Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
A
active_node_id (neuron_morphology.morphology_builder.MorphologyBuilder attribute)
add_mark() (neuron_morphology.feature_extractor.marked_feature.MarkedFeature method)
add_marker_results() (neuron_morphology.validation.report.Report method)
add_swc_results() (neuron_morphology.validation.report.Report method)
add_swc_stats() (neuron_morphology.validation.report.Report method)
affine_from_transform() (in module neuron_morphology.transforms.affine_transform)
affine_from_transform_translation() (in module neuron_morphology.transforms.affine_transform)
affine_from_translation() (in module neuron_morphology.transforms.affine_transform)
AffineTransform (class in neuron_morphology.transforms.affine_transform)
AllNeuriteCompareSpec (class in neuron_morphology.feature_extractor.feature_specialization)
AllNeuriteSpec (class in neuron_morphology.feature_extractor.feature_specialization)
AllNeuriteTypes (class in neuron_morphology.feature_extractor.mark)
apical_dendrite() (neuron_morphology.morphology_builder.MorphologyBuilder method)
ApicalDendriteCompareSpec (class in neuron_morphology.feature_extractor.feature_specialization)
ApicalDendriteSpec (class in neuron_morphology.feature_extractor.feature_specialization)
apply_casts() (in module neuron_morphology.swc_io)
aspect_ratio (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
axon() (neuron_morphology.morphology_builder.MorphologyBuilder method)
AxonCompareSpec (class in neuron_morphology.feature_extractor.feature_specialization)
AxonSpec (class in neuron_morphology.feature_extractor.feature_specialization)
B
basal_dendrite() (neuron_morphology.morphology_builder.MorphologyBuilder method)
BasalDendriteCompareSpec (class in neuron_morphology.feature_extractor.feature_specialization)
BasalDendriteSpec (class in neuron_morphology.feature_extractor.feature_specialization)
BIFURCATION (neuron_morphology.features.statistics.coordinates.COORD_TYPE attribute)
BifurcationFeatures (class in neuron_morphology.feature_extractor.mark)
BifurcationSpec (class in neuron_morphology.features.statistics.coordinates)
bin_edges (neuron_morphology.features.layer.layer_histogram.LayerHistogram attribute)
BothEmpty (neuron_morphology.features.layer.layer_histogram.EarthMoversDistanceInterpretation attribute)
BothPresent (neuron_morphology.features.layer.layer_histogram.EarthMoversDistanceInterpretation attribute)
BoundingBox (class in neuron_morphology.snap_polygons.bounding_box)
breadth_first_traversal() (neuron_morphology.morphology.Morphology method)
build() (neuron_morphology.morphology_builder.MorphologyBuilder method)
build_intermediate_nodes() (neuron_morphology.morphology.Morphology method)
C
calculate_branches_from_root() (in module neuron_morphology.features.intrinsic)
calculate_coordinate_overlap() (in module neuron_morphology.features.statistics.overlap)
calculate_coordinate_overlap_from_min_max() (in module neuron_morphology.features.statistics.overlap)
calculate_max_branch_order_from_root() (in module neuron_morphology.features.intrinsic)
calculate_max_path_distance() (in module neuron_morphology.features.path)
calculate_mean_contraction() (in module neuron_morphology.features.path)
calculate_mean_fragmentation_from_root() (in module neuron_morphology.features.intrinsic)
calculate_outer_bifs() (in module neuron_morphology.features.branching.bifurcations)
check_nodes_have_key() (in module neuron_morphology.feature_extractor.mark)
child() (neuron_morphology.morphology_builder.MorphologyBuilder method)
child_ids_by_type() (in module neuron_morphology.features.intrinsic)
children_of() (neuron_morphology.morphology.Morphology method)
clear_overlaps() (in module neuron_morphology.snap_polygons.geometries)
clone() (neuron_morphology.morphology.Morphology method)
close_bounds (neuron_morphology.snap_polygons.geometries.Geometries attribute)
closest_from_stack() (in module neuron_morphology.snap_polygons.geometries)
collect_inputs() (in module neuron_morphology.transforms.scale_correction.compute_scale_correction)
COMPARTMENT (neuron_morphology.features.statistics.coordinates.COORD_TYPE attribute)
CompartmentFeatures (class in neuron_morphology.feature_extractor.mark)
CompartmentSpec (class in neuron_morphology.features.statistics.coordinates)
convex_hull() (neuron_morphology.snap_polygons.geometries.Geometries method)
COORD_TYPE (class in neuron_morphology.features.statistics.coordinates)
coordinates (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
