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.most_probable_neuron_path method) compute_all_costs_int() (brainlit.algorithms.connect_fragments.most_probable_neuron_path method) compute_all_dists() (brainlit.algorithms.connect_fragments.viterbi_algorithm method) compute_bounds() (brainlit.algorithms.connect_fragments.most_probable_neuron_path method) (brainlit.algorithms.connect_fragments.viterbi_algorithm method) confidence_connected_threshold() (in module brainlit.algorithms.generate_fragments) connected_threshold() (in module brainlit.algorithms.generate_fragments) connection_mat (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute)

continue_registration() (brainlit.registration.Transform method) contrast_normalize() (in module brainlit.preprocessing) conversion_time (brainlit.feature_extraction.NeighborhoodFeatures attribute) cost_mat_dist (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute) cost_mat_int (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute) create_nx_graph() (brainlit.algorithms.connect_fragments.most_probable_neuron_path method) 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)

E

end_points (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute)

endpoints_from_coords_neighbors() (brainlit.algorithms.connect_fragments.most_probable_neuron_path method)

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) frags_to_lines() (brainlit.algorithms.connect_fragments.most_probable_neuron_path method) frags_to_lines_le_skel() (brainlit.algorithms.connect_fragments.viterbi_algorithm 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

image (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute)

imagize_vector() (in module brainlit.preprocessing) input_type (brainlit.utils.NeuronTrace attribute)

L

label_points() (in module brainlit.preprocessing) labels (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute) level_set_seg() (in module brainlit.algorithms.generate_fragments) line_blob_dist() (brainlit.algorithms.connect_fragments.viterbi_algorithm method)

line_int() (brainlit.algorithms.connect_fragments.most_probable_neuron_path method) line_line_dist() (brainlit.algorithms.connect_fragments.viterbi_algorithm method) load() (brainlit.registration.Transform method) (in module brainlit.registration)

M

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

most_probable_neuron_path (class in brainlit.algorithms.connect_fragments)

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) not_lines (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute) num_components (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute)

O

offset (brainlit.feature_extraction.NeighborhoodFeatures attribute)

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

P

path (brainlit.utils.NeuronTrace attribute) path_cost() (brainlit.algorithms.connect_fragments.viterbi_algorithm method) point_blob_dist() (brainlit.algorithms.connect_fragments.most_probable_neuron_path method) point_point_dist() (brainlit.algorithms.connect_fragments.most_probable_neuron_path method) point_threshold() (in module brainlit.viz)

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) reset_dists() (brainlit.algorithms.connect_fragments.most_probable_neuron_path method) resolution (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute)

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) sigma (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute) size (brainlit.feature_extraction.NeighborhoodFeatures attribute) skeleton_threshold_intersect() (in module brainlit.viz)

skeletonize() (in module brainlit.viz) snap_points() (in module brainlit.viz) somas (brainlit.algorithms.connect_fragments.viterbi_algorithm attribute) speed() (in module brainlit.algorithms.trace_analysis) split_frags() (in module brainlit.preprocessing) split_frags_place_points() (in module brainlit.preprocessing) split_frags_split_comps() (in module brainlit.preprocessing) split_frags_split_fractured_components() (in module brainlit.preprocessing) ssd() (brainlit.utils.NeuronTrace static method)

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) viterbi_algorithm (class in brainlit.algorithms.connect_fragments)

viterbi_frag() (brainlit.algorithms.connect_fragments.viterbi_algorithm method) viterbi_frag_next_layer() (brainlit.algorithms.connect_fragments.viterbi_algorithm method)

W

whiten() (in module brainlit.preprocessing)

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