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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Q
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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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Z
_
__call__() (neuron_morphology.feature_extractor.marked_feature.MarkedFeature method)
__hash__() (neuron_morphology.feature_extractor.data.Data method)
(neuron_morphology.feature_extractor.marked_feature.MarkedFeature method)
__len__() (neuron_morphology.morphology.Morphology method)
__name__ (neuron_morphology.feature_extractor.marked_feature.MarkedFeature attribute)
__repr__() (neuron_morphology.feature_extractor.marked_feature.MarkedFeature method)
(neuron_morphology.snap_polygons.bounding_box.BoundingBox method)
(neuron_morphology.validation.result.MarkerValidationError method)
(neuron_morphology.validation.result.NodeValidationError method)
__slots__ (neuron_morphology.feature_extractor.marked_feature.MarkedFeature attribute)
(neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
__str__() (neuron_morphology.validation.result.InvalidMarkerFile method)
(neuron_morphology.validation.result.InvalidMorphology method)
__version__ (in module neuron_morphology)
_add_node() (neuron_morphology.morphology_builder.MorphologyBuilder method)
_build_segment() (neuron_morphology.morphology.Morphology method)
_calculate_max_path_distance() (in module neuron_morphology.features.path)
_calculate_mean_contraction() (in module neuron_morphology.features.path)
_create_compartment_dictionary() (neuron_morphology.morphology.Morphology method)
_draw_geometries() (neuron_morphology.snap_polygons.image_outputter.ImageOutputter method)
_get_edge_and_merge() (neuron_morphology.morphology.Morphology method)
_get_node_attributes() (neuron_morphology.morphology.Morphology static method)
_get_scaling_factor() (neuron_morphology.transforms.affine_transform.AffineTransform method)
_insert_between() (neuron_morphology.morphology.Morphology method)
_make_and_insert_intermediate() (neuron_morphology.morphology.Morphology method)
_register_many() (neuron_morphology.snap_polygons.geometries.Geometries method)
A
active_node_id (neuron_morphology.morphology_builder.MorphologyBuilder attribute)
add_layer_histogram() (in module neuron_morphology.feature_extractor.feature_writer)
add_mark() (neuron_morphology.feature_extractor.marked_feature.MarkedFeature method)
add_marker_results() (neuron_morphology.validation.report.Report method)
add_run() (neuron_morphology.feature_extractor.feature_writer.FeatureWriter method)
add_swc_results() (neuron_morphology.validation.report.Report method)
add_swc_stats() (neuron_morphology.validation.report.Report method)
affine_dict (neuron_morphology.transforms.affine_transformer._schemas.ApplyAffineSchema attribute)
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)
affine_list (neuron_morphology.transforms.affine_transformer._schemas.ApplyAffineSchema attribute)
AffineDictSchema (class in neuron_morphology.transforms.affine_transformer._schemas)
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 (in module neuron_morphology.constants)
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)
ApplyAffineSchema (class in neuron_morphology.transforms.affine_transformer._schemas)
aspect_ratio (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
AXON (in module neuron_morphology.constants)
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 (in module neuron_morphology.constants)
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)
boundaries (neuron_morphology.feature_extractor._schemas.ReferenceLayerDepths attribute)
BoundingBox (class in neuron_morphology.snap_polygons.bounding_box)
bounds (neuron_morphology.layered_point_depths._schemas.Layer attribute)
breadth_first_traversal() (neuron_morphology.morphology.Morphology method)
build() (neuron_morphology.morphology_builder.MorphologyBuilder method)
build_intermediate_nodes() (neuron_morphology.morphology.Morphology method)
build_output_table() (neuron_morphology.feature_extractor.feature_writer.FeatureWriter 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)
calculate_relative_soma_depth() (in module neuron_morphology.features.soma)
calculate_soma_features() (in module neuron_morphology.features.soma)
calculate_soma_surface() (in module neuron_morphology.features.soma)
calculate_stem_exit_and_distance() (in module neuron_morphology.features.soma)
calculate_transform() (in module neuron_morphology.transforms.upright_angle.compute_angle)
ccf_path (neuron_morphology.transforms.tilt_correction._schemas.InputParameters attribute)
CCF_RESOLUTION (in module neuron_morphology.transforms.tilt_correction.compute_tilt_correction)
