processFISH {FISHalyseR} | R Documentation |
Function to automatically quantify FISH probes in cell-culture images.
processFISH(combinedImg, writedir, bgCorrMethod = list(1, 100),channelSignals = NULL, channelColours = NULL, sizeNucleus = c(5, 15000), sizeProbe = c(5, 100), gaussigma = 20, outputImageFormat = ".png")
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 |
processFISH |
does not return any value |
Karesh Arunakirinathan, Andreas Heindl
computeIlluminationCorrection, analyseParticles
## 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)