neuprint_get_meta: Get key metadata for body (including name, type, status,...

In natverse/neuprintr: R Client Utilities for Interacting with the neuPrint Connectome Analysis Service

Get key metadata for body (including name, type, status, size)

Description

Get key metadata for body (including name, type, status, size)

Usage

neuprint_get_meta(
  bodyids,
  dataset = NULL,
  all_segments = TRUE,
  conn = NULL,
  chunk = TRUE,
  progress = FALSE,
  possibleFields = NULL,
  ...
)

Arguments

bodyids	the body IDs for neurons/segments (bodies) you wish to query. This can be in any form understood by neuprint_ids.
dataset	optional, a dataset you want to query. If NULL, the default specified by your R environ file is used or, failing that the current connection, is used. See neuprint_login for details.
all_segments	if TRUE, all bodies are considered, if FALSE, only 'Neurons', i.e. bodies with a status roughly traced status.
conn	optional, a neuprintr connection object, which also specifies the neuPrint server. If NULL, the defaults set in your .Rprofile or .Renviron are used. See neuprint_login for details.
chunk	A logical specifying whether to split the query into multiple chunks or an integer specifying the size of those chunks (which defaults to 2000 when chunk=TRUE).
progress	default FALSE. If TRUE, the API is called separately for each neuron and you can assess its progress, if an error is thrown by any one bodyid, that bodyid is ignored.
possibleFields	passed to neuprint_get_fields when not NULL, otherwise a default set are used.
...	methods passed to neuprint_login

Details

Sometimes a cellBodyFiber will be present even when the soma is not, so this may be a good test of if the neuron is present in the volume. The cellBodyFiber should be matched to (hemi)lineage information .

Value

a data.frame containing the neuron's

• name

• type Cell type of the neuron

• status (Traced etc)

• statusLabel similar to status but often a bit more specific

• size size in voxels

• pre number of presynapses

• post number of postsynapses

• cropped whether the neuron is cropped by the hemibrain volume

• soma whether the neuron has a soma in the hemibrain volume

• cellBodyFiber names the tract connecting the soma to rest of neuron

Examples

da2s=neuprint_search(".*DA2.*")
neuprint_get_meta(da2s$bodyid)
# or simpler
neuprint_get_meta('DA2')

## Not run: 
neuprint_get_meta('cropped:false')

## End(Not run)

natverse/neuprintr documentation built on Sept. 15, 2023, 6:59 a.m.