lineage_clones: Download light-level lineage clone data from Ito et al. 2013...

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

Download light-level lineage clone data from Ito et al. 2013 or Yu et al. 2013

Description

Get registered light-level clonal data of central brain, secondary developmental lineages. Most neurons in the fly brain hail from one of these lineages. You can find their meta information in hemibrain_hemilineages.

Usage

lineage_clones(
  x = NULL,
  local = FALSE,
  brain = c("FAFB14", "FlyWire", "JRCFIB2018Fraw", "JRCFIB2018F", "FAFB", "JFRC2",
    "JFRC2013", "JRC2018F", "FCWB"),
  dataset = c("Ito", "Lee")
)

lineage_converter(
  x,
  from = c("ito_lee_hemilineage", "cellBodyFiber", "ito_lee_lineage",
    "hartenstein_lineage", "hartenstein_hemilineage"),
  to = "hartenstein_hemilineage"
)

Arguments

x	a specific lineage, e.g. ALlv1. If NULL, the default, all lineages are fetched
local	FALSE or path. By default (FALSE) data is read from options()$remote_connectome_data), but the user can specify an alternative path.
brain	the brainspace in which hemibrain neurons have been registered. Defaults to raw voxel space for the FlyWire project.
dataset	whether to get clonal data from Ito et al. 2013 "Ito" or Yu et al. 2013 "Lee".
from	the name system in which you can find x. One of: cellBodyFiber, ito_lee_lineage, ito_lee_hemilineage, hartenstein_lineage, hartenstein_hemilineage
to	the lineage name system you want to move to, can be multiple of: cellBodyFiber, ito_lee_lineage, ito_lee_hemilineage, hartenstein_lineage, hartenstein_hemilineage

Value

A neuronlist object containing point clouds for neuron lineage clones. In the meta-data, it might be useful for some users to note that you will get:

• "hartenstein_lineage" The Hartenstein lineage name based on expert review of light level data from the V. Hartenstein group (Wong 2013, Lovick 2013). See hemibrain_hemilineages.

• "ito_lee_lineage" Lineage name, data from the K. Ito and T. Lee groups (Yu 2013, Ito 2013). See hemibrain_hemilineages

• "side" The hemisphere of the brain onto which this clone is registered

References

Ito M, Masuda N, Shinomiya K, Endo K, Ito K. Systematic analysis of neural projections reveals clonal composition of the Drosophila brain. Curr Biol. 2013 Apr 22;23(8):644-55. doi: 10.1016/j.cub.2013.03.015. Epub 2013 Mar 28. PMID: 23541729.

Yu HH, Awasaki T, Schroeder MD, Long F, Yang JS, He Y, Ding P, Kao JC, Wu GY, Peng H, Myers G, Lee T. Clonal development and organization of the adult Drosophila central brain. Curr Biol. 2013 Apr 22;23(8):633-43. doi: 10.1016/j.cub.2013.02.057. Epub 2013 Mar 28. PMID: 23541733; PMCID: PMC3637848.

See Also

hemibrain_neurons, flywire_neurons, hemibrain_hemilineages

Examples

## Not run: 
# Loads all processed flywire neurons as a neuronlistfh object
lee.lins = lineage_clones(brain = "FAFB14", dataset = "Lee")
ito.lins = lineage_clones(brain = "FAFB14", dataset = "Ito")

# Set the scene
library(elmr)
nopen3d()
plot3d(FAFB)

# Plot WEDd1
lee.lins.wedd1 = subset(lee.lins, ito_lee_lineage == "WEDd1")
plot3d(xyzmatrix(lee.lins.wedd1),
add = TRUE, col = hemibrain_bright_colors["green"])

# Plot WEDd1 from the other clonal data set
ito.lins.wedd1 = subset(ito.lins, ito_lee_lineage == "WEDd1")
plot3d(xyzmatrix(ito.lins.wedd1),
add = TRUE, col = hemibrain_bright_colors["darkgreen"])

# Get flywire neurons
fw.neurons = flywire_neurons()
fw.neurons.wedd1 = subset(fw.neurons, ito_lee_hemilineage == "WEDd1")
plot3d(fw.neurons.wedd1,
col = hemibrain_bright_colors["marine"], soma = 4000)

# What are the equivalent hemibrain neurons?
cbf.hl = subset(hemibrain_hemilineages, ito_lee_lineage == "WEDd1")
hb.neurons = hemibrain_neurons(brain="FAFB14")
hb.neurons.wedd1 = subset(hb.neurons,cellBodyFiber%in%cbf.hl$cellBodyFiber)
plot3d(hb.neurons.wedd1,
col = hemibrain_bright_colors["orange"], soma = 4000)


## End(Not run)

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