CCF_SHAPE (in module neuron_morphology.transforms.tilt_correction.compute_tilt_correction)
ccf_soma_location (neuron_morphology.transforms.tilt_correction._schemas.InputParameters attribute)
ccf_soma_xyz (neuron_morphology.pipeline._schemas.InputParameters attribute)
cell_depth (neuron_morphology.pipeline._schemas.InputParameters attribute)
check (neuron_morphology.feature_extractor.feature_writer.FeatureFormatter attribute)
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)
COLUMN_CASTS (in module neuron_morphology.swc_io)
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)
compute_gradient() (in module neuron_morphology.transforms.streamline)
ConditionFn (in module neuron_morphology.snap_polygons.cortex_surfaces)
ConfigSchema (neuron_morphology.snap_polygons._from_lims.FromLimsSource attribute)
containing_layer() (in module neuron_morphology.layered_point_depths.__main__)
convert_coords_str() (in module neuron_morphology.lims_apical_queries)
convert_path_str_to_list() (in module neuron_morphology.transforms.pia_wm_streamlines.calculate_pia_wm_streamlines)
convex_hull() (neuron_morphology.snap_polygons.geometries.Geometries method)
COORD_TYPE (class in neuron_morphology.features.statistics.coordinates)
COORD_TYPE_SPECIALIZATIONS (in module 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)
credentials_file (neuron_morphology.pipeline._schemas.S3LandingBucket attribute)
cut() (neuron_morphology.snap_polygons.geometries.Geometries method)
CUT_DENDRITE (in module neuron_morphology.constants)
cut_thickness (neuron_morphology.pipeline._schemas.InputParameters attribute)
(neuron_morphology.transforms.scale_correction._schemas.InputParameters attribute)
D
Data (class in neuron_morphology.feature_extractor.data)
database (neuron_morphology.snap_polygons._from_lims.PostgresInputConfigSchema attribute)
deepcopy() (neuron_morphology.feature_extractor.marked_feature.MarkedFeature method)
DEFAULT_COLOR_CYCLE (neuron_morphology.snap_polygons.image_outputter.ImageOutputter attribute)
DEFAULT_FEATURE_FORMATTERS (in module neuron_morphology.feature_extractor.feature_writer)
default_features (in module neuron_morphology.features.default_features)
DEFAULT_HUMAN_ME_MET_REFERENCE_LAYER_DEPTHS (in module neuron_morphology.features.layer.reference_layer_depths)
DEFAULT_HUMAN_MTG_REFERENCE_LAYER_DEPTHS (in module neuron_morphology.features.layer.reference_layer_depths)
DEFAULT_MOUSE_ME_MET_REFERENCE_LAYER_DEPTHS (in module neuron_morphology.features.layer.reference_layer_depths)
DEFAULT_MOUSE_REFERENCE_LAYER_DEPTHS (in module neuron_morphology.features.layer.reference_layer_depths)
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 (neuron_morphology.layered_point_depths._schemas.InputParameters attribute)
depth_field_file (neuron_morphology.transforms.pia_wm_streamlines._schemas.OutputParameters attribute)
depth_field_path (neuron_morphology.layered_point_depths._schemas.DepthField attribute)
depth_first_traversal() (neuron_morphology.morphology.Morphology method)
DepthField (class in neuron_morphology.layered_point_depths._schemas)
destination_bucket (neuron_morphology.pipeline._schemas.InputParameters attribute)
determine_slice_flip() (in module neuron_morphology.transforms.tilt_correction.compute_tilt_correction)
DF_COLS (neuron_morphology.features.layer.layered_point_depths.LayeredPointDepths attribute)
dimension() (in module neuron_morphology.features.dimension)
downsample (neuron_morphology.snap_polygons._schemas.Image attribute)
(neuron_morphology.snap_polygons._schemas.OutputImage attribute)
draw_after() (neuron_morphology.snap_polygons.image_outputter.ImageOutputter method)
draw_before() (neuron_morphology.snap_polygons.image_outputter.ImageOutputter method)
E
early_branch_path() (in module neuron_morphology.features.path)
earth_movers_distance() (in module neuron_morphology.features.layer.layer_histogram)
earth_movers_distance_formatter (in module neuron_morphology.feature_extractor.feature_writer)
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)
extract_multiple() (in module neuron_morphology.feature_extractor.__main__)
F
factory() (neuron_morphology.feature_extractor.feature_specialization.FeatureSpecialization class method)
(neuron_morphology.feature_extractor.mark.Mark class method)
Feature (in module neuron_morphology.feature_extractor.marked_feature)
feature_set (neuron_morphology.feature_extractor._schemas.InputParameters attribute)
FeatureExtractionRun (class in neuron_morphology.feature_extractor.feature_extraction_run)
FeatureExtractor (class in neuron_morphology.feature_extractor.feature_extractor)
FeatureFn (in module neuron_morphology.feature_extractor.marked_feature)
FeatureFormatter (class in neuron_morphology.feature_extractor.feature_writer)
