Function reference • hemibrainr

Package Help Provides an overview of the package
`hemibrainr-package`	hemibrainr: Code for Working with Data from Janelia FlyEM's Hemibrain Project``
General skeleton functions
`hemibrain_read_neurons()` `scale_neurons()` `hemibrain_neurons()`	Read neurons from the hemibrain connectome project
`hemibrain_download_neurons()`	Download all automatically split neurons from the hemibrain project
`primary_neurite()` `primary_branchpoint()`	Retrieve the primary neurite (cell body fibre) for a neuron
`hemibrain_skeleton_check()`	Pre-process hemibrain skeletons
`hemibrain_overlap_locality()`	Calculate the overlap score between a neurons axon dendrite
`prune_vertices.neuprintneuron()`	Prune vertices from a neuprint neuron (taking care of synapse etc information)
`hemibrain_clean_skeleton()`	Remove erroneous branchlets to beautify neuron skeletons
Neuronal compartments (axons, dendrites)
`flow_centrality()`	Determine a neuron's dendrite and axon by calculating flow centrality
`plot3d_split()` `nlscan_split()` `plot3d_somas()`	Plot neurons split up by flow centrality
`axonic_points()` `dendritic_points()` `mixed_points()` `primary_dendrite_points()` `primary_neurite_points()` `axonal_endings()` `dendritic_endings()` `axonic_endings()` `primary_dendrite_endings()` `primary_neurite_endings()` `axonic_cable()` `dendritic_cable()` `arbour_cable()` `unsure_cable()` `primary_dendrite_cable()` `primary_neurite_cable()` `tract_cable()`	Extract axonic/dendritic points/cable from a neuron/neuronlist
`hemibrain_flow_centrality()`	Split neurons into axon and dendrites using pre-computed split points
`hemibrain_splitpoints()`	Get the positions of key points in a 'split' neuron
`hemibrain_use_splitpoints()`	Split a neuron using stored 'splitpoints'
`hemibrain_compartment_metrics()`	Get useful metrics for each neuron's axon and dendrite
`hemibrain_metrics` `hemibrain_metrics_polypre_centrifugal_distance` `hemibrain_metrics_polypre_centrifugal_synapses`	Neuron metrics for all neurons in the hemibrain dataset
`hemibrain_all_splitpoints` `hemibrain_splitpoints_polypre_centrifugal_distance` `hemibrain_splitpoints_pre_centrifugal_distance` `hemibrain_splitpoints_polypre_centrifugal_synapses`	Axon-dendrite split points calculated for all hemibrain neurons
`manually_assign_labels()` `hemibrain_prune_online()` `hemibrain_correctsoma()`	Manually assign the dendrite and axon to a neuron
Somas and lineages
`hemibrain_somas`	Soma / best 'root point' locations for hemibrain neurons
`hemibrain_reroot()`	Re-root (a) hemibrain neuron/neurons
`hemibrain_hemilineages`	Hemilineages names from T. Lee, K. Ito and V. Hartenstein
Synapses and neuron and ROI meshes
`hemibrain_extract_synapses()` `hemibrain_extract_connections()` `hemibrain_extract_compartment_edgelist()`	Extract synapse location and labels, and edgelists from a neuron/neuronlist
`hemibrain_remove_bad_synapses()`	Remove incorrectly placed synapses
`hemibrain_neuron_meshes()` `hemibrain_mito_meshes()`	Read hemibrain neurite or mitochondrial meshes into an R neuronlist object
`hemibrain_roi_meshes()`	Get some or all the region of interest meshes in the hemibrain project
`hemibrain.surf` `hemibrain_microns.surf`	The hemibrain mesh
`hemibrain_al.surf` `hemibrain_al_microns.surf` `hemibrain_glomeruli_summary` `odour_scenes` `flywire_al.surf`	Meshes for Antennal Lobe (AL) glomeruli
Connectivity
`grouped_adjacency()`	Flexible grouping of rows/columns of a raw adjacency matrix
`hemibrain_connectivity_similarity()` `hemibrain_connectivity_similarity_distance()` `hemibrain_connectivity_similarity_matrix()`	Calculate a connectivity similarity score between two connectivity profiles
Annotations
`hemibrain_get_meta()`	Get meta information for hemibrain neurons
`class2ids()`	Return body ids for large classes of neurons
`rn.ids` `orn.ids` `hrn.ids` `pn.ids` `upn.ids` `mpn.ids` `vppn.ids` `dan.ids` `mbon.ids` `alln.ids` `ton.ids` `lhn.ids` `dn.ids` `kc.ids` `apl.ids` `cent.ids` `lc.ids` `rn.info`	Bodyids for neuron classes
`glomerulus()`	Find the antennal lobe glomerulus for hemibrain body ids
