fafb_hemilineage_contents: Create list of FAFB neurons within a hemilineage

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

Create list of FAFB neurons within a hemilineage

Description

This functions creates a .csv file listing every neuron annotated as belonging to a certain hemilineage within the FAFB volume. A secondary hemilineage is a set of neurons born together in the late larval stage. They form ~90

To see the available hemilineages you can load the package hemibrainr and see hemibrain_hemilineages.

Usage

fafb_hemilineage_contents(
  hemilineage,
  side = c("right", "left"),
  nomenclature = c("ItoLee", "Hartenstein"),
  path = getwd(),
  return = c("data.frame", "csv"),
  ...
)

Arguments

hemilineage	a valid hemilineage name. In CATMAID FAFB v14, these appear as annotation that start either in the form ItoLee_Hemilineage or hartenstein_Hemilineage.
side	the side of the brain for which you want to get neurons. Depends on the annotation "side: left".
nomenclature	whether you are looking for hemilineages in the form ItoLee_Hemilineage or Hartenstein_Hemilineage.
path	where to save the outputted .csv file.
return	whether to return a data.frame or write to a .csv at location path.
...	methods passed to catmaid functions.

Examples

## Not run: 
## A hemilineage of mostly laterla horn neurons
df = fafb_hemilineage_contents("DL2_dorsal", side = "right")

# from a list of found hemilineages
gs = googlesheets4::read_sheet("1HI8RZJhV8aWC6hw5T0qh2
__9D8V0zKdtxx2kkDsuI8Y")
for(i in 1:nrow(gs)){
  hl = gs[i,"ItoLee_Hemilineage"]
  message("Processing ", hl)
  fafb_hemilineage_contents(hl, side = "right", return = "csv")
  fafb_hemilineage_contents(hl, side = "left", return = "csv")
}

## End(Not run)

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