navis
1.6.0
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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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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X
_
__init__() (navis.Dotprops method)
(navis.interfaces.blender.Handler method)
(navis.interfaces.neuron.comp.CompartmentModel method)
(navis.interfaces.neuron.comp.DrosophilaPN method)
(navis.interfaces.neuron.network.PointNetwork method)
,
[1]
(navis.interfaces.r.NBLASTresults method)
,
[1]
(navis.MeshNeuron method)
(navis.models.network_models.BayesianTraversalModel method)
(navis.models.network_models.TraversalModel method)
(navis.nbl.smat.Digitizer method)
(navis.nbl.smat.Lookup2d method)
(navis.nbl.smat.LookupDistDotBuilder method)
(navis.NeuronConnector method)
(navis.NeuronList method)
(navis.transforms.affine.AffineTransform method)
(navis.transforms.AffineTransform method)
(navis.transforms.AliasTransform method)
(navis.transforms.cmtk.CMTKtransform method)
(navis.transforms.CMTKtransform method)
(navis.transforms.ElastixTransform method)
(navis.transforms.h5reg.H5transform method)
(navis.transforms.H5transform method)
(navis.transforms.MovingLeastSquaresTransform method)
(navis.transforms.templates.TemplateRegistry method)
(navis.transforms.thinplate.TPStransform method)
(navis.transforms.TPStransform method)
(navis.TreeNeuron method)
(navis.Viewer method)
,
[1]
(navis.Volume method)
,
[1]
(navis.VoxelNeuron method)
A
abutting (navis.interfaces.blender.Handler attribute)
add() (navis.interfaces.blender.Handler method)
(navis.Viewer method)
add_background_noise() (navis.interfaces.neuron.network.PointNetwork method)
add_current_record() (navis.interfaces.neuron.comp.CompartmentModel method)
add_neurons() (navis.interfaces.neuron.network.PointNetwork method)
add_spike_detector() (navis.interfaces.neuron.comp.CompartmentModel method)
add_stimulus() (navis.interfaces.neuron.network.PointNetwork method)
add_synaptic_current() (navis.interfaces.neuron.comp.CompartmentModel method)
add_synaptic_input() (navis.interfaces.neuron.comp.CompartmentModel method)
add_voltage_record() (navis.interfaces.neuron.comp.CompartmentModel method)
AffineTransform (class in navis.transforms)
(class in navis.transforms.affine)
AliasTransform (class in navis.transforms)
all (navis.interfaces.blender.Handler attribute)
alpha (navis.Dotprops property)
alpha() (navis.interfaces.blender.Handler method)
(navis.interfaces.blender.ObjectList method)
apply() (navis.NeuronList method)
arbor_segregation_index() (in module navis)
authenticate() (in module navis.interfaces.insectbrain_db)
average_skeletons() (in module navis)
B
BayesianTraversalModel (class in navis.models.network_models)
bbox (navis.NeuronList property)
bending_flow() (in module navis)
betweeness_centrality() (in module navis)
bevel() (navis.interfaces.blender.Handler method)
(navis.interfaces.blender.ObjectList method)
break_fragments() (in module navis)
bridges (navis.transforms.templates.TemplateRegistry property)
C
cable_length (navis.TreeNeuron property)
cable_overlap() (in module navis)
cell_body_fiber() (in module navis)
(navis.TreeNeuron method)
clear() (navis.interfaces.blender.Handler method)
(navis.Viewer method)
clear3d() (in module navis)
,
[1]
clear_caches() (navis.transforms.templates.TemplateRegistry method)
clear_records() (navis.interfaces.neuron.comp.CompartmentModel method)
clear_stimuli() (navis.interfaces.neuron.comp.CompartmentModel method)
close() (navis.Viewer method)
close3d() (in module navis)
,
[1]
CMTKtransform (class in navis.transforms)
(class in navis.transforms.cmtk)
color() (navis.interfaces.blender.Handler method)
(navis.interfaces.blender.ObjectList method)
colorize() (navis.interfaces.blender.Handler method)
(navis.interfaces.blender.ObjectList method)
(navis.Viewer method)
combine() (navis.Volume class method)
combine_neurons() (in module navis)
CompartmentModel (class in navis.interfaces.neuron.comp)
compress_scores() (in module navis.nbl)
connect() (navis.interfaces.neuron.comp.CompartmentModel method)
