README.md

In jefferis/nat.jrcbrains: Janelia Research Campus Bridging Registrations for Drosophila Brains

nat.jrcbrains

nat.jrcbrains allows bridging registrations for Drosophila brains from Janelia Research Campus to be used with the NeuroAnatomy Toolbox suite of R packages.

Installation

You can install the development version of nat.jrcbrains from GitHub using the remotes package (part of devtools):

if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github('natverse/nat.jrcbrains')

Example

You must first download the registrations you want from

• https://www.janelia.org/open-science/jrc-2018-brain-templates

This is most easily done as follows:

library(nat.jrcbrains)
download_saalfeldlab_registrations()

To run this example you will need JRC 2018 Female - JFRC 2010, which is included as one of the downloaded bridging registrations since v0.3.1

library(nat.jrcbrains)
library(nat.templatebrains)
# sample neurons in JFRC2 space
pd2a = read.neurons("https://ars.els-cdn.com/content/image/1-s2.0-S0896627318307426-mmc5.zip")
# note use of via argument to insist on higher quality bridging registration
# to FAFB14
pd2a.fafb14=xform_brain(pd2a, sample=JFRC2, reference="FAFB14", via=c("FAFB14um"))

Registration Formats

By default nat.jrcbrains will use registrations in the Saalfeld h5 format. As an end user, support for these registrations should be installed transparently when you install nat.jrcbrains.

ANTs format registrations

If you intend to use registrations in ANTs format, then you will need to install the suggested nat.ants package. This is turn has additional dependencies that can be hard to install. See the README for https://github.com/jefferis/nat.ants for details but essentially doing

source("https://neuroconductor.org/neurocLite.R")
neuro_install("ANTsRCore")
remotes::install_github("jefferis/nat.ants")

should do the trick.

Acknowledgements

This is a thin wrapper to allow convenient download and application of bridging registrations developed by John Bogovic in Stephan Saalfeld's lab at Janelia. See:

• https://www.biorxiv.org/content/10.1101/376384v2

An unbiased template of the Drosophila brain and ventral nerve cord. John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, Geoffrey Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, Stephan Saalfeld bioRxiv 376384; doi:10.1101/376384

for details and additional downloads. Please cite their paper if you make use of these registrations.

In addition if you make use of the infrastructure in this and other natverse packages, we would be grateful if you would cite:

The natverse, a versatile toolbox for combining and analysing neuroanatomical data. A. S. Bates and J. D. Manton and S. R. Jagannathan and M. Costa and P. Schlegel and T. Rohlfing and G. S. X. E. Jefferis. eLife 9. doi:10.7554/eLife.53350

You can also get citation information from inside R for the natverse or individual packages like so:

citation('natverse')
citation('nat.jrcbrains')

Your citations will help support future tool development by the Saalfeld lab and ourselves.

jefferis/nat.jrcbrains documentation built on June 28, 2023, 4:06 a.m.