Index

A

apply_affine() (brainlit.map_neurons.CloudReg_Transform method) apply_ilastik_parallel() (brainlit.BrainLine.ApplyIlastik_LargeImage method) ApplyIlastik (class in brainlit.BrainLine) ApplyIlastik_LargeImage (class in brainlit.BrainLine)

args (brainlit.utils.NeuronTrace attribute) atlas_points (brainlit.BrainLine.SomaDistribution attribute) axis (brainlit.algorithms.trace_analysis.CubicHermiteChain attribute) AxonDistribution (class in brainlit.BrainLine)

B

brain2paths (brainlit.BrainLine.AxonDistribution attribute) (brainlit.BrainLine.SomaDistribution attribute) brainrender_axons() (brainlit.BrainLine.AxonDistribution method)

brainrender_somas() (brainlit.BrainLine.SomaDistribution method) brains (brainlit.BrainLine.ApplyIlastik attribute) brains_path (brainlit.BrainLine.ApplyIlastik attribute) Bresenham3D() (in module brainlit.viz)

C

center() (in module brainlit.preprocessing) chunk_size (brainlit.utils.NeuroglancerSession attribute) CloudReg_Transform (class in brainlit.map_neurons) collect_axon_results() (brainlit.BrainLine.ApplyIlastik_LargeImage method) collect_soma_results() (brainlit.BrainLine.ApplyIlastik_LargeImage method) 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_parameterization() (in module brainlit.algorithms.trace_analysis) compute_soma_lbls() (brainlit.algorithms.generate_fragments.state_generation method) compute_states() (brainlit.algorithms.generate_fragments.state_generation method) contrast_normalize() (in module brainlit.preprocessing) conversion_time (brainlit.feature_extraction.NeighborhoodFeatures attribute) create_tubes() (brainlit.utils.NeuroglancerSession method) CubicHermiteChain (class in brainlit.algorithms.trace_analysis) curvature() (in module brainlit.algorithms.trace_analysis) cv (brainlit.utils.NeuroglancerSession attribute) cv_annotations (brainlit.utils.NeuroglancerSession attribute) cv_segments (brainlit.utils.NeuroglancerSession attribute) czi_to_zarr() (in module brainlit.utils)

D

D() (brainlit.map_neurons.CloudReg_Transform method) (brainlit.map_neurons.Diffeomorphism_Transform method) (brainlit.map_neurons.DiffeomorphismAction method) df (brainlit.utils.NeuronTrace attribute)

diffeo_gen_ara() (in module brainlit.map_neurons) Diffeomorphism_Transform (class in brainlit.map_neurons) DiffeomorphismAction (class in brainlit.map_neurons) download_subvolumes() (in module brainlit.BrainLine) download_time (brainlit.feature_extraction.NeighborhoodFeatures attribute)

E

evaluate() (brainlit.map_neurons.CloudReg_Transform method) (brainlit.map_neurons.Diffeomorphism_Transform method) (brainlit.map_neurons.DiffeomorphismAction method)

examine_threshold() (in module brainlit.BrainLine)

F

fg_channel (brainlit.algorithms.generate_fragments.state_generation attribute) find_somas() (in module brainlit.algorithms.detect_somas)

fit_spline_tree_invariant() (brainlit.algorithms.trace_analysis.GeometricGraph method) frag_soma_dist() (brainlit.algorithms.connect_fragments.ViterBrain method) fragment_path (brainlit.algorithms.generate_fragments.state_generation attribute)

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_data_ranges() (in module brainlit.utils) 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_paths() (brainlit.utils.NeuronTrace method) 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)

