Calculation of the JD of multiple tracks. Calculation is equivalent to a single time lag point on the ensemble MSD curve, typically represented as a histogram Input is a data frame of tracks imported using readTrackMateXML() The default time step is one frame - which is the equivalent to the plot generated to show displacement versus time.
calculateJD(
dataList,
deltaT = 1,
nPop = 2,
mode = "ECDF",
init = NULL,
timeRes = 1,
breaks = 100
)list of data frame (must include at a minimum - trace (track ID), x, y and t (in real coords)) and calibration
integer to represent the multiple of frames that are to be analysed
integer (either 1,2 or 3) number of populations for the jump distance fitting
string indicated ECDF (default) or hist (histogram)
initialisation parameters for the nls fit for example list(D2 = 200, D1 = 0.1) or list(D2 = 0.01, D1=0.1, D3=10, D4=100)
time resolution per unit of jump. Frame interval is 0.5 s and jump interval is two steps, timeRes = 1.
number of bins for histogram. With ECDF breaks can be high e.g. 100, for mode = "hist" they should be low, perhaps 30.
a list of data frame of jump distances, NAs removed; and a list of parameters called jumpParam (jumptime, deltaT, nPop)
xmlPath <- system.file("extdata", "ExampleTrackMateData.xml", package="TrackMateR")
tmObj <- readTrackMateXML(XMLpath = xmlPath)
#> Units are: 1 pixel and 0.07002736 s
#> Spatial units are in pixels - consider transforming to real units
#> Collecting spot data. Using 4 cores
#> Matching track data...
#> Calculating distances...
tmObj <- correctTrackMateData(tmObj, xyscalar = 0.04)
#> Correcting XY scale.
jdObj <- calculateJD(dataList = tmObj, deltaT = 2)