Read NBLAST match results from CAVE

Query cross-species NBLAST match results stored in CAVE tables. Each table contains pairwise morphological similarity scores between BANC neurons and neurons from another connectome dataset, computed using NBLAST (Costa et al., 2016). Matches are identified by running all BANC neurons against a target dataset and retaining hits above a score threshold.

Usage

banc_nblast_matches(
  dataset = c("malecns", "fafb", "hemibrain", "manc", "fanc"),
  ...
)

Arguments

dataset

Character, which cross-species NBLAST comparison to query. One of:

"malecns"

CAVE table: banc_malecns_nblast_v2. Matches to the male CNS (Takemura et al., 2024) v0.9 dataset, covering the complete male central nervous system (~75K neurons).

"fafb"

CAVE table: banc_fafb_nblast_v2. Matches to FAFB (Zheng et al., 2018; Dorkenwald et al., 2024) FlyWire v783 dataset, a complete female Drosophila brain connectome.

"hemibrain"

CAVE table: banc_hemibrain_nblast_v2. Matches to the hemibrain (Scheffer et al., 2020) v1.2.1 dataset, a dense reconstruction of half the Drosophila brain.

"manc"

CAVE table: banc_manc_nblast_v2. Matches to the male adult nerve cord (Takemura et al., 2024) MANC v1.2.1 dataset.

"fanc"

CAVE table: banc_fanc_nblast_v2. Matches to FANC (Azevedo et al., 2024) v1116, a female adult nerve cord dataset.

...

Additional arguments passed to banc_cave_query, including live (default TRUE; set to 2 for real-time results or FALSE for the latest materialised version).

Value

A data.frame following the CAVE cell_match schema with columns:

id

CAVE annotation ID (integer).

pt_root_id

Current BANC root ID at the time of query (automatically updated by CAVE when neurons are edited).

pt_supervoxel_id

Supervoxel ID anchoring the annotation to the segmentation. Stable across root ID changes.

pt_position

3D position in voxel coordinates (resolution 4 x 4 x 45 nm) identifying the BANC neuron.

query_root_id

BANC root ID at the time the NBLAST was run. May differ from pt_root_id if the neuron has since been edited.

match_id

Identifier of the matched neuron in the target dataset. Format varies: hemibrain/maleCNS use bodyid (integer as string), FAFB uses root_783 (FlyWire root ID), MANC uses bodyid, FANC uses cell_id. Mirrored matches are prefixed with "m" (e.g. "m12345").

score

NBLAST similarity score (0-1). Higher is more similar. Typical thresholds: 0.3-0.4 for strong matches.

validation

Logical. TRUE if the match has been manually validated by a human annotator, FALSE otherwise.

Details

These tables are populated by the bancpipeline NBLAST workflow (banc-nblast-compile.R and banc-nblast-cave.R). The compile step runs NBLAST morphological comparisons and writes results to feather files; the CAVE sync step uploads new results and removes stale entries (where the BANC neuron's root ID has changed since the NBLAST was run).

Because CAVE tracks root ID changes via the pt_supervoxel_id anchor point, the pt_root_id column always reflects the current segmentation. Compare pt_root_id with query_root_id to identify entries that may need re-running (the neuron was edited after the NBLAST).

See also

banc_cave_query for the underlying CAVE query function, banc_cave_tables for listing all available CAVE tables.

Examples

if (FALSE) { # \dontrun{
# Get all maleCNS NBLAST matches
matches <- banc_nblast_matches("malecns")

# Get validated matches only
validated <- banc_nblast_matches("fafb") %>%
  dplyr::filter(validation == TRUE)

# Find matches for specific BANC neurons
my_matches <- banc_nblast_matches("hemibrain") %>%
  dplyr::filter(pt_root_id %in% my_root_ids)

# Identify stale entries (neuron edited since NBLAST)
stale <- banc_nblast_matches("manc") %>%
  dplyr::filter(pt_root_id != query_root_id)
} # }