FISHalyseR (version 1.6.2)

processFISH: FISHalyseR - Automated fluorescence in situ hybridisation quantification in R

Description

Function to automatically quantify FISH probes in cell-culture images.

Usage

processFISH(combinedImg, writedir, bgCorrMethod = list(1, 100),channelSignals = NULL, channelColours = NULL, sizeNucleus = c(5, 15000), sizeProbe = c(5, 100),  gaussigma = 20, outputImageFormat = ".png")

Arguments

combinedImg

Composite image of all available channels

writedir

Traget directory for output files

bgCorrMethod

Specifies the method used to correct for uneven background. Accepts only list types. Currently, four different methods are available: (1) Gaussian blurring, (2) Illumination correction image provided by the user, (3) multidimensional illumination correction (using a stack of images). In case no illumination correction should be applied, pass an empty list to the function

channelSignals

List of images containing the FISH probe

channelColours

List of colour vectors for each single channel

sizeNucleus

Minimum and maximum area (in pixel) of probes to be consided for further analysis

sizeProbe

Minimum and maximum area (in pixel) of probes to be considered for further analysis

gaussigma

Sigma of Gaussian used to blur the image

outputImageFormat

File format for the output image

Value

processFISH

does not return any value

See Also

computeIlluminationCorrection, analyseParticles

Examples

## Specify illumination correction image
illuCorrection = system.file( "extdata", "SampleFISHillu.jpg", package="FISHalyseR")

## Composite image containing available channels
combinedImage <- system.file( "extdata", "SampleFISH.jpg", package="FISHalyseR")

## Single FISH channels containing the probe signals
red_Og   <- system.file( "extdata", "SampleFISH_R.jpg", package="FISHalyseR")
green_Gn <- system.file( "extdata", "SampleFISH_G.jpg", package="FISHalyseR")

## Output directory
writedir = paste(tempdir(),sep='')


## Use provided illumination correction image
bgCorrMethod = list(2,illuCorrection)

## Colour vector for three different probe channels (red, green and blue)
channelColours = list(R=c(255,0,0),G=c(0,255,0))

## Add probe channels to list
channelSignals = list(red_Og,green_Gn)

## Minimum and maximum area allowed for nuclei respectively probes
sizecell = c(1000,20000)
sizeprobe= c(5,20)

## Call processFISH with the specified parameters
processFISH(combinedImage,writedir,bgCorrMethod,channelSignals,
            channelColours,sizecell,sizeprobe)