Read BANC CAVE-tables, good sources of metadata

CAVE tables query functions that track neurons across segmentation changes so that annotations and neuron entities can be stably tracked together. The Brain And Nerve Cord (BANC) dataset represents the first complete connectome including both brain and ventral nerve cord of a limbed animal, comprising approximately 160,000 neurons across the entire central nervous system.

Usage

banc_cave_tables(datastack_name = NULL, select = NULL)

banc_cave_views(datastack_name = NULL, select = NULL)

banc_edgelist(
  edgelist_view = c("synapses_250226_backbone_proofread_and_peripheral_nerves_counts",
    "synapses_250226_backbone_proofread_counts", "synapses_v1_backbone_proofread_counts"),
  ...
)

banc_mitochondria(
  rootids = NULL,
  table = "mitochondria_v1",
  rawcoords = FALSE,
  ...
)

banc_nuclei(
  rootids = NULL,
  nucleus_ids = NULL,
  table = c("both", "somas_v1a", "somas_v1b"),
  rawcoords = FALSE,
  ...
)

banc_cell_info(rootids = NULL, rawcoords = FALSE, ...)

banc_cell_ids(rootids = NULL, ...)

banc_neck_connective_neurons(
  rootids = NULL,
  table = c("neck_connective_y92500", "neck_connective_y121000"),
  ...
)

banc_peripheral_nerves(rootids = NULL, ...)

banc_backbone_proofread(rootids = NULL, ...)

banc_nt_prediction(
  rootids = NULL,
  table = "synapses_250226_nt_prediction_5",
  simplify = TRUE,
  rawcoords = TRUE,
  ...
)

banc_version()

Arguments

datastack_name: Defaults to "brain_and_nerve_cord". See https://global.daf-apis.com/info/ for other options.
select: A regex term for the name of the table you want
edgelist_view: Character, name of prepared CAVE view that computes the proofread-neuron edgelist.
...: Additional arguments passed to fafbseg::flywire_cave_query or bancr:::get_cave_table_data.
rootids: Character vector specifying one or more BANC rootids. As a convenience this argument is passed to banc_ids allowing you to pass in data.frames, BANC URLs or simple ids.
table: Character, possible alternative tables for the sort of data frame the function returns. One must be chosen.
rawcoords: Logical, whether or not to convert from raw coordinates into nanometers. Default is FALSE.
nucleus_ids: Character vector specifying one or more BANC nucleus ids. The nucleus (https://en.wikipedia.org/wiki/Cell_nucleus) contains the cell body and provides a stable reference point for neuron identification.
simplify: logical, if TRUE then the proportion of presynaptic connections for each transmitter type is returned, for each query neuron.

Value

A data.frame describing a CAVE-table related to the BANC project. In the case of banc_cave_tables, a vector is returned containing the names of all query-able cave tables.

Details

CAVE tables store rich metadata supporting analysis of distributed neural control across the entire central nervous system. For more information about CAVE infrastructure, see https://www.caveconnecto.me/CAVEclient/.

banc_edgelist returns a data frame of neuron-neuron connections where the pre (presynaptic) neuron is upstream of the post (postsynaptic) neuron. This edgelist contains synaptic connectivity data crucial for understanding distributed neural control and behaviour-centric neural modules across the brain-VNC boundary.

banc_cell_info accesses the cell_info CAVE table containing non-centralised annotations from the research community for connectome neurones. These annotations represent diverse contributions from researchers studying specific neural circuits and cell types in the BANC dataset.

Examples