API Documentation¶

FAFBseg is divided into separate modules dedicated to a single data source/type or functionality:

fafbseg.flywire for FlyWire-related functions

fafbseg.google for Google segmentation-related functions

fafbseg.synapses for querying Buhmann et al. synapse predictions

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

fafbseg.move for moving/merging data between data sets

See below for a by-module breakdown:

Flywire segmentation¶

`fafbseg.flywire.locs_to_segments`(locs[, …])	Retrieve flywire segment IDs at given location(s).
`fafbseg.flywire.encode_url`([segments, …])	Encode data as flywire neuroglancer scene.
`fafbseg.flywire.decode_url`(url[, ret])	Decode neuroglancer URL.
`fafbseg.flywire.fetch_edit_history`(x[, …])	Fetch edit history for given neuron(s).
`fafbseg.flywire.locs_to_supervoxels`(locs[, …])	Retrieve flywire supervoxel IDs at given location(s).
`fafbseg.flywire.skid_to_id`(x[, dataset, …])	Find the flywire ID(s) corresponding to given CATMAID skeleton ID(s).
`fafbseg.flywire.update_ids`(id[, sample, …])	Retrieve the most recent version of given flywire neuron(s).
`fafbseg.flywire.get_mesh_neuron`(id[, dataset])	Fetch flywire neuron as navis.MeshNeuron.
`fafbseg.flywire.skeletonize_neuron`(x[, …])	Skeletonize flywire neuron.
`fafbseg.flywire.merge_flywire_neuron`(id, …)	Merge flywire neuron into FAFB.

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.

Buhmann synapse predictions¶

`fafbseg.synapses.query_synapses`(seg_ids[, …])	Fetch synapses for given segment IDs.
`fafbseg.synapses.query_connections`(pre_ids, …)	Fetch synaptic connections between given segment IDs.
`fafbseg.synapses.get_neuron_synapses`(x[, …])	Fetch synapses for a given neuron.
`fafbseg.synapses.get_neuron_synapses`(x[, …])	Fetch synapses for a given neuron.
`fafbseg.synapses.assign_connectors`(synapses)	Collapse synapses by presynaptic connectors.

Spatial transformation¶

`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.

Merging/combining data¶

fafbseg.move.merge_into_catmaid(x, …[, …])

Merge neuron into target CATMAID instance.