ImageJ 40 by 40 box

40X40Box.ijm

//make rectange 40 by 40 in center of image

//get dimensions of image
var imageWidth, imageHeight, channels, slices, frames;
getDimensions(imageWidth, imageHeight, channels, slices, frames);

//set rectange vars
var rectangleWidth = 40;
var rectangleHeight = 40;
var rectangleX = (imageWidth - rectangleWidth)/ 2;
var rectangleY = (imageHeight - rectangleHeight)/2;
makeRectangle(rectangleX, rectangleY, rectangleWidth, rectangleHeight);