Man pages for natverse/hemibrainr
Code for Working with Data from Janelia FlyEM's Hemibrain Project and the flywire data sets``
| add_field | Add a field to neuron objects (inc. in a neuronlist) |
| add_Label | Manually add a Label annotation to a neuron |
| class2ids | Return body ids for large classes of neurons |
| classed.ids | Bodyids for neuron classes |
| extract_cable | Extract axonic/dendritic points/cable from a... |
| fafb_hemibrain_annotate | Set annotations for FAFB neurons in CATMAID based on... |
| flow_centrality | Determine a neuron's dendrite and axon by calculating flow... |
| flycircuit_neurons | Read flycircuit neurons from hemibrainr Google Drive |
| flywire_annotations_for_synapses | Generate a CSV of neuron synapses to import to a flywire... |
| flywire_googledrive_data | Read precomputed flywire data from the hemibrainr Google... |
| flywire_hemibrain_scene | Create a flywire scene that shows your chosen flywire and... |
| flywire_ids_update | Update the root_id column in a set of google sheets based on... |
| flywire_neurons | Download a large set of well-traced skeletonised neurons from... |
| flywire_synapse_simplify | Collapse Buhmann predicted flywire synapses into smaller... |
| flywire_tracing_sheet | Retrieve or go to a specific google sheet describing flywire... |
| geodesic_distance | Calculate the geodesic distance through an arbour between... |
| glomerulus | Find the antennal lobe glomerulus for hemibrain body ids |
| grouped_adjacency | Flexible grouping of rows/columns of a raw adjacency matrix |
| hemibrain_add_made_matches | Manage hemibrain-FAFB neuron matches |
| hemibrain_adjust_saved_somas | Adjust and correct hemibrain neurons somas. |
| hemibrain_adjust_saved_split | Manually review split neurons and save your results to a... |
| hemibrain_al.surf | Meshes for Antennal Lobe (AL) glomeruli |
| hemibrain_cbf | Return consistent cell body fiber annotation for neurons |
| hemibrain_clean_skeleton | Remove erroneous branchlets to beautify neuron skeletons |
| hemibrain_colours | Some nice colours used by Schlegel and Bates et al. 2020 (in... |
| hemibrain_compartment_metrics | Get useful metrics for each neuron's axon and dendrite |
| hemibrain_connectivity_similarity | Calculate a connectivity similarity score between two... |
| hemibrain_cut | Cut neurons to the hemibrain volume |
| hemibrain_download_neurons | Download all automatically split neurons from the hemibrain... |
| hemibrain_extract_connections | Extract synapse location and labels, and edgelists from a... |
| hemibrain_flow_centrality | Split neurons into axon and dendrites using pre-computed... |
| hemibrain_get_meta | Get meta information for hemibrain neurons |
| hemibrain_matched | Manually verified neuron matches between the hemibrain and... |
| hemibrain_matches | Retrieve matched up neurons between the hemibrain and FAFB |
| hemibrain_matching | Match up neurons between the hemibrain and FAFB |
| hemibrain_metrics | Neuron metrics for all neurons in the hemibrain dataset |
| hemibrain_nblast | Read precomputed NBLASTs from the hemibrainr Google Drive |
| hemibrain_neuron_meshes | Read hemibrain neurite or mitochondrial meshes into an R... |
| hemibrain_olfactory_layers | Hemibrain neurons in different Olfactory layers |
| hemibrain_overlap_locality | Calculate the overlap score between a neurons axon dendrite |
| hemibrain_precomputed_splitpoints | Axon-dendrite split points calculated for all hemibrain... |
| hemibrain_read_neurons | Read neurons from the hemibrain connectome project |
| hemibrain_reroot | Re-root (a) hemibrain/flywire neuron/neurons |
| hemibrainr_googledrive_data | Read precomputed hemibrain data from the hemibrainr Google... |
| hemibrain_roi_meshes | Get some or all the region of interest meshes in the... |
| hemibrainr-package | hemibrainr: Code for Working with Data from Janelia FlyEM's... |
| hemibrainr_set_drive | Set data source for precomputed information |
| hemibrain_skeleton_check | Pre-process hemibrain skeletons |
| hemibrain_somas | Soma / best 'root point' locations for hemibrain neurons |
| hemibrain_splitpoints | Get the positions of key points in a 'split' neuron |
| hemibrain.surf | The hemibrain mesh |
| hemibrain_tags | Set and see tags on a neuron object inc. within a neuronlist |
| hemibrain_type_plot | Plot chosen neurons and see all neurons in that type |
| hemibrain_use_splitpoints | Split a neuron using stored 'splitpoints' |
| hemibrain_view | Orient the hemibrain in an RGL viewer |
| hemilineages | Hemilineages names from T. Lee, K. Ito and V. Hartenstein |
| info | Meta information of certain neuron classes |
| lineage_clones | Download light-level lineage clone data from Ito et al. 2013... |
| manually_assign_labels | Manually assign the dendrite and axon to a neuron |
| matches_update | Update neuron match information on a google sheet |
| ngl_add_colours2 | Set colour for a specified layer properly |
| nt.cmat | Neurotransmitter prediction confidence matrices |
| paper_colours | Colours for labels used in Schlegel and Bates et al.2021 |
| plot3d_split | Plot neurons split up by flow centrality |
| plot_inspirobot | Plot motivations from InspiroBot |
| primary_neurite | Retrieve the primary neurite (cell body fibre) for a neuron |
| prune_vertices.neuprintneuron | Prune vertices from a neuprint neuron (taking care of synapse... |
| randomwords | Generate random words |
| reexports | Objects exported from other packages |
| remove_bad_synapses | Remove incorrectly placed synapses |
| soma_side | Calculate which side of the brain a neuron is on |
| standardise | Use standard names and spellings |
