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I have a folder containing many images. These are grouped into sets of three images where one filename ends in dsRed).tif, another filename ends in FITC).tif and the other filename ends in DAPI).tif.

How can I tell ImageJ to do different stuff to each image dependent on which filename ending it has?

I have tried to set up macros to run different thresholds, e.g.:

//run("Brightness/Contrast...");
setMinAndMax(0, 20000);
close();

to the different filenames based on scripts found here: http://imagej.1557.x6.nabble.com/open-file-with-specific-partial-name-td5002910.html and here: http://rsb.info.nih.gov/ij/macros/Batch_RGB_Merge.txt but I am having trouble with formatting if else functions with my three filename endings.

Jan Eglinger
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Simon C
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1 Answers1

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You can check the file names with subsequent if ... else statements:

if (endsWith(filename,"dsRed).tif") {
    // do dsRed processing here
} else if (endsWith(filename,"FITC).tif") {
    // do FITC processing here
} else if (endsWith(filename,"DAPI).tif") {
    // do DAPI processing here
}

If you want to group files that contain the same base name, loop only over one of your channels (e.g. dsRed) and use replace:

replace(filename, "dsRed).tif", "FITC).tif");

to process the respective other channel within each loop iteration.

Jan Eglinger
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  • Many thanks Jan. The macro: dir = getDirectory("image"); name=getTitle; if (endsWith(name,"dsRed).tif")) { //run dsRed stuff run("Close"); } else if (endsWith(name,"FITC).tif")) { //run FITC stuff run("Close"); } else if (endsWith(name,"DAPI).tif")) { //run DAPI stuff run("Close"); } worked nicely. – Simon C Dec 17 '15 at 16:37