`standard_transmitters()` `standard_statuses()` `standard_lineages()` `standard_compartments()` `standardise()` `standard_workflow()`	Use standard names and spellings
`hemibrain_cbf()`	Return consistent cell body fiber annotation for neurons
`fafb_hemibrain_annotate()` `fafb_set_hemilineage()` `fafb_set_transmitter()`	Set annotations for FAFB neurons in CATMAID based on hemibrain results
`hemibrain_olfactory_layers`	Hemibrain neurons in different Olfactory layers
`pn.info` `mbon.info` `ton.info` `lc.info` `alln.info` `kc.info` `cent.info` `dn.info`	Meta information of certain neuron classes
Neuron matching across datasets Includes functions for loading a range of different neuronal datasets and assigning matches between related neurons.
`hemibrain_matches()` `lm_matches()`	Retrieve matched up neurons between the hemibrain and FAFB
`hemibrain_matched` `lm_matched`	Manually verified neuron matches between the hemibrain and FAFB dataset
`matches_update()`	Update neuron match information on a google sheet
`hemibrain_task_update()` `hemibrain_adjust_saved_split()`	Manually review split neurons and save your results to a Google Sheet for everyone to use
`hemibrain_type_plot()` `hemibrain_multi3d()`	Plot chosen neurons and see all neurons in that type
`hemibrain_cut()`	Cut neurons to the hemibrain volume
Utility
`hemibrain_colours` `hemibrain_blender_colours` `hemibrain_blender_colors` `hemibrain_colors` `hemibrain_fig_colours` `hemibrain_fig_colors` `hemibrain_colour_ramp()` `hemibrain_bright_colours` `hemibrain_bright_colors` `hemibrain_bright_colour_ramp()`	Some nice colours used by Schlegel and Bates et al. 2020 (in prep.) and Li et al. 2020 (in prep)
`add_field()` `add_field_seq()`	Add a field to neuron objects (inc. in a neuronlist)
`add_Label()`	Manually add a Label annotation to a neuron
`hemibrain_settags()` `hemibrain_seetags()` `hemibrain_carryover_tags()` `metadata_add_tags()`	Set and see tags on a neuron object inc. within a neuronlist
`plot_inspirobot()`	Plot motivations from InspiroBot
`hemibrain_view()`	Orient the hemibrain in an RGL viewer
`paper_colours`	Colours for labels used in Schlegel and Bates et al.2021
R annotation pipelines
`hemibrain_adjust_saved_somas()`	Adjust and correct hemibrain neurons somas.
`LR_matching()` `hemibrain_matching()` `lm_matching()` `fafb_matching()`	Match up neurons between the hemibrain and FAFB
Set hemibrainr to work with google drive
`hemibrainr_set_drive()` `hemibrainr_team_drive()` `hemibrainr_rclone()` `hemibrainr_rclone_unmount()`	Set data source for precomputed information
Access hemibrain google drive data
`hemibrain_neuron_bodyids()` `hemibrain_elist()` `hemibrain_meta()` `hemibrain_synapses()` `hemibrain_connections()`	Read precomputed hemibrain data from the hemibrainr Google Drive
`hemibrain_nblast()`	Read precomputed NBLASTs from the hemibrainr Google Drive
Access flywire google drive data
`flywire_neurons()` `flywire_basics()` `flywire_request()`	Download a large set of well-traced skeletonised neurons from FlyWire
`flywire_meta()` `flywire_failed()` `flywire_contributions()` `flywire_ids()` `flywire_elist()` `flywire_connections()` `flywire_synapses()`	Read precomputed flywire data from the hemibrainr Google Drive
`flywire_ids_update()`	Update the root_id column in a set of google sheets based on flywire_xyz positions
Access light-level google drive data
`flycircuit_neurons()` `lm_lhns()`	Read flycircuit neurons from hemibrainr Google Drive
Manipulate googlesheets for neuron matching
`flywire_matching_rewrite()` `hemibrain_add_made_matches()` `hemibrain_matching_add()` `hemibrain_matching_transfers()` `fafb_matching_rewrite()` `hemibrain_matching_rewrite()` `flycircuit_matching_rewrite()`	Manage hemibrain-FAFB neuron matches

Reference

Package Help

General skeleton functions

Neuronal compartments (axons, dendrites)

Somas and lineages

Synapses and neuron and ROI meshes

Connectivity

Annotations

Neuron matching across datasets

Utility

R annotation pipelines

Set hemibrainr to work with google drive

Access hemibrain google drive data

Access flywire google drive data

Access light-level google drive data

Manipulate googlesheets for neuron matching