API Documentation#

FAFBseg is divided into separate modules to split functions by data source/type:

fafbseg.flywire for FlyWire functions

fafbseg.google for functions related to Google’s segmentation of FAFB

fafbseg.xform for transforming spatial data between FAFB14 and FlyWire’s FAFB14.1

See below for a by-module breakdown.

FlyWire#

Interact with the segmentation:

`fafbseg.flywire.locs_to_segments`(locs[, ...])	Retrieve FlyWire segment (i.e. root) IDs at given location(s).
`fafbseg.flywire.neuron_to_segments`(x[, ...])	Get root IDs overlapping with a given neuron.
`fafbseg.flywire.locs_to_supervoxels`(locs[, ...])	Retrieve FlyWire supervoxel IDs at given location(s).
`fafbseg.flywire.supervoxels_to_roots`(x[, ...])	Get root(s) for given supervoxel(s).
`fafbseg.flywire.skid_to_id`(x[, sample, ...])	Find the FlyWire root ID for a given (FAFB) CATMAID neuron.
`fafbseg.flywire.is_latest_root`(id[, ...])	Check if root is the current one.
`fafbseg.flywire.update_ids`(id[, stop_layer, ...])	Retrieve the most recent version of given FlyWire (root) ID(s).
`fafbseg.flywire.get_voxels`(x[, mip, sv_map, ...])	Fetch voxels making a up given root ID.
`fafbseg.flywire.is_proofread`(x[, table, ...])	Test if neuron has been set to proofread.
`fafbseg.flywire.find_common_time`(root_ids[, ...])	Find a time at which given root IDs co-existed.
`fafbseg.flywire.find_anchor_loc`(root_ids[, ...])	Find a representative coordinate.
`fafbseg.flywire.get_segmentation_cutout`(bbox)	Fetch cutout of segmentation.

Fetch neurons:

`fafbseg.flywire.get_mesh_neuron`(id[, ...])	Fetch FlyWire neuron as navis.MeshNeuron.
`fafbseg.flywire.get_somas`([x, ...])	Fetch nuclei segmentation for given neuron(s).
`fafbseg.flywire.get_skeletons`(root_id[, ...])	Fetch precomputed skeletons.
`fafbseg.flywire.skeletonize_neuron`(x[, ...])	Skeletonize FlyWire neuron.
`fafbseg.flywire.skeletonize_neuron_parallel`(ids)	Skeletonization on parallel cores.

Connectivity:

`fafbseg.flywire.synapses.get_adjacency`(sources)	Fetch adjacency matrix.
`fafbseg.flywire.synapses.get_connectivity`(x)	Fetch Buhmann et al. (2019) connectivity for given neuron(s).
`fafbseg.flywire.synapses.get_synapses`(x[, ...])	Fetch Buhmann et al. (2019) synapses for given neuron(s).
`fafbseg.flywire.synapses.get_synapse_counts`(x)	Fetch synapse counts for given root IDs.
`fafbseg.flywire.synapses.get_transmitter_predictions`(x)	Fetch neurotransmitter predictions for neurons.

L2-related functions:

`fafbseg.flywire.get_l2_info`(root_ids[, ...])	Fetch basic info for given neuron(s) using the L2 cache.
`fafbseg.flywire.get_l2_graph`(root_ids[, ...])	Fetch L2 graph(s).
`fafbseg.flywire.get_l2_dotprops`(root_ids[, ...])	Generate dotprops from L2 chunks.
`fafbseg.flywire.get_l2_skeleton`(root_id[, ...])	Generate skeleton from L2 graph.

Misc:

`fafbseg.flywire.get_edit_history`(x[, ...])	Fetch edit history for given neuron(s).
`fafbseg.flywire.get_leaderboard`([days, ...])	Fetch leader board (# of edits).
`fafbseg.flywire.get_neuropil_volumes`(neuropils)	Load FlyWire neuropil volumes.
`fafbseg.flywire.get_lineage_graph`(x[, size, ...])	Get lineage graph for given neuron.
`fafbseg.flywire.get_lr_position`(x[, coordinates])	Find out if given xyz positions are on the fly's left or right.
`fafbseg.flywire.get_voxels`(x[, mip, sv_map, ...])	Fetch voxels making a up given root ID.

For fetching annotations:

`fafbseg.flywire.search_annotations`(x[, ...])	Search hierarchical annotations (super class, cell class, cell type, etc).
`fafbseg.flywire.search_community_annotations`(x)	Search community cell identification annotations for given term/root IDs.
`fafbseg.flywire.get_hierarchical_annotations`([...])	Download (and cache) hierarchical annotations.
`fafbseg.flywire.NeuronCriteria`(*[, regex, ...])	Parses filter queries into root IDs.

For interaction with the CAVE engine:

`fafbseg.flywire.get_materialization_versions`(*)	Fetch info on the available materializations.
`fafbseg.flywire.create_cave_table`(name, ...)	Create CAVE annotation table.
`fafbseg.flywire.list_cave_tables`(*[, dataset])	Fetch available CAVE annotation tables.
`fafbseg.flywire.get_cave_table_info`(...[, ...])	Get info for given CAVE table.
`fafbseg.flywire.get_cave_table`(table_name[, ...])	Get annotations from given CAVE table.
`fafbseg.flywire.delete_annotations`(...[, ...])	Delete annotations from CAVE annotation table.
`fafbseg.flywire.upload_annotations`(...[, ...])	Upload or update annotations to CAVE table.

Utility functions:

`fafbseg.flywire.set_default_dataset`(dataset)	Set the default FlyWire dataset for this session.
`fafbseg.flywire.set_default_annotation_version`(version)	Set the default annotation version for this session.
`fafbseg.flywire.get_user_information`(user_ids)	Fetch (and cache) user information (name, affiliation, etc.) from their IDs.
`fafbseg.flywire.encode_url`([segments, ...])	Encode data as FlyWire neuroglancer scene.
`fafbseg.flywire.decode_url`(url[, format])	Decode neuroglancer URL.

Google segmentation#

`fafbseg.google.locs_to_segments`(locs[, mip, ...])	Retrieve Google segmentation IDs at given location(s).
`fafbseg.google.segments_to_neuron`(seg_ids, ...)	Retrieve autoseg neurons of given segmentation ID(s).
`fafbseg.google.segments_to_skids`(seg_ids, ...)	Retrieve skeleton IDs of neurons corresponding to given segmentation ID(s).
`fafbseg.google.neuron_to_segments`(x)	Get segment IDs overlapping with a given neuron.
`fafbseg.google.find_autoseg_fragments`(x, ...)	Find autoseg tracings constituting a given neuron.
`fafbseg.google.find_fragments`(x, remote_instance)	Find manual tracings overlapping with given autoseg neuron.
`fafbseg.google.find_missed_branches`(x, ...)	Use autoseg to find (and annotate) potential missed branches.
`fafbseg.google.get_mesh`(x, bbox[, vol])	Get mesh for given segmentation ID using CloudVolume.
`fafbseg.google.autoreview_edges`(x[, ...])	Automatically review (low-confidence) edges between nodes.
`fafbseg.google.test_edges`(x[, edges, vol, ...])	Test if edge(s) cross membranes using ray-casting.

Spatial transformation#

Note that typically you will want to use e.g. navis.xform_brain(data, source='FAFB14', target='FLYWIRE') but you can also use these low-level functions:

`fafbseg.xform.flywire_to_fafb14`(x[, ...])	Transform neurons/coordinates from flywire to FAFB V14.
`fafbseg.xform.fafb14_to_flywire`(x[, ...])	Transform neurons/coordinates from FAFB v14 to flywire.