Is is possible to read pixel data from base64 images?

In the source of the page you pointed, there's a function that uses the PNG.js and some other utilities to do what you want:

function show(data){
    var png = new PNG(data);
    var img = document.getElementById('image'), limg = document.getElementById('largeimage');
    document.getElementById('nativeimage').src = 'data:image/png;base64,' + data;
    img.innerHTML = '';
    limg.innerHTML = '';
    img.style.width = png.width + 'px';
    img.style.height = png.height + 'px';
    limg.style.width = (png.width * 3) + 'px';
    limg.style.width = (png.height * 3) + 'px';
    var line;
    while(line = png.readLine())
    {
        for (var x = 0; x < line.length; x++){
            var px = document.createElement('div'), px2 = document.createElement('div');
            px.className = px2.className = 'pixel';
            px.style.backgroundColor = px2.style.backgroundColor = '#' + line[x].toString(16).padRight('0', 6);
            img.appendChild(px);
            limg.appendChild(px2);
        }
    }
}

If you look at the loop in this function , you will notice that it's reading the PNG, line by line and ploting the pixels.

A simplified example would be:

var png = new PNG(data); // data is the base64 encoded data
var line;
var y = 0;
while(line = png.readLine())
{
    for (var x = 0; x < line.length; x++){
        var pixel = doSomethingWithPixelData(x, y, '#' + line[x].toString(16).padRight('0', 6));
    }
    y++;
}

function doSomethingWithPixelData(x, y, color) {
    // guess what? do something with pixel data here ;)
}