FeatureOutputCheck (in module neuron_morphology.feature_extractor.feature_writer)
FeatureOutputHandler (in module neuron_morphology.feature_extractor.feature_writer)
FeatureSpecialization (class in neuron_morphology.feature_extractor.feature_specialization)
FeatureWriter (class in neuron_morphology.feature_extractor.feature_writer)
fill_gaps() (neuron_morphology.snap_polygons.geometries.Geometries method)
find_closest_path() (in module neuron_morphology.transforms.tilt_correction.compute_tilt_correction)
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)
focal_plane_image_series_id (neuron_morphology.snap_polygons._from_lims.FromLimsSchema attribute)
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)
FromLimsSchema (class in neuron_morphology.snap_polygons._from_lims)
FromLimsSource (class in neuron_morphology.snap_polygons._from_lims)
Fs (in module neuron_morphology.feature_extractor.feature_specialization)
G
generate_laplace_field() (in module neuron_morphology.transforms.streamline)
Geometric (class in neuron_morphology.feature_extractor.mark)
Geometries (class in neuron_morphology.snap_polygons.geometries)
get_all_intact_apical() (in module neuron_morphology.lims_apical_queries)
get_benchmark_apical() (in module neuron_morphology.lims_apical_queries)
get_bifurcation_coordinates() (in module neuron_morphology.features.statistics.coordinates)
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_coordinates() (in module neuron_morphology.features.statistics.coordinates)
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() (in module neuron_morphology.features.statistics.coordinates)
(neuron_morphology.features.statistics.coordinates.COORD_TYPE method)
get_credentials() (in module neuron_morphology.pipeline.post_data_to_s3)
get_data() (in module neuron_morphology.lims_apical_queries)
get_dict() (neuron_morphology.snap_polygons._from_lims.FromLimsSource method)
get_dimensions() (neuron_morphology.morphology.Morphology method)
get_inputs_from_lims() (in module neuron_morphology.snap_polygons._from_lims)
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_node_coordinates() (in module neuron_morphology.features.statistics.coordinates)
get_node_intersections() (in module neuron_morphology.layered_point_depths.__main__)
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_tilt_correction() (in module neuron_morphology.transforms.tilt_correction.compute_tilt_correction)
get_tip_coordinates() (in module neuron_morphology.features.statistics.coordinates)
get_tree_list() (neuron_morphology.morphology.Morphology method)
get_upright_angle() (in module neuron_morphology.transforms.upright_angle.compute_angle)
get_vertices_from_two_lines() (in module neuron_morphology.transforms.geometry)
global_parameters (neuron_morphology.feature_extractor._schemas.InputParameters attribute)
GlobalParameters (class in neuron_morphology.feature_extractor._schemas)
gradient_field_file (neuron_morphology.transforms.pia_wm_streamlines._schemas.OutputParameters attribute)
gradient_field_path (neuron_morphology.layered_point_depths._schemas.DepthField attribute)
gradient_path (neuron_morphology.transforms.upright_angle._schemas.InputParameters attribute)
H
handler (neuron_morphology.feature_extractor.feature_writer.FeatureFormatter attribute)
has_results() (neuron_morphology.validation.report.Report method)
has_subkey() (in module neuron_morphology.feature_extractor.feature_writer)
has_type() (neuron_morphology.morphology.Morphology method)
heavy_output_path (neuron_morphology.feature_extractor._schemas.InputParameters attribute)
height (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
histogram_earth_movers_distance() (in module neuron_morphology.features.layer.layer_histogram)
host (neuron_morphology.snap_polygons._from_lims.PostgresInputConfigSchema attribute)
hydrate_parameters() (in module neuron_morphology.feature_extractor.run_feature_extraction)
I
identifier (neuron_morphology.feature_extractor._schemas.Reconstruction attribute)
Image (class in neuron_morphology.snap_polygons._schemas)
image_output_root (neuron_morphology.snap_polygons._from_lims.FromLimsSchema attribute)
ImageOutputter (class in neuron_morphology.snap_polygons.image_outputter)
images (neuron_morphology.snap_polygons._schemas.InputParameters attribute)
(neuron_morphology.snap_polygons._schemas.OutputParameters attribute)
input_path (neuron_morphology.snap_polygons._schemas.Image attribute)
(neuron_morphology.snap_polygons._schemas.OutputImage attribute)
input_swc (neuron_morphology.transforms.affine_transformer._schemas.ApplyAffineSchema attribute)
InputParameters (class in neuron_morphology.feature_extractor._schemas)
(class in neuron_morphology.layered_point_depths._schemas)
