IJROI_subset: ImageJ ROI subset localizations file

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

ImageJ ROI subset localizations file

Description

This function can be used to subset a localization file based on ROIs (Region of Interest) defined by ImageJ. This can be one or multiple ROIs.

Usage

IJROI_subset(x, file, pxsize = 5)

Arguments

x	A data.frame or list of data.frames with single molecule localizations, can be generated using SMOLR_IMPORT
file	The file location on the ROI file to be processd, either a single ROI (.roi) or multiple ROIs (.zip) can be a vector of file locations equal to the number of localizations files in a list.
pxsize	The pixel size used to create the ROI files in ImageJ defined in nanometer, default = 5 nm.

Value

Returns a list with for every ROI a data.frame.

Author(s)

Optical Imaging Centre ErasmusMC Rotterdam

See Also

read.ijroi read.ijzip

Examples

#see for example files SMoLR_data github
#https://github.com/ErasmusOIC/SMoLR_data/raw/master/IJROI_data.zip

download.file("https://github.com/ErasmusOIC/SMoLR_data/raw/master/IJROI_data.zip","IJROI_data.zip")
unzip("IJROI_data.zip")

#subset one roi
data <- IJROI_subset(smolrdata,file = "IJROI_data/IJROI.roi")

#subset to multiple ROIs
data <- IJROI_subset(smolrdata,file = "IJROI_data/RoiSet.zip")

#plot(SMOLR(data[[1]]),rgb=T)
#plot(SMOLR(data[[2]]),rgb=T)
#plot(SMOLR(data[[3]]),rgb=T)

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