copy() (neuron_morphology.snap_polygons.bounding_box.BoundingBox method)
count_number_of_independent_axons() (in module neuron_morphology.validation.morphology_statistics)
counts (neuron_morphology.features.layer.layer_histogram.LayerHistogram attribute)
cut() (neuron_morphology.snap_polygons.geometries.Geometries method)
D
Data (class in neuron_morphology.feature_extractor.data)
deepcopy() (neuron_morphology.feature_extractor.marked_feature.MarkedFeature method)
DEFAULT_COLOR_CYCLE (neuron_morphology.snap_polygons.image_outputter.ImageOutputter attribute)
default_multipolygon_resolver (neuron_morphology.snap_polygons.geometries.Geometries attribute)
default_multisurface_resolver (neuron_morphology.snap_polygons.geometries.Geometries attribute)
DendriteCompareSpec (class in neuron_morphology.feature_extractor.feature_specialization)
DendriteSpec (class in neuron_morphology.feature_extractor.feature_specialization)
depth_first_traversal() (neuron_morphology.morphology.Morphology method)
DF_COLS (neuron_morphology.features.layer.layered_point_depths.LayeredPointDepths attribute)
draw_after() (neuron_morphology.snap_polygons.image_outputter.ImageOutputter method)
draw_before() (neuron_morphology.snap_polygons.image_outputter.ImageOutputter method)
E
EarthMoversDistanceInterpretation (class in neuron_morphology.features.layer.layer_histogram)
EarthMoversDistanceResult (class in neuron_morphology.features.layer.layer_histogram)
ensure() (neuron_morphology.feature_extractor.marked_feature.MarkedFeature class method)
ensure_layers() (in module neuron_morphology.features.layer.layer_histogram)
ensure_linestring() (in module neuron_morphology.snap_polygons.types)
ensure_node_types() (in module neuron_morphology.features.layer.layer_histogram)
ensure_path() (in module neuron_morphology.snap_polygons.types)
ensure_polygon() (in module neuron_morphology.snap_polygons.types)
ensure_tuple() (in module neuron_morphology.features.layer.layer_histogram)
estimate_scale_correction() (in module neuron_morphology.transforms.scale_correction.compute_scale_correction)
euclidean_distance() (neuron_morphology.morphology.Morphology static method)
extent (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
extract() (neuron_morphology.feature_extractor.feature_extraction_run.FeatureExtractionRun method)
(neuron_morphology.feature_extractor.feature_extractor.FeatureExtractor method)
F
factory() (neuron_morphology.feature_extractor.feature_specialization.FeatureSpecialization class method)
(neuron_morphology.feature_extractor.mark.Mark class method)
feature (neuron_morphology.feature_extractor.marked_feature.MarkedFeature attribute)
FeatureExtractionRun (class in neuron_morphology.feature_extractor.feature_extraction_run)
FeatureExtractor (class in neuron_morphology.feature_extractor.feature_extractor)
FeatureSpecialization (class in neuron_morphology.feature_extractor.feature_specialization)
fill_gaps() (neuron_morphology.snap_polygons.geometries.Geometries method)
find_transition() (in module neuron_morphology.snap_polygons.cortex_surfaces)
find_vertical_surfaces() (in module neuron_morphology.snap_polygons.geometries)
first_met() (in module neuron_morphology.snap_polygons.cortex_surfaces)
fname_suffix() (in module neuron_morphology.snap_polygons.image_outputter)
from_csv() (neuron_morphology.features.layer.layered_point_depths.LayeredPointDepths class method)
from_dataframe() (neuron_morphology.features.layer.layered_point_depths.LayeredPointDepths class method)
from_dict() (neuron_morphology.transforms.affine_transform.AffineTransform class method)
from_hdf5() (neuron_morphology.features.layer.layered_point_depths.LayeredPointDepths class method)
from_list() (neuron_morphology.transforms.affine_transform.AffineTransform class method)
G
Geometric (class in neuron_morphology.feature_extractor.mark)
Geometries (class in neuron_morphology.snap_polygons.geometries)
get_branch_order_for_node() (neuron_morphology.morphology.Morphology method)
get_branch_order_for_segment() (neuron_morphology.morphology.Morphology method)
get_branching_nodes() (neuron_morphology.morphology.Morphology method)
get_ccw_vertices() (in module neuron_morphology.transforms.geometry)
get_ccw_vertices_from_two_lines() (in module neuron_morphology.transforms.geometry)
get_children() (neuron_morphology.morphology.Morphology method)
get_children_of_node_by_types() (neuron_morphology.morphology.Morphology method)
get_compartment_for_node() (neuron_morphology.morphology.Morphology method)
get_compartment_length() (neuron_morphology.morphology.Morphology method)
