fetchn_fafb: Fetch neurons from FAFB CATMAID server, transforming them as...

In jefferis/elmr: Support for working with light and electron microscopy fly brain data

Fetch neurons from FAFB CATMAID server, transforming them as appropriate

Description

fetchn_fafb is a thin wrapper around the catmaid::read.neurons.catmaid function with the additional convenience of automating conversion to a reference brain. Input can also be a pre-downloaded neuronlist.

fetchdp_fafb extends fetchn_fafb by additionally converting neurons to the dotprops representation suitable for nblast.

Usage

fetchn_fafb(
  skids,
  mirror = TRUE,
  conn = NULL,
  pid = 1,
  reference = nat.flybrains::FCWB,
  ...
)

fetchdp_fafb(skids, mirror = TRUE, conn = NULL, ...)

Arguments

skids	catmaid skeleton ids (see catmaid_skids) or a neuronlist
mirror	whether to mirror the neuron (default TRUE since FlyCircuit neurons are on fly's left and most FAFB tracings are on fly's right.)
conn	a catmaid connection object (see catmaid_connection)
pid	Project id (default 1)
reference	The reference brain to which the neurons will be transformed, either a templatebrain object such as FCWB or a character vector naming such an object.
...	Additional arguments passed to xform_brain and mirror_brain.

Examples

## Not run: 
# fetch all neurons with an annotation exactly matching "KC" and convert
# to JFRC2013 space
kcs=fetchn_fafb("annotation:^KC$", reference=JFRC2013)

# supplying a neuronlist, it will mirror and convert the neurons
# to a reference brain
dc_nl=fetchn_fafb(dense_core_neurons, reference=JFRC2013)

## End(Not run)

jefferis/elmr documentation built on Sept. 9, 2023, 1:54 p.m.