Get predicted dense core vesicle locations in the flywire dataset

Preliminary dense core vesicle (DCV) detection results from the Lee group, Stephan Gerhard and Minsu Kim.

Usage

flywire_dcvs(
  rootid,
  dataset = c("dcv.3.0", "dcv.2.0", "dcv.1.0"),
  project = "fruitfly_fafb_flywire",
  islatest = TRUE,
  simplify = TRUE,
  return = c("parsed", "text", "response"),
  token = NULL,
  simplifyVector = TRUE,
  include_headers = FALSE,
  OmitFailures = TRUE,
  cl = NULL,
  ...
)

Arguments

rootid

flywire rootid/rootids

dataset

which DCV data set from Stephan Gerhard to access. 1.0 is just for the antennal lobes of FAFB. 2.0 is the first run at the whole brain.

project

from which project to pull data. At the moment, there is only one option for DCV data.

islatest

logical, whether or not to fetch the latest root_id if the given IDs are out of date.

simplify

logical, if FALSE each rootid is a separate set of two data frames (one for DCV positions, one for the neuron's synapses). Else, a list of two combined data frames is returned.

return

One of "parsed", "text" (for raw JSON), or "response"

token

Optional chunkedgraph token (otherwise the default one for the current segmentation will be used).

simplifyVector

Whether to use jsonlite::simplifyVector

include_headers

Whether to include basic headers from the http request as attributes on the parsed JSON object (default TRUE) when parse.json=TRUE.

OmitFailures

logical, if TRUE then requests that result in a 500 error are dropped and a warning is displayed but not an error.

cl

A cluster object created by parallel::makeCluster, or an integer to indicate number of child-processes (integer values are ignored on Windows) for parallel evaluations.

...

additional arguments passed to the httr::{RETRY} function. This may include a config list other named parameters etc.

Value

A list, where the first entry contains DCV locations and the second the synapses for the given rootid, with the nearest DCV precalculated for each synapse..

See also

braincircuits_login

Examples

if (FALSE) {
# Just AL test data set
data = flywire_dcvs("720575940629166904", dataset = "dcv.1.0")
dcv = data$dcv
synapse = data$syns

# Whole brain data set
dcv = flywire_dcvs(c("720575940631973089","720575940629166904"), dataset = "dcv.2.0")
}