Read DVID body annotations for fish2 body ids

Read body annotations for the fish2 dataset from DVID.

Usage

fish_dvid_annotations(
  ids = NULL,
  node = "neutu",
  rval = c("data.frame", "list"),
  columns_show = NULL,
  cache = FALSE
)

Arguments

ids

One or more body ids, NULL (default) to fetch all annotations, or a query string (see Details).

node

The DVID node (UUID) to query. The default value of 'neutu' uses the active neutu node i.e. normally the most up to date.

rval

Whether to return a fully parsed "data.frame" (default) or an R "list".

columns_show

Whether to show all columns or only those with a '_user' or '_time' suffix. Accepted values: 'user', 'time', 'all'.

cache

Whether to cache the result for 5 minutes (default FALSE).

Value

A tibble of body annotations. See malevnc::manc_dvid_annotations for column details.

Details

This function wraps malevnc::manc_dvid_annotations for the fish2 dataset. At present this means fetching the full DVID annotation table for the chosen node and then subsetting in R, even when ids are supplied.

Query string formats for filtering DVID annotations:

"/type:RGC..*"

Match the type field with regex RGC..*.

"RGC.*"

Equivalent shorthand — bare strings default to the type field.

"/status:Traced"

Match a different field.

Regex queries are automatically anchored (^...$) unless the pattern already starts with ^. Queries fetch all annotations (with cache=TRUE) and then filter locally.

For neuprint-based id lookups, use fish_ids instead.

See also

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

Examples

if (FALSE) { # \dontrun{
# fetch annotations for specific bodies
fish_dvid_annotations(c(100003384, 100003412))
} # }
if (FALSE) { # \dontrun{
# fetch all annotations using 5m cache if possible
df <- fish_dvid_annotations(cache=TRUE)

# filter by type regex
df <- fish_dvid_annotations("/type:RGC.*", cache=T)
} # }
if (FALSE) { # \dontrun{
# shorthand for type field
df <- fish_dvid_annotations("RGC", cache=T)
df
} # }