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Make Substack vs Duplicate Loses Overlay

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Alan Brooks

Make Substack vs Duplicate Loses Overlay

This post was updated on .

If you use the Make Substack... command (ij.plugin.SubstackMaker) to duplicate a subset of a stack, you lose any Overlay content. However, if you use Duplicate... (ij.plugin.Duplicator) to accomplish the same thing, the Overlay content is preserved. This is a minor issue, but unexpected at least to me.

Here is a minimal JavaScript macro that reproduces the issue:

imp = IJ.openImage("https://imagej.net/images/flybrain.zip");
IJ.run("Labels...", "color=white font=12 draw");
IJ.run(imp, "Label...", "format=0 starting=0 interval=1 x=5 y=5 font=24 text=[] range=1-57 use use_text");
imp.setSlice(4);
imp.show();

imp2 = imp.crop("1-5");  // Duplicate... setup to get the 1st 5 slices
imp2.setSlice(4);
imp2.show()

imp3 = SubstackMaker.run(imp, "1-5");  // Make Substack... setup to get the 1st 5 slices
imp3.setSlice(4);
imp3.show()