(navis.interfaces.neuron.network.PointNetwork method)
connectivity_similarity() (in module navis)
connectivity_sparseness() (in module navis)
connectors (navis.BaseNeuron property)
(navis.interfaces.blender.Handler attribute)
convert_units() (navis.BaseNeuron method)
(navis.TreeNeuron method)
copy() (navis.BaseNeuron method)
cut_skeleton() (in module navis)
cycles (navis.TreeNeuron property)
D
data2py() (in module navis.interfaces.r)
datatables (navis.BaseNeuron property)
date (navis.interfaces.r.NBLASTresults attribute)
,
[1]
delete() (navis.interfaces.blender.ObjectList method)
despike_skeleton() (in module navis)
Digitizer (class in navis.nbl.smat)
dist_between() (in module navis)
dist_to_root() (in module navis)
distal_to() (in module navis)
Dotprops (class in navis)
downsample() (navis.TreeNeuron method)
downsample_neuron() (in module navis)
drop_fluff() (in module navis)
DrosophilaPN (class in navis.interfaces.neuron.comp)
E
edges (navis.interfaces.neuron.network.PointNetwork property)
ElastixTransform (class in navis.transforms)
emit() (navis.interfaces.blender.Handler method)
(navis.interfaces.blender.ObjectList method)
empty (navis.NeuronList property)
example_neurons() (in module navis)
example_volume() (in module navis)
extract_matches() (in module navis.nbl)
F
faces (navis.MeshNeuron property)
fetch_mesh_neuron() (in module navis.interfaces.neuprint)
fetch_neurons() (in module navis.interfaces.microns)
fetch_roi() (in module navis.interfaces.neuprint)
fetch_skeletons() (in module navis.interfaces.neuprint)
find_bridging_path() (navis.transforms.templates.TemplateRegistry method)
find_main_branchpoint() (in module navis)
find_mirror_reg() (navis.transforms.templates.TemplateRegistry method)
flow_centrality() (in module navis)
form_factor() (in module navis)
from_edge_list() (navis.interfaces.neuron.network.PointNetwork class method)
G
gapjunctions (navis.interfaces.blender.Handler attribute)
generate_network() (in module navis.interfaces.cytoscape)
,
[1]
geodesic_matrix() (in module navis)
get_available_field_values() (in module navis.interfaces.neuromorpho)
get_available_species() (in module navis.interfaces.insectbrain_db)
get_brain_meshes() (in module navis.interfaces.insectbrain_db)
get_client() (in module navis.interfaces.cytoscape)
,
[1]
get_graph_nx() (navis.TreeNeuron method)
get_igraph() (navis.TreeNeuron method)
get_neuron() (in module navis.interfaces.neuromorpho)
get_neuron_fields() (in module navis.interfaces.neuromorpho)
get_neuron_info() (in module navis.interfaces.neuromorpho)
get_neuropil() (in module navis.interfaces.r)
get_node_section() (navis.interfaces.neuron.comp.CompartmentModel method)
get_node_segment() (navis.interfaces.neuron.comp.CompartmentModel method)
get_skeletons() (in module navis.interfaces.insectbrain_db)
get_skeletons_species() (in module navis.interfaces.insectbrain_db)
get_somas() (in module navis.interfaces.microns)
get_species_info() (in module navis.interfaces.insectbrain_db)
get_spike_counts() (navis.interfaces.neuron.network.PointNetwork method)
get_viewer() (in module navis)
,
[1]
grid (navis.VoxelNeuron property)
guess_radius() (in module navis)
H
H5transform (class in navis.transforms)
(class in navis.transforms.h5reg)
Handler (class in navis.interfaces.blender)
head() (navis.NeuronList method)
heal_skeleton() (in module navis)
health_check() (in module navis)
hide() (navis.interfaces.blender.Handler method)
(navis.interfaces.blender.ObjectList method)
hide_neurons() (navis.Viewer method)
hide_others() (navis.interfaces.blender.ObjectList method)
I
id (navis.BaseNeuron property)
ids (navis.interfaces.neuron.network.PointNetwork property)
igraph (navis.TreeNeuron property)
in_volume() (in module navis)
init_rcatmaid() (in module navis.interfaces.r)
inject_current_pulse() (navis.interfaces.neuron.comp.CompartmentModel method)
insert() (navis.interfaces.neuron.comp.CompartmentModel method)
insert_nodes() (in module navis)
intersection_matrix() (in module navis)
is_degenerated (navis.NeuronList property)
is_mixed (navis.NeuronList property)
is_tree (navis.TreeNeuron property)
