There's a section about pixel manipulation in the W3C documentation.
Here's an example on how to invert an image:
var context = document.getElementById('myCanvas').getContext('2d');
// Get the CanvasPixelArray from the given coordinates and dimensions.
var imgd = context.getImageData(x, y, width, height);
var pix = imgd.data;
// Loop over each pixel and invert the color.
for (var i = 0, n = pix.length; i < n; i += 4) {
pix[i ] = 255 - pix[i ]; // red
pix[i+1] = 255 - pix[i+1]; // green
pix[i+2] = 255 - pix[i+2]; // blue
// i+3 is alpha (the fourth element)
}
// Draw the ImageData at the given (x,y) coordinates.
context.putImageData(imgd, x, y);