get_compartment_midpoint() (neuron_morphology.morphology.Morphology method)
get_compartment_surface_area() (neuron_morphology.morphology.Morphology method)
get_compartment_volume() (neuron_morphology.morphology.Morphology method)
get_compartments() (neuron_morphology.morphology.Morphology method)
get_coordinates() (neuron_morphology.features.statistics.coordinates.COORD_TYPE method)
get_dimensions() (neuron_morphology.morphology.Morphology method)
get_leaf_nodes() (neuron_morphology.morphology.Morphology method)
get_max_id() (neuron_morphology.morphology.Morphology method)
get_morphology() (in module neuron_morphology.feature_extractor.data)
get_node_by_types() (neuron_morphology.morphology.Morphology method)
get_non_soma_nodes() (neuron_morphology.morphology.Morphology method)
get_number_of_trees() (neuron_morphology.morphology.Morphology method)
get_root() (neuron_morphology.morphology.Morphology method)
get_root_for_tree() (neuron_morphology.morphology.Morphology method)
get_root_id() (neuron_morphology.morphology.Morphology method)
get_roots() (neuron_morphology.morphology.Morphology method)
get_roots_for_analysis() (neuron_morphology.morphology.Morphology method)
get_roots_for_nodes() (neuron_morphology.morphology.Morphology method)
get_segment_length() (neuron_morphology.morphology.Morphology method)
get_segment_list() (neuron_morphology.morphology.Morphology method)
get_snapped_polys() (in module neuron_morphology.snap_polygons.geometries)
get_soma() (neuron_morphology.morphology.Morphology method)
get_soma_marker_from_marker_file() (in module neuron_morphology.transforms.scale_correction.compute_scale_correction)
get_tree_list() (neuron_morphology.morphology.Morphology method)
get_vertices_from_two_lines() (in module neuron_morphology.transforms.geometry)
H
has_results() (neuron_morphology.validation.report.Report method)
has_type() (neuron_morphology.morphology.Morphology method)
height (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
hextent (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
histogram_earth_movers_distance() (in module neuron_morphology.features.layer.layer_histogram)
horigin (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
hydrate_parameters() (in module neuron_morphology.feature_extractor.run_feature_extraction)
I
ImageOutputter (class in neuron_morphology.snap_polygons.image_outputter)
interpretation (neuron_morphology.features.layer.layer_histogram.EarthMoversDistanceResult attribute)
Intrinsic (class in neuron_morphology.feature_extractor.mark)
InvalidMarkerFile
InvalidMorphology
is_node_at_beginning_of_segment() (neuron_morphology.morphology.Morphology method)
is_node_at_end_of_segment() (neuron_morphology.morphology.Morphology method)
is_soma_child() (neuron_morphology.morphology.Morphology method)
K
kwargs (neuron_morphology.feature_extractor.feature_specialization.AllNeuriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.AllNeuriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.ApicalDendriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.ApicalDendriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.AxonCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.AxonSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.BasalDendriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.BasalDendriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.DendriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.DendriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.FeatureSpecialization attribute)
(neuron_morphology.features.statistics.coordinates.BifurcationSpec attribute)
(neuron_morphology.features.statistics.coordinates.CompartmentSpec attribute)
(neuron_morphology.features.statistics.coordinates.NodeSpec attribute)
(neuron_morphology.features.statistics.coordinates.TipSpec attribute)
L
LayeredPointDepths (class in neuron_morphology.features.layer.layered_point_depths)
LayerHistogram (class in neuron_morphology.features.layer.layer_histogram)
level (neuron_morphology.validation.result.MarkerValidationError attribute)
(neuron_morphology.validation.result.NodeValidationError attribute)
M
main() (in module neuron_morphology.transforms.affine_transformer.apply_affine_transform)
(in module neuron_morphology.transforms.scale_correction.compute_scale_correction)
(in module neuron_morphology.validation.validate_reconstruction)
make_pathpatch() (in module neuron_morphology.snap_polygons.image_outputter)
make_scale() (in module neuron_morphology.snap_polygons.geometries)