(class in neuron_morphology.pipeline._schemas)
(class in neuron_morphology.snap_polygons._schemas)
(class in neuron_morphology.transforms.scale_correction._schemas)
(class in neuron_morphology.transforms.tilt_correction._schemas)
(class in neuron_morphology.transforms.upright_angle._schemas)
inputs (neuron_morphology.feature_extractor._schemas.OutputParameters attribute)
(neuron_morphology.layered_point_depths._schemas.OutputParameters attribute)
(neuron_morphology.snap_polygons._schemas.OutputParameters attribute)
(neuron_morphology.transforms.affine_transformer._schemas.OutputParameters attribute)
(neuron_morphology.transforms.pia_wm_streamlines._schemas.OutputParameters attribute)
(neuron_morphology.transforms.scale_correction._schemas.OutputParameters attribute)
(neuron_morphology.transforms.tilt_correction._schemas.OutputParameters attribute)
(neuron_morphology.transforms.upright_angle._schemas.OutputParameters attribute)
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)
is_valid() (neuron_morphology.feature_extractor._schemas.ReferenceLayerDepths class method)
item (in module neuron_morphology.feature_extractor.run_feature_extraction)
K
key (neuron_morphology.feature_extractor._schemas.ReferenceLayerDepths attribute)
known_feature_sets (in module neuron_morphology.feature_extractor.run_feature_extraction)
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
Layer (class in neuron_morphology.layered_point_depths._schemas)
layer_order (neuron_morphology.snap_polygons._schemas.InputParameters attribute)
layer_polygons (neuron_morphology.snap_polygons._schemas.InputParameters attribute)
layered_point_depths_path (neuron_morphology.feature_extractor._schemas.Reconstruction attribute)
LayeredPointDepths (class in neuron_morphology.features.layer.layered_point_depths)
LayerHistogram (class in neuron_morphology.features.layer.layer_histogram)
layers (neuron_morphology.layered_point_depths._schemas.InputParameters attribute)
level (neuron_morphology.validation.result.MarkerValidationError attribute)
(neuron_morphology.validation.result.NodeValidationError attribute)
LineType (in module neuron_morphology.snap_polygons.types)
logger (in module neuron_morphology.validation.validate_reconstruction)
M
M (in module neuron_morphology.feature_extractor.marked_feature)
main() (in module neuron_morphology.feature_extractor.__main__)
(in module neuron_morphology.layered_point_depths.__main__)
(in module neuron_morphology.pipeline.post_data_to_s3)
(in module neuron_morphology.snap_polygons.__main__)
(in module neuron_morphology.transforms.affine_transformer.apply_affine_transform)
(in module neuron_morphology.transforms.pia_wm_streamlines.calculate_pia_wm_streamlines)
(in module neuron_morphology.transforms.scale_correction.compute_scale_correction)
(in module neuron_morphology.transforms.tilt_correction.compute_tilt_correction)
(in module neuron_morphology.transforms.upright_angle.compute_angle)
(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)
marker_file (neuron_morphology.pipeline._schemas.InputParameters attribute)
marker_path (neuron_morphology.transforms.scale_correction._schemas.InputParameters attribute)
(neuron_morphology.transforms.tilt_correction._schemas.InputParameters attribute)
marker_validators (in module neuron_morphology.validation)
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.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)
max_branch_order() (in module neuron_morphology.features.intrinsic)
max_euclidean_distance() (in module neuron_morphology.features.size)
max_iter (neuron_morphology.layered_point_depths._schemas.InputParameters attribute)
max_path_distance() (in module neuron_morphology.features.path)
mean_bifurcation_angle_local() (in module neuron_morphology.features.branching.bifurcations)
mean_bifurcation_angle_remote() (in module neuron_morphology.features.branching.bifurcations)
mean_contraction() (in module neuron_morphology.features.path)
mean_diameter() (in module neuron_morphology.features.size)
mean_fragmentation() (in module neuron_morphology.features.intrinsic)
mean_parent_daughter_ratio() (in module neuron_morphology.features.size)
mesh_res (neuron_morphology.transforms.pia_wm_streamlines._schemas.PiaWmStreamlineSchema attribute)
message (neuron_morphology.validation.result.MarkerValidationError attribute)
(neuron_morphology.validation.result.NodeValidationError attribute)
midpoint() (neuron_morphology.morphology.Morphology static method)
moments() (in module neuron_morphology.features.statistics.moments)
moments_along_max_distance_projection() (in module neuron_morphology.features.statistics.moments_along_max_distance_projection)
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)
