diff --git a/DESCRIPTION b/DESCRIPTION index a499444..7555133 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -34,4 +34,4 @@ Remotes: Encoding: UTF-8 Language: en-GB LazyData: true -RoxygenNote: 6.1.1 +RoxygenNote: 7.1.0 diff --git a/NEWS.md b/NEWS.md index 3465ffc..3d1b969 100644 --- a/NEWS.md +++ b/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 diff --git a/R/JRC2018.R b/R/JRC2018.R index 12f5df2..aaa9bd5 100644 --- a/R/JRC2018.R +++ b/R/JRC2018.R @@ -1,11 +1,18 @@ -#' 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, @@ -13,17 +20,28 @@ #' 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" diff --git a/data-raw/JRC2018_UNISEX_38um_iso_16bit.nrrd b/data-raw/JRC2018_UNISEX_38um_iso_16bit.nrrd new file mode 100644 index 0000000..29f9f8a --- /dev/null +++ b/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" + diff --git a/data-raw/JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf b/data-raw/JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf new file mode 100644 index 0000000..4223b50 Binary files /dev/null and b/data-raw/JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf differ diff --git a/data-raw/JRC2018_UNISEX_surface.hx b/data-raw/JRC2018_UNISEX_surface.hx new file mode 100644 index 0000000..4418646 --- /dev/null +++ b/data-raw/JRC2018_UNISEX_surface.hx @@ -0,0 +1,516 @@ +# Amira Project 670 +# Amira +# Generated by Amira 6.7.0 +remove -all +remove "grayScale.am" "physics.icol" "labels.am" "JRC2018_UNISEX_38um_iso_16bit.nrrd" "JRC2018_UNISEX_38um_iso_16bit.to-byte" "JRC2018_UNISEX_38um_iso_16bit.resampled" "JRC2018_UNISEX_38um_iso_16bit.labels" "JRC2018_UNISEX_38um_iso_16bit.surf" "JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" "JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" "JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" "Light" "Ortho Slice" "Convert Image Type" "Resample" "Multi-Thresholding" "Generate Surface" "Surface View" "Smooth Surface" + +# Create viewers +viewer setVertical 0 + +viewer 0 setTransparencyType 6 +viewer 0 setAutoRedraw 0 +viewer 0 show +mainWindow show + +set hideNewModules 1 +[ load ${AMIRA_ROOT}/data/colormaps/grayScale.am ] setLabel "grayScale.am" +"grayScale.am" setIconPosition 0 0 +"grayScale.am" setNoRemoveAll 1 +"grayScale.am" setVar "CustomHelp" {HxColormap256} +"grayScale.am" fire +"grayScale.am" setMinMax 0 255 +"grayScale.am" flags setValue 1 +"grayScale.am" shift setMinMax -1 1 +"grayScale.am" shift setButtons 0 +"grayScale.am" shift setEditButton 1 +"grayScale.am" shift setIncrement 0.133333 +"grayScale.am" shift setValue 0 +"grayScale.am" shift setSubMinMax -1 1 +"grayScale.am" scale setMinMax 0 1 +"grayScale.am" scale setButtons 0 +"grayScale.am" scale setEditButton 1 +"grayScale.am" scale setIncrement 0.1 +"grayScale.am" scale setValue 1 +"grayScale.am" scale setSubMinMax 0 1 +"grayScale.am" fire +"grayScale.am" setViewerMask 16383 + +set hideNewModules 1 +[ load ${AMIRA_ROOT}/data/colormaps/physics.icol ] setLabel "physics.icol" +"physics.icol" setIconPosition 0 0 +"physics.icol" setNoRemoveAll 1 +"physics.icol" fire +"physics.icol" setMinMax 0 1 +"physics.icol" flags setValue 1 +"physics.icol" shift setMinMax -1 1 +"physics.icol" shift setButtons 0 +"physics.icol" shift setEditButton 1 +"physics.icol" shift setIncrement 0.133333 +"physics.icol" shift setValue 0 +"physics.icol" shift setSubMinMax -1 1 +"physics.icol" scale setMinMax 0 1 +"physics.icol" scale setButtons 0 +"physics.icol" scale setEditButton 1 +"physics.icol" scale setIncrement 0.1 +"physics.icol" scale setValue 1 +"physics.icol" scale setSubMinMax 0 1 +"physics.icol" fire +"physics.icol" setViewerMask 16383 + +set hideNewModules 1 +[ load ${AMIRA_ROOT}/data/colormaps/labels.am ] setLabel "labels.am" +"labels.am" setIconPosition 0 0 +"labels.am" setNoRemoveAll 1 +"labels.am" setVar "CustomHelp" {HxColormap256} +"labels.am" fire +"labels.am" setMinMax 1 8 +"labels.am" flags setValue 1 +"labels.am" shift setMinMax -1 1 +"labels.am" shift setButtons 0 +"labels.am" shift setEditButton 1 +"labels.am" shift setIncrement 0.133333 +"labels.am" shift setValue 0 +"labels.am" shift setSubMinMax -1 1 +"labels.am" scale setMinMax 0 1 +"labels.am" scale setButtons 0 +"labels.am" scale setEditButton 1 +"labels.am" scale setIncrement 0.1 +"labels.am" scale setValue 1 +"labels.am" scale setSubMinMax 0 1 +"labels.am" fire +"labels.am" setViewerMask 16383 + +set hideNewModules 0 +[ load ${SCRIPTDIR}/JRC2018_UNISEX_38um_iso_16bit.nrrd ] setLabel "JRC2018_UNISEX_38um_iso_16bit.nrrd" +"JRC2018_UNISEX_38um_iso_16bit.nrrd" setIconPosition 19 10 +"JRC2018_UNISEX_38um_iso_16bit.nrrd" sharedColormap disconnect +"JRC2018_UNISEX_38um_iso_16bit.nrrd" sharedColormap setDefaultColor 0.8 0.8 0.8 +"JRC2018_UNISEX_38um_iso_16bit.nrrd" sharedColormap setDefaultAlpha 0.500000 +"JRC2018_UNISEX_38um_iso_16bit.nrrd" sharedColormap activateLocalRange 1 +"JRC2018_UNISEX_38um_iso_16bit.nrrd" sharedColormap setLocalMinMax 0.000000 1.000000 +"JRC2018_UNISEX_38um_iso_16bit.nrrd" sharedColormap enableAlpha 1 +"JRC2018_UNISEX_38um_iso_16bit.nrrd" sharedColormap enableAlphaToggle 1 +"JRC2018_UNISEX_38um_iso_16bit.nrrd" sharedColormap setAutoAdjustRangeMode 1 +"JRC2018_UNISEX_38um_iso_16bit.nrrd" sharedColormap setColorbarMinMax 0 120 +"JRC2018_UNISEX_38um_iso_16bit.nrrd" fire +"JRC2018_UNISEX_38um_iso_16bit.nrrd" fire +"JRC2018_UNISEX_38um_iso_16bit.nrrd" setViewerMask 16383 + +set hideNewModules 0 +[ load ${SCRIPTDIR}/JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf ] setLabel "JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" setIconPosition 20 467 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" fire +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" LevelOfDetail setMinMax -1 -1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" LevelOfDetail setButtons 1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" LevelOfDetail setEditButton 1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" LevelOfDetail setIncrement 1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" LevelOfDetail setValue -1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" LevelOfDetail setSubMinMax -1 -1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" fire +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" setViewerMask 16383 + +set hideNewModules 0 +[ load ${SCRIPTDIR}/JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf ] setLabel "JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" setIconPosition 20 503 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" fire +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" LevelOfDetail setMinMax -1 -1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" LevelOfDetail setButtons 1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" LevelOfDetail setEditButton 1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" LevelOfDetail setIncrement 1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" LevelOfDetail setValue -1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" LevelOfDetail setSubMinMax -1 -1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" fire +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" setViewerMask 16383 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf" select + +set hideNewModules 0 +create HxLight "Light" +"Light" setIconPosition 493 10 +"Light" setNoRemoveAll 1 +"Light" setType 0 +"Light" setColor 1 1 1 +"Light" setSlave 1 +"Light" edit 1 +"Light" setDirection 0.0173025 0.0876986 -0.995997 +"Light" setLocation 3.87322 -15.8212 17.3777 +"Light" setIntensity 1 +"Light" fire +"Light" setViewerMask 16383 + +set hideNewModules 0 +create HxOrthoSlice "Ortho Slice" +"Ortho Slice" setIconPosition 302 53 +"Ortho Slice" setVar "CustomHelp" {HxOrthoSlice} +"Ortho Slice" data connect "JRC2018_UNISEX_38um_iso_16bit.nrrd" +"Ortho Slice" fire +"Ortho Slice" sliceOrientation setValue 0 +"Ortho Slice" fire +"Ortho Slice" origin setBoundingBox -3.40282e+38 3.40282e+38 -3.40282e+38 3.40282e+38 -3.40282e+38 3.40282e+38 +"Ortho Slice" origin setImmediateMode 0 +"Ortho Slice" origin setOrtho 0 +"Ortho Slice" origin showDragger 0 +"Ortho Slice" origin showPoints 0 +"Ortho Slice" origin setPointScale 1 +"Ortho Slice" origin showOptionButton 1 +"Ortho Slice" origin setNumPoints 1 1 1 +"Ortho Slice" origin setCoord 0 313.69 146.68 80.94 +"Ortho Slice" normal setBoundingBox -3.40282e+38 3.40282e+38 -3.40282e+38 3.40282e+38 -3.40282e+38 3.40282e+38 +"Ortho Slice" normal setImmediateMode 0 +"Ortho Slice" normal setOrtho 0 +"Ortho Slice" normal showDragger 0 +"Ortho Slice" normal showPoints 0 +"Ortho Slice" normal setPointScale 1 +"Ortho Slice" normal showOptionButton 1 +"Ortho Slice" normal setNumPoints 1 1 1 +"Ortho Slice" normal setCoord 0 0 0 1 +"Ortho Slice" options setValue 0 1 +"Ortho Slice" options setToggleVisible 0 1 +"Ortho Slice" options setValue 1 0 +"Ortho Slice" options