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

Description Usage Arguments Details Examples

take in a SlimFast .txt session file as input, along with several other user-configurable parameters and output options, to return a track list of all the trajectories

1 2	readSlimFa(folder, merge = F, ab.track = F, mask = F, cores = 1, frameRecord = T) .readSlimFast(file, interact = F, ab.track = F, frameRecord = F)

`file`	Full path to SlimFast .txt 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 Diatrack .mat session files output folder.
`merge`	Indicate if the output list should be merged into one- output list is divided by file names otherwise.
`mask`	Indicate if image mask should be applied to screen tracks (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 paralleled.

The naming scheme for each track is as follows:

[Last five characters of the file name].[Start frame #].[Length].[Track #]

(Note: The last five characters of the file name, excluding the extension, cannot contain “.”)

#Basic function call of .readSlimFast
trackll <- readSlimFast(folder = /FILEPATH/, cores = 2)

#Basic function call of .readSlimFast
trackl <- .readSlimFast(interact = T)