readParticleTracker-methods: readParticleTracker
In sheng-liu/smt: Single Molecule Tracking

Description Usage Arguments Details Value Examples

Read output file (tracks/trajectories in csv format) from ParticleTracker (a program of ImageJ plugin MosaicSuit).

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readParticleTracker(folder, merge = F, ab.track = F, mask = F, cores = 1, frameRecord = T)

.readParticleTracker(file, interact = F, ab.track = F, frameRecord = F)

`frameRecord`	Add a fourth column to the track list after the xyz-coordinates for the frame that coordinate point was found (especially helpful when linking frames).
`folder`	Full path to Diatrack output file.
`merge`	An logical indicate if the output list should be merged into one. Default merge = FALSE, output list is divided by file names.
`mask`	An logical indicate if image mask should be applied to screen tracks. Default False. Note the mask file should have the same name as the Diatrack output txt file with a "_MASK.tif" ending. Users can use plotMask() and plotTrackOverlay() to see the mask and its effect on screening tracks.
`cores`	Number of cores used for parallel computation. This can be the cores on a workstation, or on a cluster. Tip: each core will be assigned to read in a file when paralelled.

The usage of readParticleTracker() is equivalent to ReadDiatrack(). default merge = FALSE, so the researcher can assay variations between files. Keep both output as two level list is for simplicity of downstream analysis.

Note: the folder name should not contain ".", as it is a key character for subsequent indexing of file names.

trackID=fileID.frameID.duration.indexPerFile.indexPerTrackll

This "indexPerFile" is the index within a diatrackFile.

This "indexPerTrackll" is the index within a trackll, which is unique.

The macro used for generating the csv file is also included in ImageJ folder of the package: folder=system.file("extdata","ImageJ",package="smt")

merge = F Defult. A list of list of data.frames. First level is a list of file names in Diatrack output folder, second level is a list of data.frames from individual output file.
merge = T A list list of data.frames. First level is the folder name. second level is a list of data.frames from all Diatrack output files merged into one

# reading in tracks
folder=system.file("extdata","ImageJ",package="smt")
trackll=readParticleTracker(folder)
str(trackll,max.level=2)

# masking with image mask
trackll.masked=readParticleTracker(folder=folder,merge=F,mask=T)
str(trackll.masked,1)

# compare the masking effect
plotTrackOverlay(trackll)
plotTrackOverlay(trackll.masked)

# if Nucclear image is available
plotNucTrackOverlay(folder=folder,trackll=trackll)
plotNucTrackOverlay(folder=folder,trackll=trackll.masked)

# plot mask
plotMask(folder=folder)