R/elmr-package.R

In jefferis/elmr: Support for working with light and electron microscopy fly brain data

#' Bridge light and EM flybrain datasets
#'
#' \bold{\code{elmr}} builds on the \bold{\code{nat}} and \bold{\code{catmaid}}
#' packages to provide tools to read, analyse, plot, transform and convert
#' neuroanatomical data, especially as it relates to whole brain EM volumes
#' generated at the HHMI Janelia Research Campus (groups of Davi Bock, Stephan
#' Saalfeld and many collaborators).
#'
#' @section Interesting functions/data:
#'
#'   \itemize{
#'
#'   \item \code{\link[nat.templatebrains]{xform_brain}}
#'
#'   allows you to transform FAFB data into a large number of other template
#'   brain spaces by making use of the \code{\link{nat.templatebrains}} and
#'   \code{\link{nat.flybrains}} packages. The ability to move beyond the
#'   \code{\link[nat.flybrains]{JFRC2013}} template brain depends on having a
#'   functional CMTK installation. See \code{\link[nat]{cmtk.bindir}} for more
#'   information and advice about installation.
#'
#'   \item \code{\link{fetchn_fafb}} allows you to fetch FAFB CATMAID tracings
#'   and transform to a new template.
#'
#'   \item \code{\link{nblast_fafb}} allows you to NBLAST CATMAID tracings
#'   against a set of neuron skeletons e.g. from FlyCircuit.
#'
#'   \item \code{\link{open_fafb}} allows you to open a CATMAID session in your
#'   browser at a specific xyz location based on selecting a position in any
#'   template brain space e.g. a \code{flycircuit.tw} neuron or a JFRC2010
#'   registered GAL4 line.
#'
#'   \item \code{\link{FAFB}} a \code{\link[nat.templatebrains]{templatebrain}}
#'   object specifying the dimensions of the FAFB EM volume.
#'
#'   \item \code{\link{elm.landmarks}} a set of landmarks that can define a thin
#'   plate spline transform mapping FAFB to light level template brains.
#'
#'   }
#' @section Authentication: Interacting with a CATMAID server will normally
#'   require authentication. Please see
#'   \url{https://github.com/jefferis/rcatmaid#Authentication} for details of
#'   how to set up authentication. If you regularly use a particular CATMAID
#'   server it is recommended to put authentication in your
#'   \code{\link{Rprofile}} file.
#'
#' @section Options: There is one package option: \itemize{
#'
#'   \item \code{elmr.nblast.cores} Set the default number of cores to use for
#'   parallel NBLAST You will need to ensure that the doParallel package (a
#'   suggested but not strict dependency of elmr is installed)
#'
#'   }
#'
#'   You can set this option in your \code{\link[base]{Rprofile}} file.
#'
#' @examples
#' # position of antennal lobe glomeruli "V" in JFRC2013 template brain
#' vgloms.jfrc2013=data.frame(X=c(316,229),
#'   Y=c(143, 139),
#'   Z=c(26,22),
#'   row.names=c("V_L", "V_R"))
#' # Convert to FAFB12 coordinates
#' xform_brain(vgloms.jfrc2013, sample = JFRC2013, reference = FAFB)
#'
#' # Show state of elmr package options
#' options()[grep('^elmr', names(options()))]
#'
#' \dontrun{
#' # Conversion of neurons from FlyCircuit template
#' # NB this conversion depends on a full install of nat.flybrains and CMTK
#' library(nat)
#' kcs13.fafb=xform_brain(kcs20[1:3], sample=FCWB, reference=FAFB)
#' }
#'
#' @name elmr-package
#' @aliases elmr
#' @docType package
#' @keywords package
#' @import nat.templatebrains
#' @import nat.flybrains
#' @keywords internal
"_PACKAGE"

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