itertuples() (navis.NeuronList method)
L
labels (navis.interfaces.neuron.network.PointNetwork property)
legend_font_size (navis.Viewer attribute)
,
[1]
load_rda() (in module navis.interfaces.r)
longest_neurite() (in module navis)
Lookup2d (class in navis.nbl.smat)
LookupDistDotBuilder (class in navis.nbl.smat)
M
make_clusters() (in module navis.nbl)
make_dotprops() (in module navis)
,
[1]
map_units() (navis.BaseNeuron method)
mean() (navis.NeuronList method)
memory_usage() (navis.BaseNeuron method)
mesh() (in module navis)
,
[1]
MeshNeuron (class in navis)
mirror() (in module navis.transforms)
mirror_brain() (in module navis)
(in module navis.interfaces.r)
mirrors (navis.transforms.templates.TemplateRegistry property)
MovingLeastSquaresTransform (class in navis.transforms)
N
n_branches (navis.TreeNeuron property)
n_leafs (navis.TreeNeuron property)
n_skeletons (navis.TreeNeuron property)
n_trees (navis.TreeNeuron property)
name (navis.BaseNeuron property)
nblast() (in module navis)
(in module navis.interfaces.r)
,
[1]
nblast_align() (in module navis)
nblast_allbyall() (in module navis)
(in module navis.interfaces.r)
,
[1]
nblast_smart() (in module navis)
NBLASTresults (class in navis.interfaces.r)
,
[1]
network2igraph() (in module navis)
network2nx() (in module navis)
neuron2igraph() (in module navis)
neuron2KDTree() (in module navis)
neuron2nx() (in module navis)
neuron2py() (in module navis.interfaces.r)
neuron2r() (in module navis.interfaces.r)
NeuronConnector (class in navis)
NeuronList (class in navis)
neurons (navis.interfaces.blender.Handler attribute)
(navis.interfaces.neuron.network.PointNetwork property)
nodes (navis.TreeNeuron property)
P
param (navis.interfaces.r.NBLASTresults attribute)
,
[1]
patch_cloudvolume() (in module navis)
persistence_distances() (in module navis)
persistence_points() (in module navis)
persistence_vectors() (in module navis)
picking (navis.Viewer attribute)
,
[1]
plot1d() (in module navis)
,
[1]
plot2d() (in module navis)
,
[1]
(navis.BaseNeuron method)
plot3d() (in module navis)
,
[1]
(navis.BaseNeuron method)
(navis.Volume method)
plot_bridging_graph() (navis.transforms.templates.TemplateRegistry method)
plot_flat() (in module navis)
,
[1]
plot_raster() (navis.interfaces.neuron.network.PointNetwork method)
plot_results() (navis.interfaces.neuron.comp.CompartmentModel method)
plot_traces() (navis.interfaces.neuron.network.PointNetwork method)
PointNetwork (class in navis.interfaces.neuron.network)
points (navis.Dotprops property)
pop3d() (in module navis)
postsynapses (navis.BaseNeuron property)
(navis.interfaces.blender.Handler attribute)
presynapses (navis.BaseNeuron property)
(navis.interfaces.blender.Handler attribute)
prune_at_depth() (in module navis)
prune_by_longest_neurite() (navis.TreeNeuron method)
prune_by_strahler() (in module navis)
(navis.TreeNeuron method)
prune_by_volume() (navis.TreeNeuron method)
prune_distal_to() (navis.TreeNeuron method)
prune_proximal_to() (navis.TreeNeuron method)
prune_twigs() (in module navis)
(navis.TreeNeuron method)
Q
query (navis.interfaces.r.NBLASTresults attribute)
,
[1]
R
read_json() (in module navis)
read_mesh() (in module navis)
read_nml() (in module navis)
read_nmx() (in module navis)
read_nrrd() (in module navis)
read_parquet() (in module navis)
read_precomputed() (in module navis)
read_rda() (in module navis)
read_swc() (in module navis)
read_tiff() (in module navis)
register_path() (navis.transforms.templates.TemplateRegistry method)
register_templatebrain() (navis.transforms.templates.TemplateRegistry method)
register_transform() (navis.transforms.templates.TemplateRegistry method)
register_transformfile() (navis.transforms.templates.TemplateRegistry method)
reload() (navis.TreeNeuron method)
remove_duplicates() (navis.NeuronList method)
remove_log_handlers() (in module navis.config)
remove_nodes() (in module navis)
reroot() (navis.TreeNeuron method)
reroot_skeleton() (in module navis)
resample() (navis.TreeNeuron method)
resample_along_axis() (in module navis)
resample_skeleton() (in module navis)
resize() (navis.Volume method)
