## ----SetParameters,include=FALSE,eval=TRUE------------------------------- library(knitr) opts_chunk$set( concordance=TRUE ) TempDir<-dirname(system.file( "extdata", "SampleFISHgray.jpg", package="FISHalyseR")) ## ----LoadPackage--------------------------------------------------------- library(FISHalyseR) ## ----ComputeProbeMask,results='hide'------------------------------------- f = system.file( "extdata", "SampleFISHgray.jpg", package="FISHalyseR") img = readImage(f) t = calculateMaxEntropy(img) img[img=t] <- 1 ## ----echo=FALSE, results='hide'------------------------------------------ TargetFileName<-paste(TempDir,'exImgMaxEntropyProbes1.jpg',sep='/') writeImage(img, TargetFileName) ## ----ComputeCellMask,results='hide'-------------------------------------- f = system.file( "extdata", "SampleFISHgray.jpg", package="FISHalyseR") img = readImage(f) t = calculateThreshold(img) img[img=t] <- 1 ## ----echo=FALSE, results='hide'------------------------------------------ TargetFileName<-paste(TempDir,'exImgOtsuCellMask.jpg',sep='/') writeImage(img, TargetFileName) ## ----RemoveSmallParticlesProbeMask,results='hide'------------------------ fProbes1 = paste(TempDir,'/',"exImgMaxEntropyProbes1.jpg",sep='') img = readImage(fProbes1) anaImg <- analyseParticles(img, 20, 5,0) ## ----echo=FALSE, results='hide'------------------------------------------ TargetFileName<-paste(TempDir,'exImgProbes1Clean.jpg',sep='/') writeImage(anaImg, TargetFileName) ## ----RemoveSmallParticlesCellMask,results='hide'------------------------- f = paste(TempDir,'/',"exImgOtsuCellMask.jpg", sep='') img = readImage(f) anaImg <- analyseParticles(img, 20000, 1000,0) ## ----echo=FALSE, results='hide'------------------------------------------ TargetFileName2<-paste(TempDir,'exImgCellMaskClean.jpg',sep='/') writeImage(anaImg, TargetFileName2) ## ----ExampleGaussianBlurring,results='hide'------------------------------ bgCorrMethod = list(1,100) ## ----ExampleSepcifiedIlluminationImage,results='hide'-------------------- # path to illumination image illumPath = "../IllCorr.jpg" bgCorrMethod = list(2,illumPath) ## ----ExampleMultidimensionalIlluminationCorrection,results='hide'-------- bgCorrMethod = list(3,"/path/to/stack","*.jpg",6) ## ----SelectProbeChannels,results='hide'---------------------------------- red_Og <- system.file( "extdata", "SampleFISH_R.jpg", package="FISHalyseR") green_Gn <- system.file( "extdata", "SampleFISH_G.jpg", package="FISHalyseR") #Create colour vector list channelColours = list(R=c(255,0,0),G=c(0,255,0)) channelSignals = list(red_Og,green_Gn) ## ----UseRGBImageAsProbeSource-------------------------------------------- combinedImage <- system.file( "extdata", "SampleFISH.jpg", package="FISHalyseR") channelSignals = list(combinedImage) ## ----RunProcessFISH,results='hide'--------------------------------------- illuCorrection = system.file( "extdata", "SampleFISHillu.jpg", package="FISHalyseR") combinedImage <- system.file( "extdata", "SampleFISH.jpg", package="FISHalyseR") red_Og <- system.file( "extdata", "SampleFISH_R.jpg", package="FISHalyseR") green_Gn <- system.file( "extdata", "SampleFISH_G.jpg", package="FISHalyseR") # directory where all the files will be saved writedir = paste(TempDir,sep='') bgCorrMethod = list(0,'') channelColours = list(R=c(255,0,0),G=c(0,255,0)) channelSignals = list(red_Og,green_Gn) sizecell = c(1000,20000) sizeprobe= c(5,20) processFISH(combinedImage,writedir,bgCorrMethod,channelSignals, channelColours,sizecell,sizeprobe) ## ----results='hide',echo=FALSE------------------------------------------- OverlayFile<-paste(TempDir,'SampleFISH.jpg/SampleFISH',sep='') TargetFileName<-paste(TempDir,'SampleFISH.jpg',sep='/')