MorphologyLike (in module neuron_morphology.feature_extractor.data)
Mr (in module neuron_morphology.feature_extractor.mark)
multipolygon_error_threshold (neuron_morphology.snap_polygons._schemas.InputParameters attribute)
MultiPolygonResolverType (in module neuron_morphology.snap_polygons.types)
MultiSurfaceResolvertype (in module neuron_morphology.snap_polygons.types)
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.feature_writer.FeatureFormatter 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)
(neuron_morphology.layered_point_depths._schemas.Layer attribute)
(neuron_morphology.pipeline._schemas.S3LandingBucket attribute)
(neuron_morphology.snap_polygons._schemas.SimpleGeometry attribute)
names (neuron_morphology.feature_extractor._schemas.ReferenceLayerDepths attribute)
neighbors (neuron_morphology.transforms.upright_angle._schemas.InputParameters attribute)
nested_specialize() (in module neuron_morphology.feature_extractor.marked_feature)
NEURITE_COMPARISON_SPECIALIZATIONS (in module neuron_morphology.feature_extractor.feature_specialization)
NEURITE_SPECIALIZATIONS (in module neuron_morphology.feature_extractor.feature_specialization)
NeuriteTypeComparison (class in neuron_morphology.feature_extractor.mark)
neuron_morphology (module)
neuron_morphology.constants (module)
neuron_morphology.feature_extractor (module)
neuron_morphology.feature_extractor.__main__ (module)
neuron_morphology.feature_extractor._schemas (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.feature_writer (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.moments_along_max_distance_projection (module)
neuron_morphology.features.statistics.overlap (module)
neuron_morphology.layered_point_depths (module)
neuron_morphology.layered_point_depths.__main__ (module)
neuron_morphology.layered_point_depths._schemas (module)
neuron_morphology.lims_apical_queries (module)
neuron_morphology.marker (module)
neuron_morphology.morphology (module)
neuron_morphology.morphology_builder (module)
neuron_morphology.pipeline (module)
neuron_morphology.pipeline._schemas (module)
neuron_morphology.pipeline.post_data_to_s3 (module)
neuron_morphology.snap_polygons (module)
neuron_morphology.snap_polygons.__main__ (module)
neuron_morphology.snap_polygons._from_lims (module)
neuron_morphology.snap_polygons._schemas (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._schemas (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.pia_wm_streamlines._schemas (module)
neuron_morphology.transforms.pia_wm_streamlines.calculate_pia_wm_streamlines (module)
neuron_morphology.transforms.scale_correction (module)
neuron_morphology.transforms.scale_correction._schemas (module)
neuron_morphology.transforms.scale_correction.compute_scale_correction (module)
neuron_morphology.transforms.streamline (module)
neuron_morphology.transforms.tilt_correction (module)
neuron_morphology.transforms.tilt_correction._schemas (module)
neuron_morphology.transforms.tilt_correction.compute_tilt_correction (module)
neuron_morphology.transforms.transform_base (module)
neuron_morphology.transforms.upright_angle (module)
neuron_morphology.transforms.upright_angle._schemas (module)
neuron_morphology.transforms.upright_angle.compute_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)
neuron_reconstruction_id (neuron_morphology.pipeline._schemas.InputParameters attribute)
next_id (neuron_morphology.morphology_builder.MorphologyBuilder attribute)
NicePathType (in module neuron_morphology.snap_polygons.types)
NO_RECONSTRUCTION (in module neuron_morphology.constants)
NODE (neuron_morphology.features.statistics.coordinates.COORD_TYPE attribute)
node (neuron_morphology.transforms.upright_angle._schemas.InputParameters 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() (in module neuron_morphology.features.layer.layer_histogram)
normalized_depth_histogram_formatter (in module neuron_morphology.feature_extractor.feature_writer)
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)
num_branches() (in module neuron_morphology.features.intrinsic)
num_nodes() (in module neuron_morphology.features.intrinsic)
num_outer_bifurcations() (in module neuron_morphology.features.branching.bifurcations)
num_processes (neuron_morphology.feature_extractor._schemas.InputParameters attribute)
num_tips() (in module neuron_morphology.features.intrinsic)
numpy_array_formatter (in module neuron_morphology.feature_extractor.feature_writer)
O
OneEmpty (neuron_morphology.features.layer.layer_histogram.EarthMoversDistanceInterpretation attribute)
only_marks (neuron_morphology.feature_extractor._schemas.InputParameters attribute)
origin (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
output_dir (neuron_morphology.transforms.pia_wm_streamlines._schemas.PiaWmStreamlineSchema attribute)
