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Download BANC automatic synapse detections as a .sqlite file

Source: R/synapses.R
banc_all_synapses.Rd

Downloads a pre-baked Zetta.ai synapse table for the BANC from gs://lee-lab_brain-and-nerve-cord-fly-connectome/neuron_connectivity/v888/ and caches it as a per-version banc_data_<version>.sqlite file. After the one-off download subsequent calls read lazily from the cache so the table is never fully loaded into memory.

Usage

banc_all_synapses(
  version = c("v2", "v1", "v3"),
  overwrite = FALSE,
  n_max = 2000,
  details = FALSE,
  path = NULL
)

Arguments

version

Character, which synapse table to download. One of "v2" (default), "v1", or "v3".

overwrite

Logical, whether or not to overwrite an extant banc_data_<version>.sqlite cache.

n_max

Numeric, the maximum number of rows to stream lazily from the CSV when previewing. Set to NULL to trigger a full download into the SQLite cache.

details

Logical. If FALSE (default) only the essential pre-side columns (id, pre_pt_root_id, pre_x, pre_y, pre_z, size) are read; if TRUE all 15 columns are kept.

path

Optional explicit override of the HTTPS URL. Normally left NULL so the path is built from version.

Value

a data.frame (or a lazy dplyr::tbl backed by SQLite when the full table has been cached).

Details

Three versions are exposed, matching the BANC CAVE annotation tables of the same name. The version-specific metadata below is taken directly from each table's CAVE description; check https://banc.community/Automated-segmentation for the column-level documentation that ships with the source files.

  • v1 (deprecated). Source gs://zetta_lee_fly_cns_001_synapse/240623_run/assignment/final_edgelist.df, created 2024-07-25. Coordinates are in nanometers (CAVE voxel_resolution = c(1, 1, 1)). The CAVE table owner notice marks this version as deprecated in favour of v2.

  • v2 (default). Source gs://zetta_lee_fly_cns_001_synapse/250226_assignment/assignment/final_edgelist.df, created 2025-08-14. Coordinates are in nanometers (CAVE voxel_resolution = c(1, 1, 1)). This is the current production synapse table.

  • v3 (in testing). Created 2026-04-10. Coordinates are reported on the synapse-detection grid with CAVE voxel_resolution = c(16, 16, 45) nm/voxel - multiply by these values to obtain nanometers. Marked "still in testing" by the table owner.

Note that v1 and v2 coordinates are already in nanometers, which differs from most BANC CAVE tables (those use the EM image grid of c(4, 4, 45) nm/voxel).

Each version's synapses_<version>_human_readable.csv.gz is large (~12 GB gzipped for v2). The 15 columns are, in order: id, pre_x, pre_y, pre_z, post_x, post_y, post_z, centroid_x, centroid_y, centroid_z, size, pre_pt_supervoxel_id, pre_pt_root_id, post_pt_supervoxel_id, post_pt_root_id.

See also

banc_partner_summary, banc_partners

Examples

if (FALSE) { # \dontrun{
# Default: v2, preview first 2000 rows lazily from the CSV
syns <- banc_all_synapses()

# Full download of v2 (~12 GB gzipped) into the per-version SQLite cache
syns_all <- banc_all_synapses(n_max = NULL)

# Switch to the deprecated v1 table or the in-testing v3 table
syns_v1 <- banc_all_synapses(version = "v1")
syns_v3 <- banc_all_synapses(version = "v3")
} # }