thresh=10000;
stack = ImagePlus.getStack(); // grab stack
for (var s=1; s<=stack.getSize(); s++)
{
IJ.write( s);
pixels = stack.getPixels(s); // grab pixel array
for (var i = 0; i < pixels.length; i++)
{
p = pixels[i];
if (p<thresh) {p=0;}
pixels[i] = p;
}
}