output_path (neuron_morphology.layered_point_depths._schemas.InputParameters attribute)
(neuron_morphology.layered_point_depths._schemas.OutputParameters attribute)
(neuron_morphology.snap_polygons._schemas.Image attribute)
(neuron_morphology.snap_polygons._schemas.OutputImage attribute)
output_swc (neuron_morphology.transforms.affine_transformer._schemas.ApplyAffineSchema attribute)
output_table_path (neuron_morphology.feature_extractor._schemas.InputParameters attribute)
OutputImage (class in neuron_morphology.snap_polygons._schemas)
OutputParameters (class in neuron_morphology.feature_extractor._schemas)
(class in neuron_morphology.layered_point_depths._schemas)
(class in neuron_morphology.snap_polygons._schemas)
(class in neuron_morphology.transforms.affine_transformer._schemas)
(class in neuron_morphology.transforms.pia_wm_streamlines._schemas)
(class in neuron_morphology.transforms.scale_correction._schemas)
(class in neuron_morphology.transforms.tilt_correction._schemas)
(class in neuron_morphology.transforms.upright_angle._schemas)
overlap() (in module neuron_morphology.features.statistics.overlap)
overlay_type (neuron_morphology.snap_polygons._schemas.OutputImage attribute)
overlay_types (neuron_morphology.snap_polygons._schemas.Image 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)
password (neuron_morphology.snap_polygons._from_lims.PostgresInputConfigSchema attribute)
path (neuron_morphology.pipeline._schemas.PathResolution attribute)
(neuron_morphology.snap_polygons._schemas.SimpleGeometry attribute)
PathResolution (class in neuron_morphology.pipeline._schemas)
PathsType (in module neuron_morphology.snap_polygons.types)
PathType (in module neuron_morphology.snap_polygons.types)
Pia (neuron_morphology.pipeline._schemas.PrimaryBoundaries attribute)
pia_fixed_value (neuron_morphology.transforms.pia_wm_streamlines._schemas.PiaWmStreamlineSchema attribute)
pia_path_str (neuron_morphology.transforms.pia_wm_streamlines._schemas.PiaWmStreamlineSchema attribute)
pia_side (neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths attribute)
pia_sign (neuron_morphology.layered_point_depths._schemas.DepthField attribute)
pia_surface (neuron_morphology.layered_point_depths._schemas.Layer attribute)
(neuron_morphology.snap_polygons._schemas.InputParameters attribute)
PiaWmStreamlineSchema (class in neuron_morphology.transforms.pia_wm_streamlines._schemas)
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)
polygons (neuron_morphology.snap_polygons._schemas.OutputParameters attribute)
PolyType (in module neuron_morphology.snap_polygons.types)
port (neuron_morphology.snap_polygons._from_lims.PostgresInputConfigSchema attribute)
post_object_to_s3() (in module neuron_morphology.pipeline.post_data_to_s3)
PostgresInputConfigSchema (class in neuron_morphology.snap_polygons._from_lims)
primary_boundaries (neuron_morphology.pipeline._schemas.InputParameters attribute)
PrimaryBoundaries (class in neuron_morphology.pipeline._schemas)
process_earth_movers_distance() (in module neuron_morphology.feature_extractor.feature_writer)
process_feature() (neuron_morphology.feature_extractor.feature_writer.FeatureWriter method)
prune_two_lines() (in module neuron_morphology.transforms.geometry)
Q
query_for_cortical_surfaces() (in module neuron_morphology.snap_polygons._from_lims)
query_for_image_dims() (in module neuron_morphology.snap_polygons._from_lims)
query_for_images() (in module neuron_morphology.snap_polygons._from_lims)
query_for_layer_polygons() (in module neuron_morphology.snap_polygons._from_lims)
QueryEngineType (in module neuron_morphology.snap_polygons._from_lims)
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_soma_marker() (in module neuron_morphology.transforms.tilt_correction.compute_tilt_correction)
read_swc() (in module neuron_morphology.swc_io)
read_with_ndimage() (in module neuron_morphology.snap_polygons.image_outputter)
Reconstruction (class in neuron_morphology.feature_extractor._schemas)
reconstructions (neuron_morphology.feature_extractor._schemas.InputParameters attribute)
reference_layer_depths (neuron_morphology.feature_extractor._schemas.GlobalParameters attribute)
ReferenceLayerDepths (class in neuron_morphology.feature_extractor._schemas)
(class in neuron_morphology.features.layer.reference_layer_depths)
region (neuron_morphology.pipeline._schemas.S3LandingBucket attribute)
register_features() (neuron_morphology.feature_extractor.feature_extractor.FeatureExtractor method)
register_formatters() (neuron_morphology.feature_extractor.feature_writer.FeatureWriter 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)
RegistrableFeature (in module neuron_morphology.feature_extractor.feature_extractor)
