Neuropil Regions from Connectome Datasets

As well as neurons and connectivity, each EM connectome is accompanied by a set of regions of interest (ROIs) — the neuropils (and, for the ventral nerve cord, tracts and nerves) used by that project to spatially organise its data. VFB loads these ROIs as image individuals, each an instance of the corresponding FBbt (Drosophila anatomy ontology) anatomy term, aligned to the same standard template as the dataset’s neurons. This lets a connectome’s own region names (e.g. AL_R, LegNp(T1)(L), PB(L3)) be resolved to ontology terms and browsed alongside its neurons.

Each region individual records the source dataset’s own region name (for example AL_R) as an exact synonym, and is asserted to be part_of the relevant organism sex and body side, so that left/right and male/female regions are distinguished.

Separately, the dataset-specific typed synonyms — name_in_hemibrain, name_in_banc and so on — are held on the FBbt anatomy classes, not on the individuals: each region term is annotated with the name that each connectome uses for it, recording cross-dataset nomenclature at the ontology level.

Summary of neuropil region sets

Region names are mapped to FBbt terms during curation. Abbreviations that are ambiguous between projects (for example PB, which can mean the protocerebral bridge or a peripheral nerve) are resolved with an explicit lookup, and antennal-lobe glomeruli are matched to their antennal lobe glomerulus … terms.

Sources

• neuprint (neuprint.janelia.org) — for the Janelia datasets (Hemibrain, MANC, male-CNS, Optic-lobe) the region list is taken from the dataset Meta node: the ROI names from roiInfo and their nesting from roiHierarchy. Individual optic-lobe columns (thousands of ME/LO/LOP columns) are excluded, as they do not correspond to FBbt terms.
• FlyWire Codex (codex.flywire.ai) — for FAFB, the lateralised neuropil names are taken from the column headers of the Codex neuropil synapse table for the FlyWire full adult female brain.
• BANC region outlines — for BANC, the regions are neuroglancer meshes from the project’s region_outlines layer, in the public Google Cloud Storage bucket gs://lee-lab_brain-and-nerve-cord-fly-connectome/region_outlines/ (region names and segment IDs in segment_properties/info; meshes under meshes/). They are reference-atlas neuropils (Ito midbrain/optic-lobe, Court and MANC VNC, Schlegel antennal-lobe glomeruli) warped into BANC space. Because more than one atlas is included, a few VNC tracts appear in both the Court and MANC parcellations and are kept as distinct regions.

Relationship to template painted domains

These connectome ROIs are distinct from the standard neuropil painted domains of the reference templates. The template painted domains provide a canonical, coarse-grained parcellation of a standard brain or VNC, whereas the connectome region sets follow each project’s own — often finer — subdivision (individual glomeruli, mushroom-body slices, neuropil layers, and so on) and are aligned into the shared template space so that they can be compared.

See also

• EM Data — the neuron and connectivity datasets these regions accompany
• Region Connectivity — per-neuron synapse tallies attached to these regions
• Templates — reference templates and their painted domains
• Dataset Versions and Deprecation — how region and neuron datasets change between releases