I

id_to_regioncounts (brainlit.BrainLine.SomaDistribution attribute) ilastik_program_path (brainlit.algorithms.generate_fragments.state_generation attribute) ilastik_project (brainlit.BrainLine.ApplyIlastik_LargeImage attribute) ilastik_project_path (brainlit.algorithms.generate_fragments.state_generation attribute) ilastk_path (brainlit.BrainLine.ApplyIlastik attribute) (brainlit.BrainLine.ApplyIlastik_LargeImage attribute)

image_chunks (brainlit.algorithms.generate_fragments.state_generation attribute) image_path (brainlit.algorithms.generate_fragments.state_generation attribute) image_shape (brainlit.algorithms.generate_fragments.state_generation attribute) imagize_vector() (in module brainlit.preprocessing) input_type (brainlit.utils.NeuronTrace attribute)

J

Jacobian() (brainlit.map_neurons.CloudReg_Transform method) (brainlit.map_neurons.Diffeomorphism_Transform method)

json_to_points() (in module brainlit.BrainLine)

L

label_points() (in module brainlit.preprocessing)

M

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

move_results() (brainlit.BrainLine.ApplyIlastik method)

N

napari_coronal_section() (brainlit.BrainLine.AxonDistribution method) (brainlit.BrainLine.SomaDistribution method) ncpu (brainlit.BrainLine.ApplyIlastik_LargeImage attribute)

NeighborhoodFeatures (class in brainlit.feature_extraction) NeuroglancerSession (class in brainlit.utils) NeuronTrace (class in brainlit.utils) new_layers_dir (brainlit.algorithms.generate_fragments.state_generation attribute)

O

object_type (brainlit.BrainLine.ApplyIlastik_LargeImage attribute)

offset (brainlit.feature_extraction.NeighborhoodFeatures attribute)

P

parallel (brainlit.algorithms.generate_fragments.state_generation attribute) path (brainlit.utils.NeuronTrace attribute) plot_results() (in module brainlit.BrainLine) predict() (brainlit.algorithms.generate_fragments.state_generation method) prob_path (brainlit.algorithms.generate_fragments.state_generation attribute) process_subvols() (brainlit.BrainLine.ApplyIlastik method)

project_path (brainlit.BrainLine.ApplyIlastik attribute) 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

region_barchart() (brainlit.BrainLine.AxonDistribution method) (brainlit.BrainLine.SomaDistribution method) region_graph (brainlit.BrainLine.AxonDistribution attribute) (brainlit.BrainLine.SomaDistribution attribute) regional_distribution_dir (brainlit.BrainLine.AxonDistribution attribute) remove_somas() (in module brainlit.preprocessing)

removed_duplicates (brainlit.algorithms.trace_analysis.GeometricGraph attribute) removeSmallCCs() (in module brainlit.preprocessing) rename_states_consecutively() (in module brainlit.preprocessing) resolution (brainlit.algorithms.generate_fragments.state_generation attribute) results_dir (brainlit.BrainLine.ApplyIlastik_LargeImage attribute) root (brainlit.algorithms.trace_analysis.GeometricGraph attribute)

S

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) show_plots (brainlit.BrainLine.AxonDistribution attribute) (brainlit.BrainLine.SomaDistribution attribute) size (brainlit.feature_extraction.NeighborhoodFeatures attribute)

skeletonize() (in module brainlit.viz) soma_coords (brainlit.algorithms.generate_fragments.state_generation attribute) SomaDistribution (class in brainlit.BrainLine) speed() (in module brainlit.algorithms.trace_analysis) spline_tree (brainlit.algorithms.trace_analysis.GeometricGraph attribute) spline_type (brainlit.algorithms.trace_analysis.GeometricGraph attribute) ssd() (brainlit.utils.NeuronTrace static method) state_generation (class in brainlit.algorithms.generate_fragments) states_path (brainlit.algorithms.generate_fragments.state_generation attribute)

T

tiered_path (brainlit.algorithms.generate_fragments.state_generation attribute)

torsion() (in module brainlit.algorithms.trace_analysis) total_axon_vols (brainlit.BrainLine.AxonDistribution attribute)

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)

Z

zarr_to_omezarr() (in module brainlit.utils)