R/JRCVNC.R

In jefferislab/nat.flybrains: Additional data for use with the NeuroAnatomy Toolbox (nat)

#' Template information and surface models for the JRC2018 reference ventral nerve chords
#'
#' @description The \code{JRCVNC2018F} reference VNC is an average template
#'   VNC constructed from VNCs labelled with brp-SNAP, dehydrated, and
#'   mounted in DPX and imaged at 0.19 x 0.19 x 0.38 microns. The image was
#'   downsampled to result in a 0.4 micron isotropic voxel size, which we
#'   take to be the standard JRCVNC2018F space.
#'
#' @details For the VNC, Bogovic and Saalfeld used 36 female
#'   individuals (72 images including left-right flips) for the female template,
#'   39 male individuals (78 image with left-right flips) for the male template,
#'   and the union of both for the unisex brain template: 75 individuals (150
#'   images with left-right flips).
#'
#'   Downloaded from
#'   \url{https://www.janelia.org/open-science/jrc-2018-brain-templates}
#' @references An unbiased template of the Drosophila brain and ventral nerve
#'   cord John A Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito,
#'   Jennifer Jeter, Geoffrey W Meissner, Aljoscha Nern, Jennifer Colonell, Oz
#'   Malkesman, Kei Ito, Stephan Saalfeld bioRxiv 376384; doi:
#'   \href{https://doi.org/10.1101/376384}{doi:10.1101/376384}
#' @name JRCVNC2018
#' @aliases JRCVNC2018F
#' @rdname JRCVNC
#' @docType data
"JRCVNC2018F"




#' @description The \code{JRCVNC2018U} reference VNC was constructed as for
#'   \code{JRCVNC2018F} VNC but pooling both male and female brains.
#' @rdname JRCVNC
#' @name JRCVNC2018U
#' @docType data
"JRCVNC2018U"

#' @description \code{JRCVNC2018F.surf}, was generated in
#'   Amira from a 2 micron downsampled, Lanczos filtered version of the
#'   respective template VNC. A surface was then generated with a threshold
#'   level of 2800 and then smoothed and downsampled.
#'
#' @name JRCVNC2018F.surf
#' @rdname JRCVNC
#' @docType data
#' @examples
#' JRCVNC2018F
#' dim(JRCVNC2018F)
#' voxdims(JRCVNC2018F)
#' boundingbox(JRCVNC2018F)
#'
#' \dontrun{
#' library(nat)
#' plot3d(JRCVNC2018F)
#' plot3d(JRCVNC2018F.surf)
#' plot3d(JRCVNC2018F.surf, col='red', alpha=0.3)
#' }
"JRCVNC2018F.surf"

#' @description \code{JRCVNC2018U.surf}, was generated in
#'   Amira from a 2 micron downsampled, Lanczos filtered 8 bit version of the
#'   respective template VNC. A surface was then generated with a threshold
#'   level of 20 and then smoothed and downsampled.
#'
#' @name JRCVNC2018U.surf
#' @rdname JRCVNC
#' @docType data
#' @seealso \code{\link{JRCVNC2018F}}
#' @examples
#' JRCVNC2018U
#' dim(JRCVNC2018U)
#' voxdims(JRCVNC2018U)
#' boundingbox(JRCVNC2018U)
#'
#' \dontrun{
#' library(nat)
#' plot3d(JRCVNC2018U)
#' plot3d(JRCVNC2018U.surf)
#' plot3d(JRCVNC2018U.surf, col='red', alpha=0.3)
#' }
"JRCVNC2018U.surf"