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Dera all,
hereby a macro I wrote, it works fine but it probably might be improved
thanks in advance for comments and suggestions,
Fabrice.
--
Senger Fabrice
//Fabrice Senger 09/07/09
//Adapted from :
// recursiveTiffConvert.txt
// Written by Curtis Rueden
// Last updated on 2008 May 6
// Recursively converts files to TIFF using Bio-Formats.
// It was originally written to convert Gatan DM3 files, but you can easily
// change the code to work with any or all extensions of your choice.
ext = "zvi"; // this variable controls the extension of source files
requires("1.39u");
inDir = getDirectory("Choose Directory Containing " + ext + " Files ");
outDir = getDirectory("Choose Directory for TIFF Output ");
setBatchMode(true);
processFiles(inDir, outDir, "");
print("-- Done --");
function processFiles(inBase, outBase, sub) {
list = getFileList(inBase + sub);
File.makeDirectory(outBase + sub);
for (i=0; i<list.length; i++) {
path = sub + list[i];
if (endsWith(path, "/")) {
// recurse into subdirectories
processFiles(inBase, outBase, path);
}
{
print("-- Processing file: " + path + " --");
run("Bio-Formats Importer", "open='" + inBase + path + "' autoscale split_channels view=[Standard ImageJ] stack_order=Default");
name = getTitle;
dotIndex = indexOf(name, ".");
joe = substring(name, 0, dotIndex);
n=nImages;
for (j=0; j<n; j++) {
run("Misc...", "divide=Infinity hide");
selectImage(j+1);
run("Duplicate...", "duplicate range=[] title=Channel"+j+1);
}
run("Merge Channels...", "red=Channel3 green=Channel2 blue=Channel1 gray=*None*");
saveAs("tiff", outDir+joe);
}
}
}
exit()
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