make_translation() (in module neuron_morphology.snap_polygons.geometries)
Mark (class in neuron_morphology.feature_extractor.mark)
marked() (in module neuron_morphology.feature_extractor.marked_feature)
MarkedFeature (class in neuron_morphology.feature_extractor.marked_feature)
Marker (class in neuron_morphology.marker)
marker (neuron_morphology.validation.result.MarkerValidationError attribute)
MarkerValidationError (class in neuron_morphology.validation.result)
marks (neuron_morphology.feature_extractor.feature_specialization.AllNeuriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.AllNeuriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.ApicalDendriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.ApicalDendriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.AxonCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.AxonSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.BasalDendriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.BasalDendriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.DendriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.DendriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.FeatureSpecialization attribute)
(neuron_morphology.feature_extractor.marked_feature.MarkedFeature attribute)
(neuron_morphology.features.statistics.coordinates.BifurcationSpec attribute)
(neuron_morphology.features.statistics.coordinates.CompartmentSpec attribute)
(neuron_morphology.features.statistics.coordinates.NodeSpec attribute)
(neuron_morphology.features.statistics.coordinates.TipSpec attribute)
message (neuron_morphology.validation.result.MarkerValidationError attribute)
(neuron_morphology.validation.result.NodeValidationError attribute)
midpoint() (neuron_morphology.morphology.Morphology static method)
Morphology (class in neuron_morphology.morphology)
morphology_from_swc() (in module neuron_morphology.swc_io)
morphology_statistics() (in module neuron_morphology.validation.morphology_statistics)
morphology_to_swc() (in module neuron_morphology.swc_io)
MorphologyBuilder (class in neuron_morphology.morphology_builder)
N
name (neuron_morphology.feature_extractor.feature_specialization.AllNeuriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.AllNeuriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.ApicalDendriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.ApicalDendriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.AxonCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.AxonSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.BasalDendriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.BasalDendriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.DendriteCompareSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.DendriteSpec attribute)
(neuron_morphology.feature_extractor.feature_specialization.FeatureSpecialization attribute)
(neuron_morphology.feature_extractor.marked_feature.MarkedFeature attribute)
(neuron_morphology.features.statistics.coordinates.BifurcationSpec attribute)
(neuron_morphology.features.statistics.coordinates.CompartmentSpec attribute)
(neuron_morphology.features.statistics.coordinates.NodeSpec attribute)
(neuron_morphology.features.statistics.coordinates.TipSpec attribute)
nested_specialize() (in module neuron_morphology.feature_extractor.marked_feature)
NeuriteTypeComparison (class in neuron_morphology.feature_extractor.mark)
neuron_morphology (module)
neuron_morphology.constants (module)
neuron_morphology.feature_extractor (module)
neuron_morphology.feature_extractor.data (module)
neuron_morphology.feature_extractor.feature_extraction_run (module)
neuron_morphology.feature_extractor.feature_extractor (module)
neuron_morphology.feature_extractor.feature_specialization (module)
neuron_morphology.feature_extractor.mark (module)
neuron_morphology.feature_extractor.marked_feature (module)
neuron_morphology.feature_extractor.run_feature_extraction (module)
neuron_morphology.feature_extractor.utilities (module)
neuron_morphology.features (module)
neuron_morphology.features.branching (module)
neuron_morphology.features.branching.bifurcations (module)
neuron_morphology.features.default_features (module)
neuron_morphology.features.dimension (module)
neuron_morphology.features.intrinsic (module)
neuron_morphology.features.layer (module)
neuron_morphology.features.layer.layer_histogram (module)
neuron_morphology.features.layer.layered_point_depths (module)
neuron_morphology.features.layer.reference_layer_depths (module)
neuron_morphology.features.path (module)
