extr_ISBatch - veeninglab/BactMAP GitHub Wiki

Upload ISBatch/Peakfitter data into R

Usage

extr.ISBatch(dataloc, seperator=",", cellList=FALSE)

Arguments

  • dataloc Path to the results table from the “peakfitter” option of the ISBatch imageJ plugin saved as .CSV or tab-delimited .TXT.

  • seperator When .CSV is not comma-separated but by something else, indicate this here.

  • cellList When cellList=TRUE, cellList (see below) will be part of the returned values.

Value

  • cellList copy of original data as dataframe

  • spotframe when data is made using ISBatch’s peak fitter only, this data frame contains only x, y -coordinates and frame numbers. When trajectories are recorded, it also contains the squared-displacement, trajectory ID and trajectory length.

References

http://singlemolecule.github.io/iSBatch/

Caldas, V.E., Punter, C.M., Ghodke, H., Robinson, A. and van Oijen, A.M., 2015. iSBatch: a batch-processing platform for data analysis and exploration of live-cell single-molecule microscopy images and other hierarchical datasets. Molecular BioSystems, 11(10), pp.2699-2708.

See Also

Use spotsInBox to combine the spot data with segmentation data from another program.

Examples

##Choose ISBatch peakfitter output file
dataloc <- file.choose()
##Convert to dataframe
spotframe <- extr.ISBatch(dataloc)

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