Read Clio body annotations for fish2 body ids

Read live body annotations for the fish2 dataset from Clio.

Usage

fish_clio_annotations(
  ids = NULL,
  query = NULL,
  json = FALSE,
  config = NULL,
  cache = FALSE,
  update.bodyids = FALSE,
  test = FALSE,
  show.extra = c("none", "user", "time", "all"),
  ...
)

Arguments

ids

One or more body ids, NULL (default) to fetch all annotations, or anything accepted by fish_ids.

query

A json query string (see examples or documentation) or an R list with field names as elements.

json

Whether to return unparsed JSON rather than an R list (default FALSE).

config

An optional httr::config (expert use only, must include a bearer token)

cache

Whether to cache the result of this call for 5 minutes.

update.bodyids

Whether to update the bodyid associated with annotations based on the position field. The default value of this has been switched to FALSE as of Feb 2022.

test

Whether to unset the clio-store test server (default FALSE)

show.extra

Extra columns to show with user/timestamp information.

...

Additional arguments passed to pblapply.

Value

A data.frame of body annotations. See malevnc::manc_body_annotations for further details.

Details

This function wraps malevnc::manc_body_annotations for the active fish dataset. When ids are supplied they are first resolved with fish_ids, so you can pass fish body ids or simple neuprint-backed queries such as cell types. Leave ids=NULL to use the query argument directly, as in malevnc::manc_body_annotations. When querying numeric fields such as group, use numeric values rather than quoted strings.

See also

Other live-annotations: fish_annotate(), fish_dvid_annotations()

Examples

if (FALSE) { # \dontrun{
fish_clio_annotations(ids = 100003384)
fish_clio_annotations(ids = "RGC")
fish_clio_annotations(query = list(group = 100003384))
} # }