neuron_morphology.features.size (module)
neuron_morphology.features.soma (module)
neuron_morphology.features.statistics (module)
neuron_morphology.features.statistics.coordinates (module)
neuron_morphology.features.statistics.moments (module)
neuron_morphology.features.statistics.overlap (module)
neuron_morphology.layered_point_depths (module)
neuron_morphology.marker (module)
neuron_morphology.morphology (module)
neuron_morphology.morphology_builder (module)
neuron_morphology.pipeline (module)
neuron_morphology.snap_polygons (module)
neuron_morphology.snap_polygons.bounding_box (module)
neuron_morphology.snap_polygons.cortex_surfaces (module)
neuron_morphology.snap_polygons.geometries (module)
neuron_morphology.snap_polygons.image_outputter (module)
neuron_morphology.snap_polygons.types (module)
neuron_morphology.swc_io (module)
neuron_morphology.transforms (module)
neuron_morphology.transforms.affine_transform (module)
neuron_morphology.transforms.affine_transformer (module)
neuron_morphology.transforms.affine_transformer.apply_affine_transform (module)
neuron_morphology.transforms.geometry (module)
neuron_morphology.transforms.pia_wm_streamlines (module)
neuron_morphology.transforms.scale_correction (module)
neuron_morphology.transforms.scale_correction.compute_scale_correction (module)
neuron_morphology.transforms.tilt_correction (module)
neuron_morphology.transforms.transform_base (module)
neuron_morphology.transforms.upright_angle (module)
neuron_morphology.validation (module)
neuron_morphology.validation.bits_validation (module)
neuron_morphology.validation.marker_validation (module)
neuron_morphology.validation.morphology_statistics (module)
neuron_morphology.validation.radius_validation (module)
neuron_morphology.validation.report (module)
neuron_morphology.validation.resample_validation (module)
neuron_morphology.validation.result (module)
neuron_morphology.validation.structure_validation (module)
neuron_morphology.validation.type_validation (module)
neuron_morphology.validation.validate_reconstruction (module)
neuron_morphology.vis (module)
neuron_morphology.vis.morphovis (module)
next_id (neuron_morphology.morphology_builder.MorphologyBuilder attribute)
NODE (neuron_morphology.features.statistics.coordinates.COORD_TYPE attribute)
node_by_id() (neuron_morphology.morphology.Morphology method)
node_ids (neuron_morphology.validation.result.NodeValidationError attribute)
NodeSpec (class in neuron_morphology.features.statistics.coordinates)
NodeValidationError (class in neuron_morphology.validation.result)
normalized_depth_histogram_within_layer() (in module neuron_morphology.features.layer.layer_histogram)
normalized_depth_histograms_across_layers (in module neuron_morphology.features.layer.layer_histogram)
O
OneEmpty (neuron_morphology.features.layer.layer_histogram.EarthMoversDistanceInterpretation attribute)
origin (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
OVERLAY_TYPES (neuron_morphology.snap_polygons.image_outputter.ImageOutputter attribute)
P
parent_daughter_ratio_visitor() (in module neuron_morphology.features.size)
parent_id (neuron_morphology.morphology_builder.MorphologyBuilder attribute)
parent_of() (neuron_morphology.morphology.Morphology method)
parse_arguments() (in module neuron_morphology.validation.validate_reconstruction)
partial() (neuron_morphology.feature_extractor.marked_feature.MarkedFeature method)
pia_side (neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths attribute)
plot_cortical_boundary() (in module neuron_morphology.vis.morphovis)
plot_depth_field() (in module neuron_morphology.vis.morphovis)
plot_gradient_field() (in module neuron_morphology.vis.morphovis)
plot_morphology_xy() (in module neuron_morphology.vis.morphovis)
plot_morphology_zy() (in module neuron_morphology.vis.morphovis)
plot_soma() (in module neuron_morphology.vis.morphovis)
prune_two_lines() (in module neuron_morphology.transforms.geometry)
R
rasterize() (in module neuron_morphology.snap_polygons.geometries)
(neuron_morphology.snap_polygons.geometries.Geometries method)
read() (neuron_morphology.features.layer.layered_point_depths.LayeredPointDepths class method)
read_image() (in module neuron_morphology.snap_polygons.image_outputter)
read_jp2() (in module neuron_morphology.snap_polygons.image_outputter)
read_marker_file() (in module neuron_morphology.marker)
read_swc() (in module neuron_morphology.swc_io)
read_with_ndimage() (in module neuron_morphology.snap_polygons.image_outputter)
