In the original example, we saw how to load one dataset and recalibrate.
library(ggplot2)
library(TrackMateR)
# an example file is provided, otherwise use file.choose()
xmlPath <- system.file("extdata", "ExampleTrackMateData.xml", package="TrackMateR")
# read the TrackMate XML file into R using
tmObj <- readTrackMateXML(XMLpath = xmlPath)
# Pixel size is 0.04 um and original data was 1 pixel, xyscalar = 0.04
tmObj <- correctTrackMateData(dataList = tmObj, xyscalar = 0.04, xyunit = "um")For the example file, the spatial units are 1 pixel and not the real
value which is 0.04 um per pixel. So to convert we can specify
xyscalar to change 1 to 0.04 and specify
xyunit to change from “pixel” to “um”. If the file had 2
pixels as the spatial unit (for some reason), to convert to 0.04 um we
would need to use xyscalar = 0.02, xyunit = "um"
The units (xyunit and tunit) can be any
arbitrary string. The use of “um” is preferred over “µm” because the mu
character prints inconsistently in R graphics across platforms.
If the time scaling of the file is 0.07 s and we would prefer ms as the unit,
tmObj <- correctTrackMateData(dataList = tmObj, xyscalar = 0.04, xyunit = "um", tscalar = 1000, tunit = "ms")this is because the file is loaded in and scaled at 1 s, so the
conversion needs to be 1000 ms. If we wanted to switch to minutes, we
would use tscale = 1/60, tunit = "min".
If the time scaling is incorrect, e.g. 1 frame, we would need to
rescale using tscale = 0.07, tunit = "s",
tscale = 70, tunit = "ms", or
tscale = 0.07/60, tunit = "min".
When using compareDatasets(), it is possible to
recalibrate TrackMate XML files en masse by using a CSV file in
the condition subfolder containing the XML files, see
vignette("comparison"). To recalibrate, a separate CSV file
is needed for each condition. Any conditions that do not need
recalibrating simply do not need a CSV file present. The CSV file can
have any name but must follow this format.
value,unit
0.04,um
0.07,s
Using this file, all XML files in the folder will be recalibrated if they are not already at 0.04 micron pixel size and 0.07 s per frame. Adjustments smaller than 2.5% are ignored.
Note that the calibration file should give the correct final scaling required for all files in the folder.
When the rescaling is done using a file like this, TrackMateR will work out the scalar for you. So the file needs to specify what final scaling is required.
In the situation where you have datasets with differing (but correct) timescales and spatial units need to be corrected, use 0 for the value corresponding to time (time rescaling will be ignored) and spatial rescaling will go ahead. Similarly, if you have differening (but correct) spatial scaling between datasets you can rescale time only by using 0 for the spatial value. If you have datasets that need calibrating differently, you will need to group them into condition-level subfolders with a single csv file to specify the correct parameters. Alternatively, consider going back and retracking in TrackMate and specifying the correct parameters.