Download MANC (EM) to JRC (light level) registrations — download_manc

John Bogovic and Stephan Saalfeld have constructed a series of bridging registrations from both light level and EM brains imaged at HHMI Janelia Research Campus. This function downloads the VNC registrations to your local machine to allow you to convert data between this different template spaces.

Usage

download_manc_registrations()

Details

It downloads publicly available registrations: MANC to JRC2018VNCM https://figshare.com/s/7f003353c24741136df3 JRC2018VNCM <> JRC2018VNCU https://figshare.com/s/42ad71eb14e7dd51e81a RC2018VNCF <> JRC2018VNCU https://figshare.com/s/c4589cef9180e1dd4ee1

It requires installation of a suggested dependency nat.jrcbrains. These transformations operate in units of microns. Therefore, any point coordinates must be converted to micron units before applying.

In order to use the registrations you need to load the nat.jrcbrains.

References

See Bogovic et al. (2018) doi:10.1101/376384

Examples


if (FALSE) { # \dontrun{
# one time install of optional package if you don't have it
if(!requireNamespace('nat.jrcbrains'))
  natmanager::install(pkgs = 'nat.jrcbrains')
# load this to use bridging registrations to JRC templates
library(nat.jrcbrains)

# one time download of large (~1.4 GB) bridging registrations
if(!"MANC" %in% allreg_dataframe()$reference)
  download_manc_registrations()

DNa02s=read_manc_meshes('DNa02')
# nb convert from nm to microns
DNa02s.jrcvnc2018u=xform_brain(DNa02s/1e3, reference = "JRCVNC2018U", sample="MANC")
plot3d(DNa02s.jrcvnc2018u)
plot3d(JRCVNC2018U)
} # }