setToggleVisible 1 1 +"Ortho Slice" options setValue 2 0 +"Ortho Slice" options setToggleVisible 2 1 +"Ortho Slice" mappingType setIndex 0 0 +"Ortho Slice" contrastLimit setMinMax 0 -16777216 16777216 +"Ortho Slice" contrastLimit setValue 0 7 +"Ortho Slice" colormap connect "grayScale.am" +"Ortho Slice" colormap setDefaultColor 1 0.8 0.5 +"Ortho Slice" colormap setDefaultAlpha 1.000000 +"Ortho Slice" colormap activateLocalRange 1 +"Ortho Slice" colormap setLocalMinMax 0.000000 19288.000000 +"Ortho Slice" colormap enableAlpha 1 +"Ortho Slice" colormap enableAlphaToggle 1 +"Ortho Slice" colormap setAutoAdjustRangeMode 1 +"Ortho Slice" colormap setColorbarMinMax 0 64000 +"Ortho Slice" sliceNumber setMinMax 0 455 +"Ortho Slice" sliceNumber setButtons 1 +"Ortho Slice" sliceNumber setEditButton 1 +"Ortho Slice" sliceNumber setIncrement 1 +"Ortho Slice" sliceNumber setValue 213 +"Ortho Slice" sliceNumber setSubMinMax 0 455 +"Ortho Slice" transparency setValue 0 +"Ortho Slice" alpha setMinMax 0 -16777216 16777216 +"Ortho Slice" alpha setValue 0 0 +"Ortho Slice" alpha setMinMax 1 -16777216 16777216 +"Ortho Slice" alpha setValue 1 255 +"Ortho Slice" frameSettings setState {item 0 1 item 2 1 color 3 1 0.5 0 } +"Ortho Slice" embossingOnOff setValue 0 +"Ortho Slice" depth setMinMax -60 60 +"Ortho Slice" depth setButtons 0 +"Ortho Slice" depth setEditButton 1 +"Ortho Slice" depth setIncrement 8 +"Ortho Slice" depth setValue 2 +"Ortho Slice" depth setSubMinMax -60 60 +"Ortho Slice" fire + +"Ortho Slice" fire +"Ortho Slice" setViewerMask 16383 +"Ortho Slice" setShadowStyle 0 +"Ortho Slice" setPickable 1 + +set hideNewModules 0 +create HxCastField "Convert Image Type" +"Convert Image Type" setIconPosition 122 85 +"Convert Image Type" setVar "CustomHelp" {HxCastField} +"Convert Image Type" data connect "JRC2018_UNISEX_38um_iso_16bit.nrrd" +"Convert Image Type" colormap disconnect +"Convert Image Type" colormap setDefaultColor 1 0.8 0.5 +"Convert Image Type" colormap setDefaultAlpha 0.500000 +"Convert Image Type" colormap activateLocalRange 1 +"Convert Image Type" colormap setLocalMinMax 0.000000 30306.000000 +"Convert Image Type" colormap enableAlpha 1 +"Convert Image Type" colormap enableAlphaToggle 1 +"Convert Image Type" colormap setAutoAdjustRangeMode 1 +"Convert Image Type" colormap setColorbarMinMax 0 30306 +"Convert Image Type" fire +"Convert Image Type" outputType setIndex 0 0 +"Convert Image Type" scaling setMinMax 0 -3.40282346638529e+38 3.40282346638529e+38 +"Convert Image Type" scaling setValue 0 0.00840336084365845 +"Convert Image Type" scaling setMinMax 1 -3.40282346638529e+38 3.40282346638529e+38 +"Convert Image Type" scaling setValue 1 0 +"Convert Image Type" voxelGridOptions setValue 0 1 +"Convert Image Type" voxelGridOptions setToggleVisible 0 1 +"Convert Image Type" colorFieldOptions setIndex 0 0 +"Convert Image Type" applyTransformToResult 1 +"Convert Image Type" fire +"Convert Image Type" setViewerMask 16383 +"Convert Image Type" setPickable 1 + +set hideNewModules 0 +[ {Convert Image Type} create result ] setLabel "JRC2018_UNISEX_38um_iso_16bit.to-byte" +"JRC2018_UNISEX_38um_iso_16bit.to-byte" setIconPosition 20 121 +"JRC2018_UNISEX_38um_iso_16bit.to-byte" master connect "Convert Image Type" "result" 0 +"JRC2018_UNISEX_38um_iso_16bit.to-byte" sharedColormap disconnect +"JRC2018_UNISEX_38um_iso_16bit.to-byte" sharedColormap setDefaultColor 0.8 0.8 0.8 +"JRC2018_UNISEX_38um_iso_16bit.to-byte" sharedColormap setDefaultAlpha 0.500000 +"JRC2018_UNISEX_38um_iso_16bit.to-byte" sharedColormap activateLocalRange 1 +"JRC2018_UNISEX_38um_iso_16bit.to-byte" sharedColormap setLocalMinMax 0.000000 1.000000 +"JRC2018_UNISEX_38um_iso_16bit.to-byte" sharedColormap enableAlpha 1 +"JRC2018_UNISEX_38um_iso_16bit.to-byte" sharedColormap enableAlphaToggle 1 +"JRC2018_UNISEX_38um_iso_16bit.to-byte" sharedColormap setAutoAdjustRangeMode 1 +"JRC2018_UNISEX_38um_iso_16bit.to-byte" sharedColormap setColorbarMinMax 0 254 +"JRC2018_UNISEX_38um_iso_16bit.to-byte" fire +"JRC2018_UNISEX_38um_iso_16bit.to-byte" fire +"JRC2018_UNISEX_38um_iso_16bit.to-byte" setViewerMask 16383 + +set hideNewModules 0 +create HxResample "Resample" +"Resample" setIconPosition 160 157 +"Resample" setVar "CustomHelp" {HxResample} +"Resample" data connect "JRC2018_UNISEX_38um_iso_16bit.to-byte" +"Resample" fire +"Resample" filter setIndex 0 4 +"Resample" mode setValue 1 +"Resample" resolution setMinMax 0 1 2147483648 +"Resample" resolution setValue 0 314 +"Resample" resolution setMinMax 1 1 2147483648 +"Resample" resolution setValue 1 147 +"Resample" resolution setMinMax 2 1 2147483648 +"Resample" resolution setValue 2 87 +"Resample" voxelSize setMinMax 0 -3.40282346638529e+38 3.40282346638529e+38 +"Resample" voxelSize setValue 0 2 +"Resample" voxelSize setMinMax 1 -3.40282346638529e+38 3.40282346638529e+38 +"Resample" voxelSize setValue 1 2 +"Resample" voxelSize setMinMax 2 -3.40282346638529e+38 3.40282346638529e+38 +"Resample" voxelSize setValue 2 2 +"Resample" average setMinMax 0 1 32 +"Resample" average setValue 0 2 +"Resample" average setMinMax 1 1 32 +"Resample" average setValue 1 2 +"Resample" average setMinMax 2 1 32 +"Resample" average setValue 2 1 +"Resample" applyTransformToResult 1 +"Resample" fire +"Resample" setViewerMask 16383 +"Resample" setPickable 1 + +set hideNewModules 0 +[ {Resample} create result ] setLabel "JRC2018_UNISEX_38um_iso_16bit.resampled" +"JRC2018_UNISEX_38um_iso_16bit.resampled" setIconPosition 20 192 +"JRC2018_UNISEX_38um_iso_16bit.resampled" master connect "Resample" "result" 0 +"JRC2018_UNISEX_38um_iso_16bit.resampled" sharedColormap disconnect +"JRC2018_UNISEX_38um_iso_16bit.resampled" sharedColormap setDefaultColor 0.8 0.8 0.8 +"JRC2018_UNISEX_38um_iso_16bit.resampled" sharedColormap setDefaultAlpha 0.500000 +"JRC2018_UNISEX_38um_iso_16bit.resampled" sharedColormap activateLocalRange 1 +"JRC2018_UNISEX_38um_iso_16bit.resampled" sharedColormap setLocalMinMax 0.000000 1.000000 +"JRC2018_UNISEX_38um_iso_16bit.resampled" sharedColormap enableAlpha 1 +"JRC2018_UNISEX_38um_iso_16bit.resampled" sharedColormap enableAlphaToggle 1 +"JRC2018_UNISEX_38um_iso_16bit.resampled" sharedColormap setAutoAdjustRangeMode 1 +"JRC2018_UNISEX_38um_iso_16bit.resampled" sharedColormap setColorbarMinMax 0 1 +"JRC2018_UNISEX_38um_iso_16bit.resampled" fire +"JRC2018_UNISEX_38um_iso_16bit.resampled" setTransform 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 +"JRC2018_UNISEX_38um_iso_16bit.resampled" fire +"JRC2018_UNISEX_38um_iso_16bit.resampled" setViewerMask 16383 + +set hideNewModules 0 +create HxLabelVoxel "Multi-Thresholding" +"Multi-Thresholding" setIconPosition 162 231 +"Multi-Thresholding" setVar "CustomHelp" {HxLabelVoxel} +"Multi-Thresholding" data connect "JRC2018_UNISEX_38um_iso_16bit.resampled" +"Multi-Thresholding" fire +"Multi-Thresholding" regions setState {Exterior Inside} +"Multi-Thresholding" boundary01 setMinMax 0 228 +"Multi-Thresholding" boundary01 setButtons 1 +"Multi-Thresholding" boundary01 setEditButton 1 +"Multi-Thresholding" boundary01 setIncrement 10 +"Multi-Thresholding" boundary01 setValue 20 +"Multi-Thresholding" boundary01 setSubMinMax 0 228 +"Multi-Thresholding" boundary12 setMinMax 0 228 +"Multi-Thresholding" boundary12 setButtons 1 +"Multi-Thresholding" boundary12 setEditButton 1 +"Multi-Thresholding" boundary12 setIncrement 10 +"Multi-Thresholding" boundary12 setValue 228 +"Multi-Thresholding" boundary12 setSubMinMax 0 228 +"Multi-Thresholding" boundary23 setMinMax 0 228 +"Multi-Thresholding" boundary23 setButtons 1 +"Multi-Thresholding" boundary23 setEditButton 1 +"Multi-Thresholding" boundary23 setIncrement 10 +"Multi-Thresholding" boundary23 setValue 228 +"Multi-Thresholding" boundary23 setSubMinMax 0 228 +"Multi-Thresholding" boundary34 setMinMax 0 228 +"Multi-Thresholding" boundary34 setButtons 1 +"Multi-Thresholding" boundary34 setEditButton 1 +"Multi-Thresholding" boundary34 setIncrement 10 +"Multi-Thresholding" boundary34 setValue 228 +"Multi-Thresholding" boundary34 setSubMinMax 0 228 +"Multi-Thresholding" options setValue 0 1 +"Multi-Thresholding" options setToggleVisible 0 1 +"Multi-Thresholding" options setValue 1 0 +"Multi-Thresholding" options setToggleVisible 1 1 +"Multi-Thresholding" options setValue 2 0 +"Multi-Thresholding" options setToggleVisible 2 1 +"Multi-Thresholding" applyTransformToResult 1 +"Multi-Thresholding" fire +"Multi-Thresholding" setViewerMask 16383 +"Multi-Thresholding" setPickable 1 + +set hideNewModules 0 +[ "Multi-Thresholding" create + ] setLabel "JRC2018_UNISEX_38um_iso_16bit.labels" +"JRC2018_UNISEX_38um_iso_16bit.labels" setIconPosition 20 267 +"JRC2018_UNISEX_38um_iso_16bit.labels" master connect "Multi-Thresholding" "result" 0 +"JRC2018_UNISEX_38um_iso_16bit.labels" sharedColormap connect "labels.am" +"JRC2018_UNISEX_38um_iso_16bit.labels" sharedColormap setDefaultColor 