readParticleTracker-methods: readParticleTracker

In snjy9182/smt: Single Molecule Tracking

Description

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

Usage

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

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

Arguments

file	Full path to Diatrack .mat session file.
interact	Open menu to interactively choose file.
ab.track	Use absolute coordinates for tracks.
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 ImageJ .csv files output folder.
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 paralleled.

Details

The usage of readParticleTracker() is equivalent to ReadDiatrack().

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")

Examples

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

snjy9182/smt documentation built on May 24, 2019, 7:19 a.m.