Package index • TrackMateR

Loading and correcting TrackMate data

To start, TrackMate XML data needs to be read into R. It may need recalibrating if the data were captured with incorrect parameters.

readTrackMateXML(): Read TrackMate XML output files.
correctTrackMateData(): Correct distance and time of imported TrackMate data.

Automated reports

TrackMateR can be used manually to have fine control over your analysis, however if you just want to analyse your data with default parameters, these two functions will process one dataset, or many

reportDataset(): Report Dataset
compareDatasets(): Compare datasets
compareDatasetValues(): Compare dataset values

Analysing track dynamics

To analyse track dynamics, there are several functions to calculate them. These functions are called (with set parameters) in the automated workflows and all of them must be called to make a report.

calculateAlpha(): Calculate alpha (relationship between MSD and normal diffusion)
calculateCVE(): Calculate CVE (covariance-based estimator)
calculateFD(): Calculate fractal dimension (FD)
calculateJD(): Calculate Jump Distance (JD)
calculateMSD(): Calculate Mean Squared Displacement (MSD)
calculateTrackDensity(): Calculate density of tracks
fittingJD(): Fitting jump distance (JD) data

Generating reports and summaries

Reports and summaries are collections of plots. They can be generated automatically using the automated workflows, or they can be made manually after fine-tuning the analysis of track dynamics.

makeSummaryReport(): Make Summary Report
makeComparison(): Make Comparison Plots

Plotting functions

The autoimated workflows and the reports that can be generated with TrackMateR use several different plotting functions.

plot_tm_MSD(): Make a plot of MSD data
plot_tm_NMSD(): Plot several (n) MSD curves
plot_tm_allTracks(): Make a plot of all tracks
plot_tm_alpha(): Make a histogram of alpha values
plot_tm_cumdistOverTime(): Make a plot of cumulative distance over time
plot_tm_dee(): Make a histogram of D values
plot_tm_displacementHist(): Make a histogram of displacements
plot_tm_displacementOverTime(): Make a plot of displacement over time
plot_tm_durationHist(): Make a histogram of track durations
plot_tm_fd(): Make a histogram of fractal dimension
plot_tm_intensityHist(): Make a histogram of intensities
plot_tm_neighbours(): Make a histogram of track density (number of neighbours)
plot_tm_speed(): Make a histogram of average speed
plot_tm_width(): Make a histogram of the largest point-to-point distance in each track

Analysis of non-TrackMate data

TrackMateR can read and process csv files in a similar way to TrackMate XML outputs. These are typically “ground truth” data sets that have been generated synthetically, but could come from some other package.

compareGTDatasets(): Compare ground truth datasets
readGTFile(): Read a ground truth csv file