ReferenceLayerDepths (class in neuron_morphology.features.layer.reference_layer_depths)
register_features() (neuron_morphology.feature_extractor.feature_extractor.FeatureExtractor method)
register_polygon() (neuron_morphology.snap_polygons.geometries.Geometries method)
register_polygons() (neuron_morphology.snap_polygons.geometries.Geometries method)
register_surface() (neuron_morphology.snap_polygons.geometries.Geometries method)
register_surfaces() (neuron_morphology.snap_polygons.geometries.Geometries method)
remove_duplicates() (in module neuron_morphology.snap_polygons.cortex_surfaces)
Report (class in neuron_morphology.validation.report)
RequiresApical (class in neuron_morphology.feature_extractor.mark)
RequiresAxon (class in neuron_morphology.feature_extractor.mark)
RequiresBasal (class in neuron_morphology.feature_extractor.mark)
RequiresDendrite (class in neuron_morphology.feature_extractor.mark)
RequiresLayerAnnotations (class in neuron_morphology.feature_extractor.mark)
RequiresLayeredPointDepths (class in neuron_morphology.feature_extractor.mark)
RequiresRadii (class in neuron_morphology.feature_extractor.mark)
RequiresReferenceLayerDepths (class in neuron_morphology.feature_extractor.mark)
RequiresRegularPointSpacing (class in neuron_morphology.feature_extractor.mark)
RequiresRelativeSomaDepth (class in neuron_morphology.feature_extractor.mark)
RequiresRoot (class in neuron_morphology.feature_extractor.mark)
RequiresSoma (class in neuron_morphology.feature_extractor.mark)
resolve_reference_layer_depths() (in module neuron_morphology.feature_extractor.run_feature_extraction)
result (neuron_morphology.features.layer.layer_histogram.EarthMoversDistanceResult attribute)
root() (neuron_morphology.morphology_builder.MorphologyBuilder method)
rotation_from_angle() (in module neuron_morphology.transforms.affine_transform)
round() (neuron_morphology.snap_polygons.bounding_box.BoundingBox method)
run_feature_extraction() (in module neuron_morphology.feature_extractor.run_feature_extraction)
run_scale_correction() (in module neuron_morphology.transforms.scale_correction.compute_scale_correction)
S
safe_linemerge() (in module neuron_morphology.snap_polygons.geometries)
scale (neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths attribute)
select_features() (neuron_morphology.feature_extractor.feature_extraction_run.FeatureExtractionRun method)
select_largest_subpolygon() (in module neuron_morphology.snap_polygons.geometries)
select_marks() (neuron_morphology.feature_extractor.feature_extraction_run.FeatureExtractionRun method)
sequential() (neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths class method)
serialize() (neuron_morphology.feature_extractor.feature_extraction_run.FeatureExtractionRun method)
setup_data() (in module neuron_morphology.feature_extractor.run_feature_extraction)
shared_faces() (in module neuron_morphology.snap_polygons.geometries)
slope_linear_regression_branch_order_avg_radius() (in module neuron_morphology.validation.radius_validation)
specialize() (in module neuron_morphology.feature_extractor.marked_feature)
(neuron_morphology.feature_extractor.marked_feature.MarkedFeature method)
split_pathstring() (in module neuron_morphology.snap_polygons.types)
swap_nodes_edges() (neuron_morphology.morphology.Morphology method)
T
thickness (neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths attribute)
TIP (neuron_morphology.features.statistics.coordinates.COORD_TYPE attribute)
TipFeatures (class in neuron_morphology.feature_extractor.mark)
TipSpec (class in neuron_morphology.features.statistics.coordinates)
to_csv() (neuron_morphology.features.layer.layered_point_depths.LayeredPointDepths method)
to_dict() (neuron_morphology.transforms.affine_transform.AffineTransform method)
to_dict_human_readable() (neuron_morphology.features.layer.layer_histogram.EarthMoversDistanceResult method)
to_json() (neuron_morphology.snap_polygons.geometries.Geometries method)
(neuron_morphology.validation.report.Report method)
to_list() (neuron_morphology.transforms.affine_transform.AffineTransform method)
transform() (neuron_morphology.snap_polygons.bounding_box.BoundingBox method)
(neuron_morphology.snap_polygons.geometries.Geometries method)
(neuron_morphology.transforms.affine_transform.AffineTransform method)
(neuron_morphology.transforms.transform_base.TransformBase method)
transform_morphology() (neuron_morphology.transforms.affine_transform.AffineTransform method)
(neuron_morphology.transforms.transform_base.TransformBase method)
TransformBase (class in neuron_morphology.transforms.transform_base)