0.8 0.8 0.8 +"JRC2018_UNISEX_38um_iso_16bit.labels" sharedColormap setDefaultAlpha 0.500000 +"JRC2018_UNISEX_38um_iso_16bit.labels" sharedColormap activateLocalRange 1 +"JRC2018_UNISEX_38um_iso_16bit.labels" sharedColormap setLocalMinMax 1.000000 8.000000 +"JRC2018_UNISEX_38um_iso_16bit.labels" sharedColormap enableAlpha 1 +"JRC2018_UNISEX_38um_iso_16bit.labels" sharedColormap enableAlphaToggle 1 +"JRC2018_UNISEX_38um_iso_16bit.labels" sharedColormap setAutoAdjustRangeMode 1 +"JRC2018_UNISEX_38um_iso_16bit.labels" sharedColormap setColorbarMinMax 1 8 +"JRC2018_UNISEX_38um_iso_16bit.labels" fire +"JRC2018_UNISEX_38um_iso_16bit.labels" primary setIndex 0 0 +"JRC2018_UNISEX_38um_iso_16bit.labels" fire +"JRC2018_UNISEX_38um_iso_16bit.labels" setViewerMask 16383 + +set hideNewModules 0 +create HxGMC "Generate Surface" +"Generate Surface" setIconPosition 118 315 +"Generate Surface" setVar "CustomHelp" {HxGMC} +"Generate Surface" data connect "JRC2018_UNISEX_38um_iso_16bit.labels" +"Generate Surface" fire +"Generate Surface" smoothing setIndex 0 2 +"Generate Surface" smoothingExtent setMinMax 1 9 +"Generate Surface" smoothingExtent setButtons 0 +"Generate Surface" smoothingExtent setEditButton 1 +"Generate Surface" smoothingExtent setIncrement 0.533333 +"Generate Surface" smoothingExtent setValue 5 +"Generate Surface" smoothingExtent setSubMinMax 1 9 +"Generate Surface" options setState {item 0 1 item 1 0 } +"Generate Surface" borderOnOff setValue 1 +"Generate Surface" algorithmMode setIndex 0 0 +"Generate Surface" borderSettings setValue 0 1 +"Generate Surface" borderSettings setToggleVisible 0 1 +"Generate Surface" borderSettings setValue 1 0 +"Generate Surface" borderSettings setToggleVisible 1 1 +"Generate Surface" borderSettings setValue 2 0 +"Generate Surface" borderSettings setToggleVisible 2 1 +"Generate Surface" borderSettings setValue 3 0 +"Generate Surface" borderSettings setToggleVisible 3 1 +"Generate Surface" materialList setIndex 0 0 +"Generate Surface" smoothMaterial setIndex 0 2 +"Generate Surface" applyTransformToResult 1 +"Generate Surface" fire +"Generate Surface" setViewerMask 16383 +"Generate Surface" setPickable 1 + +set hideNewModules 0 +[ load ${SCRIPTDIR}/JRC2018_UNISEX_38um_iso_16bit.surf ] setLabel "JRC2018_UNISEX_38um_iso_16bit.surf" +"JRC2018_UNISEX_38um_iso_16bit.surf" setIconPosition 21 353 +"JRC2018_UNISEX_38um_iso_16bit.surf" master connect "Generate Surface" "result" 0 +"JRC2018_UNISEX_38um_iso_16bit.surf" fire +"JRC2018_UNISEX_38um_iso_16bit.surf" LevelOfDetail setMinMax -1 -1 +"JRC2018_UNISEX_38um_iso_16bit.surf" LevelOfDetail setButtons 1 +"JRC2018_UNISEX_38um_iso_16bit.surf" LevelOfDetail setEditButton 1 +"JRC2018_UNISEX_38um_iso_16bit.surf" LevelOfDetail setIncrement 1 +"JRC2018_UNISEX_38um_iso_16bit.surf" LevelOfDetail setValue -1 +"JRC2018_UNISEX_38um_iso_16bit.surf" LevelOfDetail setSubMinMax -1 -1 +"JRC2018_UNISEX_38um_iso_16bit.surf" fire +"JRC2018_UNISEX_38um_iso_16bit.surf" setViewerMask 16383 + +set hideNewModules 0 +create HxDisplaySurface "Surface View" +"Surface View" setIconPosition 444 353 +"Surface View" setVar "CustomHelp" {HxDisplaySurface} +"Surface View" data connect "JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf" +"Surface View" colormap disconnect +"Surface View" colormap setDefaultColor 1 0.1 0.1 +"Surface View" colormap setDefaultAlpha 0.500000 +"Surface View" colormap activateLocalRange 1 +"Surface View" colormap setLocalMinMax 0.000000 1.000000 +"Surface View" colormap enableAlpha 1 +"Surface View" colormap enableAlphaToggle 1 +"Surface View" colormap setAutoAdjustRangeMode 1 +"Surface View" colormap setColorbarMinMax 0 120 +"Surface View" fire +"Surface View" drawStyle setValue 1 +"Surface View" fire +"Surface View" drawStyle setSpecularLighting 1 +"Surface View" drawStyle setTexture 1 +"Surface View" drawStyle setAlphaMode 1 +"Surface View" drawStyle setCullingMode 0 +"Surface View" drawStyle setNormalBinding 2 +"Surface View" drawStyle setSortingMode 1 +"Surface View" drawStyle setLineWidth 1.000000 +"Surface View" drawStyle setOutlineColor 0 0 0.2 +"Surface View" textureWrap setIndex 0 1 +"Surface View" selectionMode setIndex 0 0 +"Surface View" patch setMinMax 0 1 +"Surface View" patch setButtons 1 +"Surface View" patch setEditButton 1 +"Surface View" patch setIncrement 1 +"Surface View" patch setValue 0 +"Surface View" patch setSubMinMax 0 1 +"Surface View" boundaryId setIndex 0 -1 +"Surface