remove_duplicates() (in module neuron_morphology.snap_polygons.cortex_surfaces)
Report (class in neuron_morphology.validation.report)
required_marks (neuron_morphology.feature_extractor._schemas.InputParameters attribute)
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)
resolution (neuron_morphology.pipeline._schemas.PathResolution attribute)
(neuron_morphology.transforms.pia_wm_streamlines._schemas.PiaWmStreamlineSchema attribute)
resolve_reference_layer_depths() (in module neuron_morphology.feature_extractor.run_feature_extraction)
result (neuron_morphology.features.layer.layer_histogram.EarthMoversDistanceResult attribute)
results (neuron_morphology.feature_extractor._schemas.OutputParameters 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_layered_point_depths() (in module neuron_morphology.layered_point_depths.__main__)
run_scale_correction() (in module neuron_morphology.transforms.scale_correction.compute_scale_correction)
run_snap_polygons() (in module neuron_morphology.snap_polygons.__main__)
run_streamlines() (in module neuron_morphology.transforms.pia_wm_streamlines.calculate_pia_wm_streamlines)
run_tilt_correction() (in module neuron_morphology.transforms.tilt_correction.compute_tilt_correction)
run_upright_angle() (in module neuron_morphology.transforms.upright_angle.compute_angle)
S
S3LandingBucket (class in neuron_morphology.pipeline._schemas)
safe_linemerge() (in module neuron_morphology.snap_polygons.geometries)
scale (neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths attribute)
scale_correction (neuron_morphology.transforms.scale_correction._schemas.OutputParameters attribute)
scale_transform (neuron_morphology.transforms.scale_correction._schemas.OutputParameters 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)
setup_interpolator() (in module neuron_morphology.layered_point_depths.__main__)
setup_layers() (in module neuron_morphology.layered_point_depths.__main__)
shared_faces() (in module neuron_morphology.snap_polygons.geometries)
SimpleGeometry (class in neuron_morphology.snap_polygons._schemas)
slice_image_flip (neuron_morphology.pipeline._schemas.InputParameters attribute)
(neuron_morphology.transforms.tilt_correction._schemas.InputParameters attribute)
slice_transform (neuron_morphology.pipeline._schemas.InputParameters attribute)
slice_transform_dict (neuron_morphology.transforms.tilt_correction._schemas.InputParameters attribute)
slice_transform_list (neuron_morphology.transforms.tilt_correction._schemas.InputParameters attribute)
slope_linear_regression_branch_order_avg_radius() (in module neuron_morphology.validation.radius_validation)
solve_laplace_2d() (in module neuron_morphology.transforms.streamline)
SOMA (in module neuron_morphology.constants)
Soma (neuron_morphology.pipeline._schemas.PrimaryBoundaries attribute)
soma_depth (neuron_morphology.transforms.scale_correction._schemas.InputParameters attribute)
soma_origin (neuron_morphology.layered_point_depths._schemas.DepthField attribute)
soma_path_str (neuron_morphology.transforms.pia_wm_streamlines._schemas.PiaWmStreamlineSchema attribute)
SPACING (in module neuron_morphology.constants)
SpecializationOption (in module neuron_morphology.feature_extractor.feature_specialization)
SpecializationSet (in module neuron_morphology.feature_extractor.feature_specialization)
SpecializationSets (in module neuron_morphology.feature_extractor.feature_specialization)
specialize() (in module neuron_morphology.feature_extractor.marked_feature)
(neuron_morphology.feature_extractor.marked_feature.MarkedFeature method)
specimen_id (neuron_morphology.pipeline._schemas.InputParameters attribute)
split_pathstring() (in module neuron_morphology.snap_polygons.types)
step (neuron_morphology.transforms.upright_angle._schemas.InputParameters attribute)
step_from_node() (in module neuron_morphology.layered_point_depths.__main__)
step_size (neuron_morphology.layered_point_depths._schemas.InputParameters attribute)
surface_distance_threshold (neuron_morphology.snap_polygons._schemas.InputParameters attribute)
surfaces (neuron_morphology.snap_polygons._schemas.OutputParameters attribute)
swap_nodes_edges() (neuron_morphology.morphology.Morphology method)
SWC_COLUMNS (in module neuron_morphology.swc_io)
swc_file (neuron_morphology.pipeline._schemas.InputParameters attribute)
swc_path (neuron_morphology.feature_extractor._schemas.Reconstruction attribute)
(neuron_morphology.layered_point_depths._schemas.InputParameters attribute)
(neuron_morphology.transforms.scale_correction._schemas.InputParameters attribute)
(neuron_morphology.transforms.tilt_correction._schemas.InputParameters attribute)
(neuron_morphology.transforms.upright_angle._schemas.InputParameters attribute)