trim_coords() (in module neuron_morphology.snap_polygons.cortex_surfaces)
trim_to_close() (in module neuron_morphology.snap_polygons.cortex_surfaces)
U
unnest() (in module neuron_morphology.feature_extractor.utilities)
up() (neuron_morphology.morphology_builder.MorphologyBuilder method)
update() (neuron_morphology.snap_polygons.bounding_box.BoundingBox method)
V
valid_dendrite_parent() (in module neuron_morphology.validation.type_validation)
validate() (in module neuron_morphology.validation.bits_validation)
(in module neuron_morphology.validation.marker_validation)
(in module neuron_morphology.validation.radius_validation)
(in module neuron_morphology.validation.resample_validation)
(in module neuron_morphology.validation.structure_validation)
(in module neuron_morphology.validation.type_validation)
(neuron_morphology.feature_extractor.mark.Mark class method)
(neuron_morphology.feature_extractor.mark.RequiresApical class method)
(neuron_morphology.feature_extractor.mark.RequiresAxon class method)
(neuron_morphology.feature_extractor.mark.RequiresBasal class method)
(neuron_morphology.feature_extractor.mark.RequiresDendrite class method)
(neuron_morphology.feature_extractor.mark.RequiresLayerAnnotations class method)
(neuron_morphology.feature_extractor.mark.RequiresLayeredPointDepths class method)
(neuron_morphology.feature_extractor.mark.RequiresRadii class method)
(neuron_morphology.feature_extractor.mark.RequiresReferenceLayerDepths class method)
(neuron_morphology.feature_extractor.mark.RequiresRelativeSomaDepth class method)
(neuron_morphology.feature_extractor.mark.RequiresRoot class method)
(neuron_morphology.feature_extractor.mark.RequiresSoma class method)
(neuron_morphology.morphology.Morphology method)
validate_children_nodes_appear_before_parent_nodes() (in module neuron_morphology.validation.structure_validation)
validate_constrictions() (in module neuron_morphology.validation.radius_validation)
validate_coordinates_corresponding_to_axon_tip() (in module neuron_morphology.validation.marker_validation)
validate_coordinates_corresponding_to_dendrite_tip() (in module neuron_morphology.validation.marker_validation)
validate_count_node_parent() (in module neuron_morphology.validation.type_validation)
validate_distance_between_connected_nodes() (in module neuron_morphology.validation.resample_validation)
validate_expected_name() (in module neuron_morphology.validation.marker_validation)
validate_expected_types() (in module neuron_morphology.validation.type_validation)
validate_extreme_taper() (in module neuron_morphology.validation.radius_validation)
validate_immediate_children_of_soma_cannot_branch() (in module neuron_morphology.validation.type_validation)
validate_independent_axon_has_more_than_four_nodes() (in module neuron_morphology.validation.bits_validation)
validate_marker() (in module neuron_morphology.validation)
validate_morphology() (in module neuron_morphology.validation)
validate_multiple_axon_initiation_points() (in module neuron_morphology.validation.type_validation)
validate_no_reconstruction_count() (in module neuron_morphology.validation.marker_validation)
validate_node_parent() (in module neuron_morphology.validation.type_validation)
validate_number_of_soma_nodes() (in module neuron_morphology.validation.type_validation)
validate_radius_has_negative_slope_dendrite() (in module neuron_morphology.validation.radius_validation)
validate_radius_threshold() (in module neuron_morphology.validation.radius_validation)
validate_type_thirty_count() (in module neuron_morphology.validation.marker_validation)
validate_types_three_four_traceable_back_to_soma() (in module neuron_morphology.validation.bits_validation)
validation_errors (neuron_morphology.validation.result.InvalidMarkerFile attribute)
(neuron_morphology.validation.result.InvalidMorphology attribute)
vextent (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
vorigin (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
W
width (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
wm_side (neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths attribute)
write_figure() (in module neuron_morphology.snap_polygons.image_outputter)
write_images() (neuron_morphology.snap_polygons.image_outputter.ImageOutputter method)
write_swc() (in module neuron_morphology.swc_io)
neuron morphology
Navigation
- Feature Extraction
- IVSCC Spatial Transformation
- Installation
- Reference
- Github
- Allen Institute
Related Topics
Documentation overview
Quick search