//INPUT/OUPUT
#@ String (label=" ", value="Oligodendrocyte Differentiation
Pre-processing", visibility=MESSAGE, persist=false) heading
#@ File(label="Select an input directory:", style="directory") inDir
#@ String (label=" ", value="![](\"http://www.crm.ed.ac.uk/sites/default/themes/website/logo.png\")
", visibility=MESSAGE, persist=false) logo1
myList=getFileList(inDir);
outDir=inDir+"_pre-processed";
File.makeDirectory(outDir);
//CLEAR LOG
print("\\Clear");
print("Running pre-processing");
// CLOSE ALL OPEN IMAGES
while (nImages>0) {
selectImage(nImages);
close();
}
//SET BATCH MODE
setBatchMode(true);
setOption("ExpandableArrays", true);
//FILE MANAGEMENT
batchFiles=0;
for (i=0; i0) {
//create an array containing only the names of the ND2 files in the directory path
nd2Array=newArray(nd2Files);
count=0;
for (j=0; j