celltrackR: Motion Trajectory Analysis

#' Two-Photon Data: B Cells in a Lymph Node
#'
#' GFP-labelled B cells were injected retro-orbitally in healthy CD11c-YFP mice, and 
#' intravitally imaged (using two-photon microscopy) inside a cervical lymph
#' node. These data illustrate the characteristic "random-walk-like" motion pattern 
#' of B cells in lymph nodes. For full method details, see references below. 
#'
#' @format ## `BCells`
#' An S3 object of class "tracks"; a list with 74 elements. Each 
#' element name identifies a cell track. Each element is a matrix
#' containing the following three columns.
#' \describe{
#' 	\item{\code{t}}{the time (in seconds)}
#' 	\item{\code{x}}{The X coordinate (in micrometers)}
#'  \item{\code{y}}{The Y coordinate (in micrometers)}
#' }
#' @source Data were generated in 2021 in the Mark J. Miller Lab, Department of Medicine, Washington University in St Louis, USA.
#' @references
#' Miller MJ and Wei SH and Parker I and Cahalan MD (2002), 
#' Two-photon imaging of lymphocyte motility and antigen response in intact lymph node.
#' \emph{Science}, \bold{296}(5574):1869--1873. doi:10.1126/science.1070051
#' 
#' Wortel IMN and Liu AY and Dannenberg K and Berry JC and Miller MJ and Textor J (2021),
#' CelltrackR: an R package for fast and flexible analysis of immune cell migration data.
#' \emph{ImmunoInformatics}, \bold{1-2}:100003. doi:10.1016/j.immuno.2021.100003
#' 
#' @keywords datasets
#'
#' @usage data("BCells")
#' 
#' @examples
#'   ## load the tracks
#'   data(BCells)
#'
#'   ## visualize the tracks (calls function plot.tracks)
#'   plot(BCells)
#' 
"BCells"

#' Two-Photon Data: T Cells in a Lymph Node
#'
#' RFP-labelled T cells were injected retro-orbitally in healthy CD11c-YFP mice, and 
#' intravitally imaged (using two-photon microscopy) inside a cervical lymph
#' node. These data illustrate the characteristic "random-walk-like" motion pattern 
#' of T cells in lymph nodes. For full method details, see references below. 
#'
#' @format ## `TCells`
#' An S3 object of class "tracks"; a list with 199 elements. Each 
#' element name identifies a cell track. Each element is a matrix
#' containing the following three columns.
#' \describe{
#' 	\item{\code{t}}{the time (in seconds)}
#' 	\item{\code{x}}{The X coordinate (in micrometers)}
#'  \item{\code{y}}{The Y coordinate (in micrometers)}
#' }
#' @source Data were generated in 2021 in the Mark J. Miller Lab, Department of Medicine, Washington University in St Louis, USA.
#' @references
#' Miller MJ and Wei SH and Parker I and Cahalan MD (2002), 
#' Two-photon imaging of lymphocyte motility and antigen response in intact lymph node.
#' \emph{Science}, \bold{296}(5574):1869--1873. doi:10.1126/science.1070051
#' 
#' Wortel IMN and Liu AY and Dannenberg K and Berry JC and Miller MJ and Textor J (2021),
#' CelltrackR: an R package for fast and flexible analysis of immune cell migration data.
#' \emph{ImmunoInformatics}, \bold{1-2}:100003. doi:10.1016/j.immuno.2021.100003
#' 
#' @keywords datasets
#'
#' @usage data("TCells")
#' 
#' @examples
#'   ## load the tracks
#'   data(TCells)
#'
#'   ## visualize the tracks (calls function plot.tracks)
#'   plot(TCells)
#' 
"TCells"

#' Two-Photon Data: Neutrophils responding to an infection in the ear
#'
#' LysM-GFP mice were infected with S. aureus on their ear, and intravitally
#' imaged using two-photon microscopy proximal to the infection. 
#' These cells display a fairly directed kind of motion, as they move towards 
#' infection foci. For method details, see the references below.
#'
#' @format ## `Neutrophils`
#' An S3 object of class "tracks"; a list with 411 elements. Each 
#' element name identifies a cell track. Each element is a matrix
#' containing the following three columns.
#' \describe{
#' 	\item{\code{t}}{the time (in seconds)}
#' 	\item{\code{x}}{The X coordinate (in micrometers)}
#'  \item{\code{y}}{The Y coordinate (in micrometers)}
#' }
#' @source Data were generated in 2021 in the Mark J. Miller Lab, Department of Medicine, Washington University in St Louis, USA.
#' @references
#' Lin A and Loughman JA and Zinselmeyer BH and Miller MJ and Caparon MG (2009), 
#' Streptolysin S inhibits neutrophil recruitment during the early stages of streptococcus pyogenes infection.
#' \emph{Infect Immun}, \bold{77}(11):5190--5201. doi:10.1128/IAI.00420-09
#'
#' Wang B and Zinselmeyer BH and McDole JR and Gieselman PA and Miller MJ (2010), 
#' Non-invasive imaging of leukocyte homing and migration in vivo.
#' \emph{J Vis Exp}, \bold{46}:e2062. doi:10.3791/2062
#'
#' Graham DB and Zinselmeyer BH and Mascarenhas F and Delgado R and Miller MJ and Swat W (2009), 
#' Itam signaling by Vav family Rho Guanine nucleotide exchange factors regulates interstitial transit rates of neutrophils in vivo.
#' \emph{PLOS ONE}, \bold{2}(2):1--5. doi:10.1371/journal.pone.0004652
#' 
#' Wortel IMN and Liu AY and Dannenberg K and Berry JC and Miller MJ and Textor J (2021),
#' CelltrackR: an R package for fast and flexible analysis of immune cell migration data.
#' \emph{ImmunoInformatics}, \bold{1-2}:100003. doi:10.1016/j.immuno.2021.100003
#' 
#' @keywords datasets
#'
#' @usage data("Neutrophils")
#' 
#' @examples
#'   ## load the tracks
#'   data(Neutrophils)
#'
#'   ## visualize the tracks (calls function plot.tracks)
#'   plot(Neutrophils)
#' 
"Neutrophils"