extr_ISBatch: Import ISBatch/Peakfitter data into R

In vrrenske/shinyspots: Visualization and Analysis of Bacterial Cell Segmentation and Fluorescence Data

Import ISBatch/Peakfitter data into R

Description

Import ISBatch/Peakfitter spot coordinates and/or trajectories from a .txt or .csv 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 TRUE, the value cellList is part of the returned output (see below).

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.

Author(s)

Renske van Raaphorst

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

## Not run: 
##Choose ISBatch peakfitter output file
dataloc <- file.choose()
##Convert to dataframe
spotframe <- extr_ISBatch(dataloc)

## End(Not run)

vrrenske/shinyspots documentation built on Oct. 28, 2023, 12:26 p.m.