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An ImageJ macro that performs image registration using the [StackReg](http://bigwww.epfl.ch/thevenaz/stackreg/) plugin on all the TIFF movies in a folder.
// "BatchStackreg" by James Ackman June 7, 2007
//
// This macro batch processes all the files in a folder and any
// subfolders in that folder. In this example, it runs the Stackreg plugin for automatic
// image registration of multipageTIFF files. Stackreg plugin must be installed.
// For other kinds of processing, edit the processFile() function at the end of this macro.
// Based on the BatchProcessFolders.txt macro on the ImageJ website.
requires("1.33s");
dir = getDirectory("Choose a Directory ");
//setBatchMode(true);
count = 0;
countFiles(dir);
n = 0;
processFiles(dir);
print(count+" files processed");
function countFiles(dir) {
list = getFileList(dir);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/"))
countFiles(""+dir+list[i]);
else
count++;
}
}
function processFiles(dir) {
list = getFileList(dir);
for (i=0; i<list.length; i++) {
if (endsWith(list[i], "/"))
processFiles(""+dir+list[i]);
else {
showProgress(n++, count);
path = dir+list[i];
processFile(path);
}
}
}
function processFile(path) {
if (endsWith(path, ".tif")) {
open(path);
num=nSlices;
if (num >200) {
run("StackReg ", "transformation=[Rigid Body]");
}
//run("Subtract Background...", "rolling=50 white");
save(path);
close();
}
}
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