results (navis.interfaces.r.NBLASTresults attribute)
,
[1]
rewire_skeleton() (in module navis)
root (navis.TreeNeuron property)
run_simulation() (navis.interfaces.neuron.network.PointNetwork method)
S
sampling_resolution (navis.MeshNeuron property)
(navis.TreeNeuron property)
sc (navis.interfaces.r.NBLASTresults attribute)
,
[1]
scan_parquet() (in module navis)
scan_paths() (navis.transforms.templates.TemplateRegistry method)
scr (navis.interfaces.r.NBLASTresults attribute)
,
[1]
screenshot() (in module navis)
,
[1]
(navis.Viewer method)
search_neurons() (in module navis.interfaces.insectbrain_db)
segment_analysis() (in module navis)
segment_length() (in module navis)
segments (navis.TreeNeuron property)
segregation_index() (in module navis)
select() (navis.interfaces.blender.Handler method)
(navis.interfaces.blender.ObjectList method)
selected (navis.interfaces.blender.Handler attribute)
(navis.Viewer attribute)
,
[1]
set_colors() (navis.Viewer method)
set_default_connector_colors() (in module navis)
set_labels() (navis.interfaces.neuron.network.PointNetwork method)
set_loggers() (in module navis)
set_pbars() (in module navis)
shape (navis.NeuronList property)
(navis.VoxelNeuron property)
sholl_analysis() (in module navis)
shortest_bridging_seq() (navis.transforms.templates.TemplateRegistry method)
show() (navis.Viewer method)
show_legend (navis.Viewer attribute)
,
[1]
simple (navis.TreeNeuron property)
simplify_mesh() (in module navis)
skeletonize() (in module navis)
,
[1]
(navis.MeshNeuron method)
smooth_mesh() (in module navis)
smooth_skeleton() (in module navis)
smooth_voxels() (in module navis)
snap() (navis.Dotprops method)
(navis.MeshNeuron method)
(navis.TreeNeuron method)
soma (navis.interfaces.blender.Handler attribute)
soma_pos (navis.TreeNeuron property)
split_axon_dendrite() (in module navis)
split_into_fragments() (in module navis)
stitch_skeletons() (in module navis)
strahler_index() (in module navis)
strip() (navis.VoxelNeuron method)
subset_neuron() (in module navis)
subtrees (navis.TreeNeuron property)
sum() (navis.NeuronList method)
summary() (navis.BaseNeuron method)
(navis.NeuronList method)
(navis.transforms.templates.TemplateRegistry method)
symmetrize_brain() (in module navis)
synapse_flow_centrality() (in module navis)
synapse_similarity() (in module navis)
synblast() (in module navis)
T
tail() (navis.NeuronList method)
target (navis.interfaces.r.NBLASTresults attribute)
,
[1]
TemplateRegistry (class in navis.transforms.templates)
to_skeleton() (navis.Dotprops method)
toggle_bounds() (navis.Viewer method)
tortuosity() (in module navis)
TPStransform (class in navis.transforms)
(class in navis.transforms.thinplate)
transforms (navis.transforms.templates.TemplateRegistry property)
TraversalModel (class in navis.models.network_models)
tree2meshneuron() (in module navis.conversion)
TreeNeuron (class in navis)
trimesh (navis.MeshNeuron property)
type (navis.BaseNeuron property)
types (navis.NeuronList property)
U
unhide() (navis.interfaces.blender.Handler method)
(navis.interfaces.blender.ObjectList method)
unhide_neurons() (navis.Viewer method)
uninsert() (navis.interfaces.neuron.comp.CompartmentModel method)
units (navis.BaseNeuron property)
unmix() (navis.NeuronList method)
update_scores() (in module navis.nbl)
use_transparency() (navis.interfaces.blender.Handler method)
(navis.interfaces.blender.ObjectList method)
V
validate() (navis.MeshNeuron method)
(navis.Volume method)
vect (navis.Dotprops property)
vertices (navis.MeshNeuron property)
Viewer (class in navis)
,
[1]
Volume (class in navis)
,
[1]
volume (navis.MeshNeuron property)
(navis.TreeNeuron property)
voxelize() (in module navis)
,
[1]
VoxelNeuron (class in navis)
voxels (navis.VoxelNeuron property)
voxels2mesh() (in module navis.conversion)
W
write_json() (in module navis)
write_mesh() (in module navis)
write_nrrd() (in module navis)
write_parquet() (in module navis)
write_precomputed() (in module navis)
write_swc() (in module navis)
X
xform() (in module navis)
xform_brain() (in module navis)
(in module navis.interfaces.r)