Index

A

args (brainlit.utils.NeuronTrace attribute)

B

Bresenham3D() (in module brainlit.viz)

C

center() (in module brainlit.preprocessing) chunk_size (brainlit.utils.NeuroglancerSession attribute) compute_all_costs_dist() (brainlit.algorithms.connect_fragments.ViterBrain method) compute_all_costs_int() (brainlit.algorithms.connect_fragments.ViterBrain method) compute_bfs() (brainlit.algorithms.generate_fragments.state_generation method) compute_edge_weights() (brainlit.algorithms.generate_fragments.state_generation method) compute_frags() (brainlit.algorithms.generate_fragments.state_generation method) (in module brainlit.preprocessing) compute_image_tiered() (brainlit.algorithms.generate_fragments.state_generation method) compute_soma_lbls() (brainlit.algorithms.generate_fragments.state_generation method)

compute_states() (brainlit.algorithms.generate_fragments.state_generation method) confidence_connected_threshold() (in module brainlit.algorithms.generate_fragments) connected_threshold() (in module brainlit.algorithms.generate_fragments) continue_registration() (brainlit.registration.Transform method) contrast_normalize() (in module brainlit.preprocessing) conversion_time (brainlit.feature_extraction.NeighborhoodFeatures attribute) create_tubes() (brainlit.utils.NeuroglancerSession method) curvature() (in module brainlit.algorithms.trace_analysis) cv (brainlit.utils.NeuroglancerSession attribute) cv_annotations (brainlit.utils.NeuroglancerSession attribute) cv_segments (brainlit.utils.NeuroglancerSession attribute)

D

df (brainlit.utils.NeuronTrace attribute)

download_time (brainlit.feature_extraction.NeighborhoodFeatures attribute)

F

fast_marching_seg() (in module brainlit.algorithms.generate_fragments) find_somas() (in module brainlit.algorithms.detect_somas)

fit_spline_tree_invariant() (brainlit.algorithms.trace_analysis.GeometricGraph method) frag_frag_dist() (brainlit.algorithms.connect_fragments.ViterBrain method) frag_soma_dist() (brainlit.algorithms.connect_fragments.ViterBrain method)

G

gabor_filter() (in module brainlit.preprocessing) generate_df_subset() (brainlit.utils.NeuronTrace method) GeometricGraph (class in brainlit.algorithms.trace_analysis) get_bfs_subgraph() (brainlit.utils.NeuronTrace method) get_df() (brainlit.utils.NeuronTrace method) get_df_arguments() (brainlit.utils.NeuronTrace method) get_df_voxel() (brainlit.utils.NeuronTrace method) get_graph() (brainlit.utils.NeuronTrace method) get_img_T1() (in module brainlit.algorithms.generate_fragments)

get_lddmm_dict() (brainlit.registration.Transform method) get_paths() (brainlit.utils.NeuronTrace method) get_seed() (in module brainlit.algorithms.generate_fragments) get_segments() (brainlit.utils.NeuroglancerSession method) get_skel() (brainlit.utils.NeuronTrace method) get_sub_neuron() (brainlit.utils.NeuronTrace method) get_sub_neuron_paths() (brainlit.utils.NeuronTrace method) getLargestCC() (in module brainlit.preprocessing) gmm_seg() (in module brainlit.algorithms.generate_fragments)

H

heatslices() (in module brainlit.registration)

I

imagize_vector() (in module brainlit.preprocessing)

input_type (brainlit.utils.NeuronTrace attribute)

L

label_points() (in module brainlit.preprocessing) level_set_seg() (in module brainlit.algorithms.generate_fragments)

load() (brainlit.registration.Transform method) (in module brainlit.registration)

M

mip (brainlit.utils.NeuroglancerSession attribute) (brainlit.utils.NeuronTrace attribute)

N

neighborhood_connected_threshold() (in module brainlit.algorithms.generate_fragments) NeighborhoodFeatures (class in brainlit.feature_extraction)

NeuroglancerSession (class in brainlit.utils) NeuronTrace (class in brainlit.utils)

O

offset (brainlit.feature_extraction.NeighborhoodFeatures attribute)

otsu() (in module brainlit.algorithms.generate_fragments)

P

path (brainlit.utils.NeuronTrace attribute) point_threshold() (in module brainlit.viz) predict() (brainlit.algorithms.generate_fragments.state_generation method) pull_bounds_img() (brainlit.utils.NeuroglancerSession method)

pull_bounds_seg() (brainlit.utils.NeuroglancerSession method) pull_chunk() (brainlit.utils.NeuroglancerSession method) pull_vertex_list() (brainlit.utils.NeuroglancerSession method) pull_voxel() (brainlit.utils.NeuroglancerSession method) push() (brainlit.utils.NeuroglancerSession method)

R

register() (brainlit.registration.Transform method) remove_somas() (in module brainlit.preprocessing)

removeSmallCCs() (in module brainlit.preprocessing) rename_states_consecutively() (in module brainlit.preprocessing)

S

save() (brainlit.registration.Transform method) (in module brainlit.registration) scales (brainlit.utils.NeuroglancerSession attribute) seg_id (brainlit.utils.NeuronTrace attribute) segment_url (brainlit.feature_extraction.NeighborhoodFeatures attribute) set_url_segments() (brainlit.utils.NeuroglancerSession method) shortest_path() (brainlit.algorithms.connect_fragments.ViterBrain method)

size (brainlit.feature_extraction.NeighborhoodFeatures attribute) skeleton_threshold_intersect() (in module brainlit.viz) skeletonize() (in module brainlit.viz) snap_points() (in module brainlit.viz) speed() (in module brainlit.algorithms.trace_analysis) ssd() (brainlit.utils.NeuronTrace static method) state_generation (class in brainlit.algorithms.generate_fragments)

T

thres_from_gmm() (in module brainlit.algorithms.generate_fragments) torsion() (in module brainlit.algorithms.trace_analysis)

Transform (class in brainlit.registration) transform_image() (brainlit.registration.Transform method) transform_points() (brainlit.registration.Transform method)

U

undo_pad() (in module brainlit.preprocessing) url (brainlit.feature_extraction.NeighborhoodFeatures attribute) (brainlit.utils.NeuroglancerSession attribute)

url_segments (brainlit.utils.NeuroglancerSession attribute)

V

vectorize_img() (in module brainlit.preprocessing)

ViterBrain (class in brainlit.algorithms.connect_fragments)

W

whiten() (in module brainlit.preprocessing)

window_pad() (in module brainlit.preprocessing) write_time (brainlit.feature_extraction.NeighborhoodFeatures attribute)