SMOLR_KDE: 2D kernel density estimation from a single molecule dataset

In ErasmusOIC/SMoLR: Single Molecule Localization Microscopy visualization and analysis in R

2D kernel density estimation from a single molecule dataset

Description

Fits a 2D kernel density estimation to single molecule localization data based on bkde2de from the kernsmooth package

Usage

SMOLR_KDE(x, y, ch, prec, bandwidth, input_xsize, input_ysize, px, threshold, fit, file, output)

Arguments

x	X coordinates in nm, a localizations data.frame or a list of data.frames.
y	Y coordinates in nm
ch	Channel number (default=1)
prec	Precision in nm (default=20)
bandwidth	Bandwidth of the kernel used to fit, typically a bandwidth of around the precision is used. The bandwidth is a vector containing an x and a y size. (default = c(20,20))
xlim	Vector with the upper and lower limit of x axis (x coordinates outside limits will be discarded if fit=TRUE)
ylim	Vector with the upper and lower limit of y axis (y coordinates outside limits will be discarded if fit=TRUE)
px	Pixelsize in nm
threshold	Threshold for the kde in localizations per squared nm, used to create binary image of the single molecule data
fit	If fit=TRUE all coordinates that lie outside of indicated xlim and ylim values are discarded
file	Path and name of file to save tif to (i.e. file="D:/test.tif", will return the files test_kde.tif and test_kde_bin.tif)
output	Set output to "tiff" to output tiff files of the KDE

Value

kde	Array containing the kernel density estimation
kde_binary	Array containing the binary thresholded image
parameters	Parameters of the input
int	list of intensities from the kde per localization, unique feature id per localization
inputs	list of values that were the input in the function, for reference

Author(s)

Optical Imaging Centre ErasmusMC Rotterdam

References

Kernel density estimation uses the bkde2D algorithm from the kernsmooth package

See Also

bkde2D

Examples

test_kde <- SMOLR_KDE(smolrdata)
plot(test_kde)
plot(test_kde)
plot(test_kde,contrast = 2,saturate = 0.05,brightness = 0)
SMOLR_PLOT(smolrdata,color=SMOLR_KDE(smolrdata)[[4]][,2],split_ch=TRUE)

ErasmusOIC/SMoLR documentation built on Aug. 20, 2024, 8:50 p.m.