders attribute)
(neurom.core._soma.SomaSimpleContour attribute)
(neurom.core._soma.SomaSinglePoint attribute)
check_wrapper() (in module neurom.check)
CheckResult (class in neurom.check)
COL_COUNT (neurom.core.dataformat.COLS attribute)
COLS (class in neurom.core.dataformat)
compare_two() (in module neurom.stats)
ConfigError
count() (neurom.core.point.Point method)
(neurom.stats.FitResults method)
CUSTOM (neurom.core.dataformat.POINT_TYPE attribute)
D
dendrite_filter() (in module neurom.core.types)
dict_if_none() (in module neurom.view.common)
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)
FileOrder (neurom.core.types.NeuriteIter attribute)
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
generate_cylindrical_points() (in module neurom.view.common)
get() (in module neurom.fst)
(neurom.io.utils.NeuronLoader method)
get_back_tracking_neurites() (in module neurom.check.morphtree)
get_figure() (in module neurom.view.common)
get_files_by_path() (in module neurom.io.utils)
get_flat_neurites() (in module neurom.check.morphtree)
get_morph_files() (in module neurom.io.utils)
get_nonmonotonic_neurites() (in module neurom.check.morphtree)
get_test() (in module neurom.stats)
get_version() (in module neurom.io.hdf5)
graft_neuron() (in module neurom.core._neuron)
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_dangling_branch() (in module neurom.check.neuron_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_no_narrow_neurite_section() (in module neurom.check.neuron_checks)
has_no_narrow_start() (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
ibifurcation_point() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
ID (neurom.core.dataformat.COLS attribute)
IDSequenceError
iforking_point() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
ileaf() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
index() (neurom.core.point.Point method)
(neurom.stats.FitResults method)
interpolate_radius() (in module neurom.morphmath)
InvalidDrawModeError
ipostorder() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
ipreorder() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
is_back_tracking() (in module neurom.check.morphtree)
is_bifurcation_point() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
is_flat() (in module neurom.check.morphtree)
is_forking_point() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
is_leaf() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
is_monotonic() (in module neurom.check.morphtree)
is_root() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
is_single_tree() (in module neurom.check.structural_checks)
iter() (neurom.core._soma.Soma method)
(neurom.core._soma.SomaCylinders method)
(neurom.core._soma.SomaNeuromorphoThreePointCylinders method)
(neurom.core._soma.SomaSimpleContour method)
(neurom.core._soma.SomaSinglePoint method)
iter_neurites() (in module neurom.core._neuron)
iter_sections() (in module neurom.core._neuron)
(neurom.core._neuron.Neurite method)
iter_segments() (in module neurom.core._neuron)
iupstream() (neurom.core._neuron.Section method)
(neurom.core.tree.Tree method)
K
ks (neurom.stats.StatTests attribute)
L
length (neurom.core._neuron.Neurite attribute)
(neurom.core._neuron.Section attribute)
linear_interpolate() (in module neurom.morphmath)
load_data() (in module neurom.io.utils)
load_neuron() (in module neurom.io.utils)
load_neurons() (in module neurom.io.utils)
locate_segment_position() (in module neurom.fst.sectionfunc)
M
make_soma() (in module neurom.core._soma)
MissingParentError
MultipleTrees
N
Neurite (class in neurom.core._neuron)
NeuriteIter (class in neurom.core.types)
NEURITES (neurom.core.dataformat.POINT_TYPE attribute)
NeuriteType (class in neurom.core.types)
neurom (module)
neurom.check (module)
neurom.check.morphtree (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._neuron)
NeuronLoader (class in neurom.io.utils)
no_missing_parents() (in module neurom.check.structural_checks)
NotDrawableError
NRN (neurom.core.types.NeuriteIter attribute)
O
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_id_offset() (in module neurom.morphmath)
path_fraction_point() (in module neurom.morphmath)
pca() (in module neurom.morphmath)
plot_cylinder() (in module neurom.view.common)
plot_dendrogram() (in module neurom.view.view)
plot_labels() (in module neurom.view.common)
plot_legend() (in module neurom.view.common)
plot_neuron() (in module neurom.view.view)
plot_neuron3d() (in module neurom.view.view)
plot_soma() (in module neurom.view.view)
plot_soma3d() (in module neurom.view.view)
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)
plot_tree() (in module neurom.view.view)
plot_tree3d() (in module neurom.view.view)
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._soma.Soma attribute)
(neurom.core._soma.SomaCylinders attribute)
(neurom.core._soma.SomaNeuromorphoThreePointCylinders attribute)
(neurom.core._soma.SomaSimpleContour attribute)
(neurom.core._soma.SomaSinglePoint attribute)
polygon_diameter() (in module neurom.morphmath)
principal_direction_extent() (in module neurom.morphmath)
project_cylinder_onto_2d() (in module neurom.view.common)
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)
register_neurite_feature() (in module neurom.fst)
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._neuron)
section_area() (in module neurom.fst.sectionfunc)
section_end_distance() (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)
Soma (class in neurom.core._soma)
SOMA (neurom.core.dataformat.POINT_TYPE attribute)
soma (neurom.core.types.NeuriteType attribute)
SomaCylinders (class in neurom.core._soma)
SomaError
SomaNeuromorphoThreePointCylinders (class in neurom.core._soma)
SomaSimpleContour (class in neurom.core._soma)
SomaSinglePoint (class in neurom.core._soma)
sphere_area() (in module neurom.morphmath)
StatTests (class in neurom.stats)
strahler_order() (in module neurom.fst.sectionfunc)
T
t (neurom.core.point.Point attribute)
taper_rate() (in module neurom.morphmath)
total_score() (in module neurom.stats)
transform() (neurom.core._neuron.Neurite method)
Tree (class in neurom.core.tree)
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.types.NeuriteType attribute)
update_plot_limits() (in module neurom.view.common)
V
vector() (in module neurom.morphmath)
vector_projection() (in module neurom.morphmath)
ViewerError
volume (neurom.core._neuron.Neurite 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)
XY (neurom.core.dataformat.COLS attribute)
XYZ (neurom.core.dataformat.COLS attribute)
XYZR (neurom.core.dataformat.COLS attribute)
XZ (neurom.core.dataformat.COLS attribute)
Y
Y (neurom.core.dataformat.COLS attribute)
y (neurom.core.point.Point attribute)
YZ (neurom.core.dataformat.COLS attribute)
Z
Z (neurom.core.dataformat.COLS attribute)
z (neurom.core.point.Point attribute)
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