you can do this using setInterval method:-
var interval=500,i=0;
setInterval(function(){
i++;
if (i % 2 !== 0) {
document.getElementById('square1').style.visibility = 'visible';
document.getElementById('square2').style.visibility = 'hidden';
} else {
document.getElementById('square1').style.visibility = 'hidden';
document.getElementById('square2').style.visibility = 'visible';
}
},interval);
if you want it to go active after it reached a point on the page use an if construct to verify the scrollTop of the page:-
if(document.body.scrollTop>=500){
...
//do some stuff
}
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