catmaid_controlled_upload: Interactively upload neuron(s) to CATMAID

In alexanderbates/catnat: Analyse neuronal morphology and connectivity (extends catmaid and nat)

Interactively upload neuron(s) to CATMAID

Description

Uploads neurons to CATMAID, names them and annotates them, from the environment specified with conn to that specified by conn2. Please use with caution, as you could be heavily adding to a live tracing environment. When neurons are shown, potential join sites / locations of join tags are shown as spheres.

Usage

catmaid_controlled_upload(
  x,
  tolerance = 0.15,
  name = "v14-seg neuron upload",
  annotations = "v14-seg upload",
  avoid = "v14",
  avoid.join = NULL,
  join.only = NULL,
  include.potential.duplicates = FALSE,
  include.tags = TRUE,
  include.connectors = TRUE,
  search.range.nm = 1000,
  join = FALSE,
  join.tag = "TODO",
  lock = TRUE,
  fafbseg = FALSE,
  downsample = 2,
  min_nodes = 2,
  brain = NULL,
  return.uploaded.skids = TRUE,
  duplication.range.nm = 20,
  pid = 1,
  conn = NULL,
  pid2 = 1,
  conn2 = fafb_seg_conn(),
  ...
)

Arguments

x	either skeleton IDs in the environment specified by conn2 (by default, the v14-seg CATMAID instance), or a neuronlist object to upload to the CATMAID instance specified when you use catmaid::catmaid_login(), if conn is NULL, else specified by conn$server
tolerance	how many potentially duplicated nodes you will tolerate
name	whatever you want to name your uploaded neurons. If a single character, then it will be added to all uploaded neurons. Else, can be a character vector the same length as swc.
annotations	a character vector of annotations, to be added to all of the uploaded neurons
avoid	a character vector. If a neuron contains an annotation specified by avoid, it will not be considered for upload
include.potential.duplicates	whether or not to include skeletons from the instance specified by conn2, that have the annotation "duplicated"
include.tags	whether of not to transfer each neuron's tags to its newly uploaded cognate
include.connectors	whether of not to transfer each neuron's connectors to its newly uploaded cognate
search.range.nm	the maximum distance from which to search from the TODO point tag to find potential mergers
join	whether or not to attempt to join each uploaded neuron to neurons within the new CATMAID instance, based on the placement of join.tags specified using the next argument
join.tag	a single character specifying a tag that has been used to signify a potential merge point
lock	if TRUE, neurons in the CATMAID instance specified by conn2 (i.e. the environment from which you are uploading) will be 'locked' so other users cannot edit them (via addition of a 'locked' annotation)
fafbseg	whether or not to use fafbseg::read_brainmaps_meshes on the TODO tag locations and restrict possible merges to neurons within the search range and within the cognate auto-segmented volume
downsample	if downsample > 1, a sample of number.of.points/downsample is taken from the neuron, and only these points are used to assess duplication. Speeds things up
min_nodes	the minimum number of nodes a potential merger skeleton needs to have
brain	the brain to plot while visualising potential mergers using rgl. Defaults to NULL, no brain plotted.
return.uploaded.skids	whether or not to returns the skeleton IDs of uploaded neurons. If FALSE, nothing is returned
duplication.range.nm	the radius around each node of a skeleton you are looking to upload, in which to search for other CATMAID skeletons that might represent a duplication of the same neuron
pid	project id for conn. Defaults to 1
conn	CATMAID connection object, see ?catmaid::catmaid_login for details
pid2	project id for conn2. Defaults to 1
conn2	CATMAID connection object, see ?catmaid::catmaid_login for details
...	methods passed to catmaid::catmaid_fetch

Examples

## Not run: 
# This function, first, gets the neurons we want from the v14-seg CATMAID instance
# Then it checks that we have not already uploaded to v14-seg using the annotations you specify with the avoid argument
# Then it will seek to upload them in a controlled way, that gives us options to have their tags, connectors, and make joins, as well as trying to check for possible duplication.
# Be aware that the interactive join will often suggest the same neuron multiple times at different join sites.
# The join sites are indicated by spheres - you may need to zoom in in order to see them.
# If lock = TRUE, the neurons we just uploaded will be locked, to lessen the chance someone else will connect stuff to them and want to upload them AGAIN later...
uploaded = catmaid_controlled_upload(x = "name:ASB Tester", join = TRUE, name = "ASB Tester from v14-seg", duplication.range.nm = 10,
search.range.nm = 1000, annotations = "ASB Test v14-seg Upload", brain = elmr::FAFB14)
# Note that CATMAID links will also be supplied, so you can inspect a merge site in CATMAID. If you join in CATMAID, do not join in the interactive window, ad this will throw an errror, just keep hitting 'n' for no, until all options are exhausted.
# Oops, did you make a mistake in uploading this neuron?
catmaid_delete_neurons("annotation:ASB Tester from v14-seg")
# Be careful wen deleting, especially if you have merged your fragment during the interactive join.
# Phew.

## End(Not run)

alexanderbates/catnat documentation built on Sept. 5, 2023, 4:51 a.m.