swc_validators (in module neuron_morphology.validation)
T
thickness (neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths attribute)
tilt_correction (neuron_morphology.transforms.tilt_correction._schemas.OutputParameters attribute)
tilt_transform_dict (neuron_morphology.transforms.tilt_correction._schemas.OutputParameters 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)
total_length() (in module neuron_morphology.features.size)
total_surface_area() (in module neuron_morphology.features.size)
total_volume() (in module neuron_morphology.features.size)
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)
transformed_swc (neuron_morphology.transforms.affine_transformer._schemas.OutputParameters attribute)
TransformType (in module neuron_morphology.snap_polygons.types)
translate_field() (in module neuron_morphology.layered_point_depths.__main__)
translation (neuron_morphology.transforms.pia_wm_streamlines._schemas.OutputParameters attribute)
trim_coords() (in module neuron_morphology.snap_polygons.cortex_surfaces)
trim_to_close() (in module neuron_morphology.snap_polygons.cortex_surfaces)
tuplize() (in module neuron_morphology.layered_point_depths.__main__)
tvr_00 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_01 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_02 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_03 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_04 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_05 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_06 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_07 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_08 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_09 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_10 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
tvr_11 (neuron_morphology.transforms.affine_transformer._schemas.AffineDictSchema attribute)
TYPE_30 (in module neuron_morphology.constants)
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)
upright_angle (neuron_morphology.transforms.upright_angle._schemas.OutputParameters attribute)
upright_transform_dict (neuron_morphology.transforms.upright_angle._schemas.OutputParameters attribute)
user (neuron_morphology.snap_polygons._from_lims.PostgresInputConfigSchema attribute)
V
valid_dendrite_parent() (in module neuron_morphology.validation.type_validation)
valid_types (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_input_affine() (in module neuron_morphology.transforms.affine_transformer._schemas)
(in module neuron_morphology.transforms.tilt_correction._schemas)
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_neighbors() (in module neuron_morphology.transforms.upright_angle._schemas)
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_point_depths_path() (in module neuron_morphology.feature_extractor._schemas)
validate_radius_has_negative_slope_dendrite() (in module neuron_morphology.validation.radius_validation)
validate_radius_threshold() (in module neuron_morphology.validation.radius_validation)
validate_schema_input() (neuron_morphology.transforms.affine_transformer._schemas.ApplyAffineSchema method)
(neuron_morphology.transforms.tilt_correction._schemas.InputParameters method)
(neuron_morphology.transforms.upright_angle._schemas.InputParameters method)
validate_table_extension() (neuron_morphology.feature_extractor.feature_writer.FeatureWriter method)
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)
version_path (in module neuron_morphology)
W
well_known_marks (in module neuron_morphology.feature_extractor.run_feature_extraction)
WELL_KNOWN_REFERENCE_LAYER_DEPTHS (in module neuron_morphology.features.layer.reference_layer_depths)
White_Matter (neuron_morphology.pipeline._schemas.PrimaryBoundaries attribute)
width (neuron_morphology.snap_polygons.bounding_box.BoundingBox attribute)
wm_fixed_value (neuron_morphology.transforms.pia_wm_streamlines._schemas.PiaWmStreamlineSchema attribute)
wm_path_str (neuron_morphology.transforms.pia_wm_streamlines._schemas.PiaWmStreamlineSchema attribute)
wm_side (neuron_morphology.features.layer.reference_layer_depths.ReferenceLayerDepths attribute)
wm_surface (neuron_morphology.layered_point_depths._schemas.Layer attribute)
(neuron_morphology.snap_polygons._schemas.InputParameters attribute)
working_scale (neuron_morphology.snap_polygons._schemas.InputParameters attribute)
write() (neuron_morphology.feature_extractor.feature_writer.FeatureWriter method)
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)
write_table() (neuron_morphology.feature_extractor.feature_writer.FeatureWriter method)
Z
zip_files() (in module neuron_morphology.pipeline.post_data_to_s3)
neuron morphology
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