View" materials setIndex 0 1 +"Surface View" materials setIndex 1 0 +"Surface View" colorMode setIndex 0 0 +"Surface View" baseTrans setMinMax 0 1 +"Surface View" baseTrans setButtons 0 +"Surface View" baseTrans setEditButton 1 +"Surface View" baseTrans setIncrement 0.1 +"Surface View" baseTrans setValue 0.8 +"Surface View" baseTrans setSubMinMax 0 1 +"Surface View" VRMode setIndex 0 0 +"Surface View" colorFieldMappingType setValue 0 +"Surface View" setLighting 1 +"Surface View" fire +"Surface View" hideBox 1 +"Surface View" selectTriangles zab HIJMONNLABANAADAAIAELBHHDGPPKKNIKGACBCFKAFGHOAKKAAAAIAANJCNDJNAAAAAAAAAAAAAAAAAACMJFKHLLABAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAICLPFPFPOOOJMOGN +"Surface View" fire +"Surface View" setViewerMask 16383 +"Surface View" setShadowStyle 0 +"Surface View" setPickable 1 + +set hideNewModules 0 +create HxSurfaceSmooth "Smooth Surface" +"Smooth Surface" setIconPosition 138 395 +"Smooth Surface" setVar "CustomHelp" {HxSurfaceSmooth} +"Smooth Surface" data connect "JRC2018_UNISEX_38um_iso_16bit.surf" +"Smooth Surface" fire +"Smooth Surface" parameters setMinMax 0 -3.40282346638529e+38 3.40282346638529e+38 +"Smooth Surface" parameters setValue 0 2 +"Smooth Surface" parameters setMinMax 1 -3.40282346638529e+38 3.40282346638529e+38 +"Smooth Surface" parameters setValue 1 0.600000023841858 +"Smooth Surface" applyTransformToResult 1 +"Smooth Surface" fire +"Smooth Surface" setViewerMask 16383 +"Smooth Surface" setPickable 1 + +set hideNewModules 0 +[ load ${SCRIPTDIR}/JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am ] setLabel "JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" setIconPosition 21 431 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" master connect "Smooth Surface" "result" 0 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" fire +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" LevelOfDetail setMinMax -1 -1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" LevelOfDetail setButtons 1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" LevelOfDetail setEditButton 1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" LevelOfDetail setIncrement 1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" LevelOfDetail setValue -1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" LevelOfDetail setSubMinMax -1 -1 +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" fire +"JRC2018_UNISEX_38um_iso_16bit.smooth.surf.100k.am" setViewerMask 16383 + +set hideNewModules 0 + +viewer 0 setCameraOrientation -0.998421 0.0171618 0.0534953 3.37539 +viewer 0 setCameraPosition 275.851 67.2608 -226.609 +viewer 0 setCameraFocalDistance 346.053 +viewer 0 setCameraNearDistance -61.0608 +viewer 0 setCameraFarDistance 460.028 +viewer 0 setCameraType orthographic +viewer 0 setCameraHeight 391.955 +viewer 0 setAutoRedraw 1 +viewer 0 redraw + +"Ortho Slice" data connectTo "AutomaticPointProbe" data +correlationPanel closeTabs +correlationPanel setTabName 0 "Correlation 1" +correlationPanel 0 setLogScalingOnAxis 0 0 +correlationPanel 0 setLogScalingOnAxis 1 0 + +histogramPanel closeTabs +histogramPanel setTabName 0 "Histogram 1" +histogramPanel 0 setLogScalingOnAxis 0 0 +histogramPanel 0 setLogScalingOnAxis 1 1 + +theObjectPool setSelectionOrder JRC2018_UNISEX_38um_iso_16bit.smooth.surf.18k.surf diff --git a/data-raw/jrc2018u.R b/data-raw/jrc2018u.R new file mode 100644 index 0000000..aaa6ba5 --- /dev/null +++ b/data-raw/jrc2018u.R @@ -0,0 +1,16 @@ +library(nat) +JRC2018U.surf=read.hxsurf('data-raw/JRC2018_UNISEX_38um_iso_16bit.smooth.surf.25k.surf') +library(devtools) +use_data(JRC2018U.surf, overwrite = T) + +library(nat.templatebrains) +JRC2018U <- + as.templatebrain('data-raw/JRC2018_UNISEX_38um_iso_16bit.nrrd', + regName = 'JRC2018U', + type = 'Average template brain', + sex = 'Intersex', + doi = 'https://doi.org/10.1101/376384', + description="Average template brain constructed from brains labelled with brp-SNAP presynaptic marker,dehydrated, and mounted in DPX and then imaged by confocal microscope. There were 36 female individuals (72 images including left-right flips) and 26 male individuals (52 image with left-right flips) for a total of 62 individuals (124 images with left-right flips)." + ) + +use_data(JRC2018U, overwrite = T) diff --git a/data/JRC2018U.rda b/data/JRC2018U.rda new file mode 100644 index 0000000..59ea52f Binary files /dev/null and b/data/JRC2018U.rda differ diff --git a/data/JRC2018U.surf.rda b/data/JRC2018U.surf.rda new file mode 100644 index 0000000..0eec94c Binary files /dev/null and b/data/JRC2018U.surf.rda differ diff --git a/man/Dmel.Rd b/man/Dmel.Rd index f1053d9..8ed1604 100644 --- a/man/Dmel.Rd +++ b/man/Dmel.Rd @@ -24,7 +24,9 @@ plot3d(Dmel.surf) } } \seealso{ -Other Drosophilid-Brains: \code{\link{DsecI}}, - \code{\link{Dsim}}, \code{\link{Dvir}} +Other Drosophilid-Brains: +\code{\link{DsecI}}, +\code{\link{Dsim}}, +\code{\link{Dvir}} } \concept{Drosophilid-Brains} diff --git a/man/DsecI.Rd b/man/DsecI.Rd index dbe5d9b..62b3ea7 100644 --- a/man/DsecI.Rd +++ b/man/DsecI.Rd @@ -24,7 +24,9 @@ plot3d(DsecI) } } \seealso{ -Other Drosophilid-Brains: \code{\link{Dmel}}, - \code{\link{Dsim}}, \code{\link{Dvir}} +Other Drosophilid-Brains: +\code{\link{Dmel}}, +\code{\link{Dsim}}, +\code{\link{Dvir}} } \concept{Drosophilid-Brains} diff --git a/man/Dsim.Rd b/man/Dsim.Rd index be405da..0e8e4d6 100644 --- a/man/Dsim.Rd +++ b/man/Dsim.Rd @@ -24,7 +24,9 @@ plot3d(Dsim.surf) } } \seealso{ -Other Drosophilid-Brains: \code{\link{Dmel}}, - \code{\link{DsecI}}, \code{\link{Dvir}} +Other Drosophilid-Brains: +\code{\link{Dmel}}, +\code{\link{DsecI}}, +\code{\link{Dvir}} } \concept{Drosophilid-Brains} diff --git a/man/Dvir.Rd b/man/Dvir.Rd index 5ba362c..f436df8 100644 --- a/man/Dvir.Rd +++ b/man/Dvir.Rd @@ -24,7 +24,9 @@ plot3d(Dvir.surf) } } \seealso{ -Other Drosophilid-Brains: \code{\link{Dmel}}, - \code{\link{DsecI}}, \code{\link{Dsim}} +Other Drosophilid-Brains: +\code{\link{Dmel}}, +\code{\link{DsecI}}, +\code{\link{Dsim}} } \concept{Drosophilid-Brains} diff --git a/man/FCWB.Rd b/man/FCWB.Rd index 672da5b..7d05d7b 100644 --- a/man/FCWB.Rd +++ b/man/FCWB.Rd @@ -5,7 +5,9 @@ \alias{FCWB} \alias{FCWB.surf} \title{Template information and Surface model of the FCWB FlyCircuit reference brain} -\format{An object of class \code{templatebrain} of dimension 1769 x 1026 x 108.} +\format{ +An object of class \code{templatebrain} of dimension 1769 x 1026 x 108. +} \usage{ FCWB } diff --git a/man/IBN.Rd b/man/IBN.Rd index e30a468..aadc971 100644 --- a/man/IBN.Rd +++ b/man/IBN.Rd @@ -5,7 +5,9 @@ \name{IBN} \alias{IBN} \title{Template information for the Insect Brain Nomenclature reference brain} -\format{An object of class \code{templatebrain} of dimension 512 x 512 x 135.} +\format{ +An object of class \code{templatebrain} of dimension 512 x 512 x 135. +} \usage{ IBN } diff --git a/man/IBNWB.Rd b/man/IBNWB.Rd index eaa32f1..eaa5d14 100644 --- a/man/IBNWB.Rd +++ b/man/IBNWB.Rd @@ -7,7 +7,9 @@ \alias{IBNWB.surf} \title{Template information for the Insect Brain Nomenclature Whole Brain reference brain} -\format{An object of class \code{templatebrain} of dimension 905 x 513 x 136.} +\format{ +An object of class \code{templatebrain} of dimension 905 x 513 x 136. +} \usage{ IBNWB } diff --git a/man/IS2.Rd b/man/IS2.Rd index 66d14f1..4ca053c 100644 --- a/man/IS2.Rd +++ b/man/IS2.Rd @@ -4,7 +4,9 @@ \name{IS2} \alias{IS2} \title{Template information for the IS2 reference brain} -\format{An object of class \code{templatebrain} of dimension 768 x 768 x 173.} +\format{ +An object of class \code{templatebrain} of dimension 768 x 768 x 173. +} \usage{ IS2 } diff --git a/man/JFRC2.Rd b/man/JFRC2.Rd index 7ee9b94..e62ad8d 100644 --- a/man/JFRC2.Rd +++ b/man/JFRC2.Rd @@ -5,7 +5,9 @@ \alias{JFRC2} \alias{JFRC2.surf} \title{Template information and surface model for the JFRC2 reference brain} -\format{An object of class \code{templatebrain} of dimension 1024 x 512 x 218.} +\format{ +An object of class \code{templatebrain} of dimension 1024 x 512 x 218. +} \usage{ JFRC2 } diff --git a/man/JFRC2013.Rd b/man/JFRC2013.Rd index 5b49234..4da4b1c 100644 --- a/man/JFRC2013.Rd +++ b/man/JFRC2013.Rd @@ -8,7 +8,11 @@ \alias{JFRC2013DS} \alias{JFRC2013DS.surf} \title{Template information and surface model for the JFRC2013 reference brain} -\format{An object of class \code{templatebrain} of dimension 1450 x 725 x 436.