Merge pull request #41 from natverse/feature/jrc2018u

Feature/jrc2018u

DESCRIPTION

@@ -34,4 +34,4 @@ Remotes:
 Encoding: UTF-8
 Language: en-GB
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0

NEWS.md

@@ -1,9 +1,15 @@
+# nat.flybrains 1.7.5
+
+* Add `JRC2018U` intersex template brain and surface, from the Bogovic
+  and Saalfeld average template brains. This intersex template brain from 
+  may become the new registration standard.
+
 # nat.flybrains 1.7.4
 
 * new github organisation: natverse/nat.flybrains
 * other standard doc features for https://natverse.github.io packages
 * fix DOI link for Dsim brain
-* decription for JRC2018F brain
+* description for JRC2018F brain
 
 # nat.flybrains 1.7.3
 

R/JRC2018.R

@@ -1,29 +1,47 @@
-#' Template information and surface model for the JRC2018F reference brain
+#' Template information and surface model for the JRC2018 reference brains
 #'
-#' @description The \code{JRC2018F} reference brain is a an average template
+#' @description The \code{JRC2018F} reference brains is an average template
 #'   brain constructed from brains 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 in XY to result in a 0.38 micron isotropic voxel size, which we
 #'   take to be the standard JRC2018F space.
-#' @details Downloaded from
+#'
+#' @details For the central brain, Bogovic and Saalfeld used 36 female
+#'   individuals (72 images including left-right flips) for the female template,
+#'   26 male individuals (52 image with left-right flips) for the male template,
+#'   and the union of both for the unisex brain template: 62 individuals (124
+#'   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 JRC2018F
+#' @rdname JRC2018
 #' @docType data
 "JRC2018F"
 
 
-#' \code{JRC2018F.surf} was generated in Amira from a 2 micron downsampled and
-#' Lanczos filtered version of the JRC2018F template brain. A surface was then
-#' generated with a threshold level of 20; this was then smoothed and
-#' downsampled. See \code{data-raw/JFRC2018_FEMALE_surface.hx} for details.
+#' @description The \code{JRC2018U} reference brain was constructed as for
+#'   \code{JRC2018F} brain but pooling both male and female brains.
+#' @rdname JRC2018
+#' @name JRC2018U
+#' @docType data
+"JRC2018U"
+
+
+#' @description \code{JRC2018F.surf} and \code{JRC2018U.surf} were generated in
+#'   Amira from a 2 micron downsampled and Lanczos filtered version of the
+#'   JRC2018F template brain. A surface was then generated with a threshold
+#'   level of 20; this was then smoothed and downsampled. See
+#'   \code{data-raw/JFRC2018_FEMALE_surface.hx} or
+#'   \code{data-raw/JRC2018_UNISEX_surface.hx} for details.
 #'
 #' @name JRC2018F.surf
-#' @rdname JRC2018F
+#' @rdname JRC2018
 #' @docType data
 #' @examples
 #' dim(JRC2018F)
@@ -37,4 +55,21 @@
 #' plot3d(JRC2018F.surf)
 #' plot3d(JRC2018F.surf, col='red', alpha=0.3)
 #' }
-NULL
+"JRC2018F.surf"
+
+#' @name JRC2018U.surf
+#' @rdname JRC2018
+#' @docType data
+#' @examples
+#' dim(JRC2018U)
+#' voxdims(JRC2018U)
+#' boundingbox(JRC2018U)
+#' JRC2018U
+#'
+#' \dontrun{
+#' library(nat)
+#' plot3d(JRC2018U)
+#' plot3d(JRC2018U.surf)
+#' plot3d(JRC2018U.surf, col='red', alpha=0.3)
+#' }
+"JRC2018U.surf"

data-raw/JRC2018_UNISEX_38um_iso_16bit.nrrd

@@ -0,0 +1,11 @@
+NRRD0004
+# Created by Nrrd_Writer at Thu Jul 12 12:28:24 EDT 2018
+type: uint16
+encoding: gzip
+endian: big
+dimension: 3
+sizes: 1652 773 456
+space dimension: 3
+space directions: (0.38,0,0) (0,0.38,0) (0,0,0.38)
+space units: "microns" "microns" "microns"
+