fafb_hemibrain_annotate: Set annotations for FAFB neurons in CATMAID based on...

In natverse/hemibrainr: Code for Working with Data from Janelia FlyEM's Hemibrain Project and the flywire data sets``

Set annotations for FAFB neurons in CATMAID based on hemibrain results

Description

Set annotations for FAFB neurons in CATMAID based on matches made to hemibrain neurons. E.g. transfer information on matches and cell body fibers, and also update lineage related information. Not that catmaid::flywire_matching_rewrite() will write annotations related to flywire.

Usage

fafb_hemibrain_annotate(x, flywire = TRUE, ...)

fafb_set_hemilineage(
  find,
  ito_lee_hemilineage,
  dataset = c("FAFB", "hemibrain"),
  putative = TRUE,
  delete.find = FALSE,
  ...
)

fafb_set_transmitter(
  find,
  dataset = c("FAFB", "hemibrain"),
  putative = TRUE,
  transmitter = c("acetylcholine", "GABA", "glutamate"),
  delete.find = FALSE,
  ...
)

Arguments

x	a vector of FAFB skeleton IDs (skids) that can be read with catmaid::catmaid_skids()
flywire	logical. Whether or not to add flywire-related annotation information, e.g. a corresponding position in flywire voxel space and a matching, cognate flywire ID.
...	arguments passed to neuprintr::neuprint_get_meta and catmaid::catmaid_login.
find	an annotation/search term/vector of skids passed to catmaid::catmaid_skids.
ito_lee_hemilineage	character, the correct K. Ito / T. Lee hemilineage. Must be an entry in hemibrain_hemilineages. If set to 'wipe' all lineage related annotations will be removed.
dataset	either FAFB or hemibrain. If hemibrain, then find must be a vector of valid bodyids. Matches to FAFB neurons will be annotated for these bodyids, using hemibrain_matches.
putative	if TRUE the word 'putative' is added to all lineage annotations to indicate to users that the labelled neurons may not have been given the correct lineages. More work may need to be done to solidify these assignments.
delete.find	logical, is TRUE then if find is an annotation, it will be wiped from the neuron after this function is used (if you have permission to remove it)
transmitter	character, the known or putative transmitter identity of the neurons that will be fetched using find.

Value

annotations set on CATMAID neurons in specified CATMAID instance, see your catmaid::catmaid_connection()

See Also

hemibrain_get_meta

Examples

## Not run: 

# Transfer information on the VA6 uPN
fafb_hemibrain_annotate("16")

# Annotate all GABAergic MBONs in FAFB as GABAergic
bodyids = c(1016835041,
         1048215779,
        1078693835,
         672352543,
         613719036,
         581678043,
         673085197,
         706840303,
         768555687,
         5812982924,
         424767514,
         517518166);
fafb_set_transmitter(find=bodyids,dataset="hemibrain",transmitter="GABA", putative = FALSE)


## End(Not run)

natverse/hemibrainr documentation built on Nov. 27, 2024, 9:01 p.m.