} +\format{ +An object of class \code{templatebrain} of dimension 1450 x 725 x 436. + +An object of class \code{templatebrain} of dimension 1184 x 592 x 218. +} \usage{ JFRC2013 diff --git a/man/JRC2018.Rd b/man/JRC2018.Rd new file mode 100644 index 0000000..b7c8db7 --- /dev/null +++ b/man/JRC2018.Rd @@ -0,0 +1,86 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/JRC2018.R +\docType{data} +\name{JRC2018F} +\alias{JRC2018F} +\alias{JRC2018U} +\alias{JRC2018F.surf} +\alias{JRC2018U.surf} +\title{Template information and surface model for the JRC2018 reference brains} +\format{ +An object of class \code{templatebrain} of dimension 1652 x 768 x 479. + +An object of class \code{templatebrain} of dimension 1652 x 773 x 456. + +An object of class \code{hxsurf} (inherits from \code{list}) of length 4. + +An object of class \code{hxsurf} (inherits from \code{list}) of length 4. +} +\usage{ +JRC2018F + +JRC2018U + +JRC2018F.surf + +JRC2018U.surf +} +\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. + +The \code{JRC2018U} reference brain was constructed as for + \code{JRC2018F} brain but pooling both male and female brains. + +\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. +} +\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} +} +\examples{ +dim(JRC2018F) +voxdims(JRC2018F) +boundingbox(JRC2018F) +JRC2018F + +\dontrun{ +library(nat) +plot3d(JRC2018F) +plot3d(JRC2018F.surf) +plot3d(JRC2018F.surf, col='red', alpha=0.3) +} +dim(JRC2018U) +voxdims(JRC2018U) +boundingbox(JRC2018U) +JRC2018U + +\dontrun{ +library(nat) +plot3d(JRC2018U) +plot3d(JRC2018U.surf) +plot3d(JRC2018U.surf, col='red', alpha=0.3) +} +} +\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} +} +\keyword{datasets} diff --git a/man/JRC2018F.Rd b/man/JRC2018F.Rd deleted file mode 100644 index c4a8147..0000000 --- a/man/JRC2018F.Rd +++ /dev/null @@ -1,43 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/JRC2018.R -\docType{data} -\name{JRC2018F} -\alias{JRC2018F} -\alias{JRC2018F.surf} -\title{Template information and surface model for the JRC2018F reference brain} -\format{An object of class \code{templatebrain} of dimension 1652 x 768 x 479.} -\usage{ -JRC2018F -} -\description{ -The \code{JRC2018F} reference brain is a 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 - \url{https://www.janelia.org/open-science/jrc-2018-brain-templates} -} -\examples{ -dim(JRC2018F) -voxdims(JRC2018F) -boundingbox(JRC2018F) -JRC2018F - -\dontrun{ -library(nat) -plot3d(JRC2018F) -plot3d(JRC2018F.surf) -plot3d(JRC2018F.surf, col='red', alpha=0.3) -} -} -\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} -} -\keyword{datasets} diff --git a/man/T1.Rd b/man/T1.Rd index 66418fa..95a7ed4 100644 --- a/man/T1.Rd +++ b/man/T1.Rd @@ -5,7 +5,9 @@ \alias{T1} \alias{T1.surf} \title{Template information and surface model for the T1 reference brain} -\format{An object of class \code{templatebrain} of dimension 768 x 768 x 165.} +\format{ +An object of class \code{templatebrain} of dimension 768 x 768 x 165. +} \usage{ T1 } diff --git a/man/VNCIS1.Rd b/man/VNCIS1.Rd index 19fe7c7..08d6374 100644 --- a/man/VNCIS1.Rd +++ b/man/VNCIS1.Rd @@ -5,7 +5,9 @@ \alias{VNCIS1} \alias{VNCIS1.surf} \title{Template information and surface model for the VNCIS1 reference neuropil} -\format{An object of class \code{templatebrain} of dimension 1024 x 768 x 163.} +\format{ +An object of class \code{templatebrain} of dimension 1024 x 768 x 163. +} \usage{ VNCIS1 } diff --git a/man/download_jefferislab_registrations.Rd b/man/download_jefferislab_registrations.Rd index 6f168a4..d409049 100644 --- a/man/download_jefferislab_registrations.Rd +++ b/man/download_jefferislab_registrations.Rd @@ -4,8 +4,10 @@ \alias{download_jefferislab_registrations} \title{Download (or update) and install Jefferis lab registrations} \usage{ -download_jefferislab_registrations(repos = c("BridgingRegistrations", - "MirrorRegistrations", "DrosophilidBridgingRegistrations")) +download_jefferislab_registrations( + repos = c("BridgingRegistrations", "MirrorRegistrations", + "DrosophilidBridgingRegistrations") +) } \arguments{ \item{repos}{character vector of Jefferis Lab GitHub repositories to download diff --git a/man/nat.flybrains-package.Rd b/man/nat.flybrains-package.Rd index ed9e188..aa3224f 100644 --- a/man/nat.flybrains-package.Rd +++ b/man/nat.flybrains-package.Rd @@ -78,11 +78,11 @@ researchers working with fly data. \code{\link[nat]{nat}, \link{nat.templatebrains}} } \author{ -\strong{Maintainer}: James Manton \email{ajd.manton@googlemail.com} (0000-0001-9260-3156) +\strong{Maintainer}: James Manton \email{ajd.manton@googlemail.com} (\href{https://orcid.org/0000-0001-9260-3156}{ORCID}) Authors: \itemize{ - \item Gregory Jefferis \email{jefferis@gmail.com} (0000-0002-0587-9355) + \item Gregory Jefferis \email{jefferis@gmail.com} (\href{https://orcid.org/0000-0002-0587-9355}{ORCID}) } }