Man pages for natverse/fafbseg
Support Functions for Analysis of FAFB EM Segmentation
| add_celltype_info | Fetch flytable cell type information to a dataframe with... |
| as.mesh3d | Convert a raw neuroglancer mesh into a mesh3d object |
| braincircuits_login | Create and log into a braincircuits account |
| brainmaps_auth | Generate a token to enable access to brainmaps API |
| brainmaps_fetch | GET/POST from brainmaps API with optional retry / cache |
| brainmaps_listfragments | Low level call to brainmaps API to list mesh fragment ids for... |
| brainmaps_skeleton | Low level function to fetch skeleton from brainmaps API |
| brainmaps_volume | Extract brainmaps volume identifier |
| brainmaps_xyz2id | Convert 3D x,y,z locations in brainmaps volumes to... |
| catmaid2ngl | Convert CATMAID things (eg neurons) into Neuroglancer... |
| choose_segmentation | Choose or (temporarily) use a FAFB autosegmentation |
| compare_ng_neuron | Compare a neuroglancer mesh object with a regular neuron |
| download_flywire_release_data | Download FlyWire connectivity and annotations from public... |
| dr_fafbseg | Print information about fafbseg setup including tokens and... |
| fafb14_to_flywire_ids | Get flywire IDs that map onto CATMAID neurons |
| fafbseg-ids | Convert between filenames and neuroglancer ids |
| fafbseg-package | fafbseg: Support Functions for Analysis of FAFB EM... |
| fct2nginfo | Convert flytable cell type information into a neuroglancer... |
| fetch_all_curl | Fetch data specified by a set of curl shell commands (e.g.... |
| find_merged_segments | Find all merged segment ids for a given starting google... |
| find_merged_segments_slow | Find all merged segment ids for a given starting google... |
| flytable_cell_types | Fetch (memoised) flywire cell type information from flytable |
| flytable_list_selected | List selected rows from flytable |
| flytable_login | Low level functions to access the flytable metadata service |
| flytable-queries | Flytable database queries |
| flytable_set_celltype | Set the flytable cell type and other columns for a set of... |
| flytable_update_rows | Update or append rows in a flytable database |
| flywire2fafb | Map points between FlyWire v1 and FAFB14 space (xyz nm) |
| flywire_adjacency_matrix | Fetch the synaptic adjacency matrix for a set of flywire... |
| flywire_adjacency_matrix2 | Fast adjacency matrices based on flywire connectome dumps |
| flywire_cave_client | Low level access to the Flywire CAVE annotation system |
| flywire_cave_query | Query the FlyWire CAVE annotation system |
| flywire_change_log | Summarise edits for one or more FlyWire segment ids |
| flywire_cloudvolume | Low level access to FlyWire data via Python cloudvolume... |
| flywire_connectome_data | Access precomputed flywire connectivity data |
| flywire_dcvs | Get predicted dense core vesicle locations in the flywire... |
| flywire_fetch | GET/POST from flywire (graphene) servers with appropriate... |
| flywire_ids | Flexible specification of flywire ids (including from... |
| flywire_islatest | Check that one or more FlyWire root ids have not been further... |
| flywire_l2ids | Return level 2 supervoxel ids for neurons |
| flywire_last_modified | Check when a root id was last edited |
| flywire_latestid | Find the most up to date FlyWire rootid for one or more input... |
| flywire_leaves | Find all the supervoxel (leaf) ids that are part of a FlyWire... |
| flywire_neurons_add_synapses | Attach synapses to flywire neuron skeletons |
| flywire_ntplot | Plot neurotransmitter prediction summaries or synapses in 3D |
| flywire_ntpred | Return raw neurotransmitter prediction results for output of... |
| flywire_nuclei | Queries for information about flywire nuclei (helpful for... |
| flywire_partners | Find the input/output partners for a flywire neuron |
| flywire_partner_summary2 | Rapid flywire connectivity summaries using cached connectome... |
| flywire_rootid | Find the root_id of a FlyWire segment / supervoxel. |
| flywire_scene | Return a sample Neuroglancer scene URL for FlyWire dataset |
| flywire_set_token | Record (and if necessary create) a FlyWire chunkedgraph token |
| flywire_shortenurl | Shorten or expand neuroglancer URLs |
| flywire_sirepo_file | Read or return path to FlyWire annotations manuscript... |
| flywire_timestamp | Find standard UTC timestamp for flywire materialisation... |
| flywire_updateids | Update flywire root ids to any timestamp using XYZ position... |
| flywire_user_info | Fetch information for one or more users |
| flywire_voxdims | Handle raw and nm calibrated flywire coordinates |
| flywire_xyz2id | Find FlyWire root or supervoxel (leaf) ids for XYZ locations |
| make_merge_graph | Graph representation of the agglomeration (merge) between raw... |
| meshparty_skeletonize | Skeletonize neurons using meshparty python library |
| ngl_add_colours | Add colours to the neuroglancer scene |
| ngl_annotation_layers | Construct one or more neuroglancer annotation layers |
| ngl_annotations | Extract annotations from a neuroglancer scene into a... |
| ngl_blank_scene | Return a blank neuroglancer scene based on a specified... |
| ngl_decode_scene | Decode and manipulate Neuroglancer scenes (from URLs or JSON... |
| ngl_encode_url | Encode scene information into a neuroglancer URL |
| ngl_layers | Extract and manipulate layers in a neuroglancer scene |
| ngl_segments | Helper function to turn diverse inputs into neuroglancer... |
| open_fafb_ngl | Construct Neuroglancer URL based on 3D location data |
| read_brainmaps_meshes | Read 3D meshes via the brainmaps API |
| read_cloudvolume_meshes | Read meshes from chunked graph (graphene) server via... |
| read_l2skel | Read L2 skeleton or dotprops for FlyWire data sources using... |
| read_mergeinfo | Read CSV files containing raw agglomeration (merge)... |
| read.neuron.brainmaps | Read skeleton(s) from brainmaps API into a 'nat::neuron'... |
| read_ng_dump | Read neuroglancer data dump from disk / web |
| read_ng_raw | Read raw neuroglancer data - currently only supports mesh... |
| read_segments | Read skeletons for segments by extracting from the... |
| read_topn | Find and read the largest n segments from one or more... |
| simple_python | Simple Python installation for use with R/fafbseg/FlyWire |
| skeletor | Skeletonise neuron meshes using skeletor |
| skelsforsegment | Find all skeleton fragments for one segment |
| tabify_coords | Convert coordinates to tab separated values. Useful for... |
| voxdims.ngscene | Extract voxel dimensions from a neuroglancer scene |
| write_nginfo | Read and write neuroglancer annotation info json files |
| xform.ngscene | Add a transformation to one or more layers in a neuroglancer... |
| xyzmatrix | Extract the XYZ coordinates from neuroglancer mesh objects |
