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);

Try the getImageData method:

var data = context.getImageData(x, y, 1, 1).data;
var rgb = [ data[0], data[1], data[2] ];

Yup, check out getImageData(). Here's an example of breaking CAPTCHA with JavaScript using canvas:

OCR and Neural Nets in JavaScript

Note that getImageData returns a snapshot. Implications are:

• Changes will not take effect until subsequent putImageData
• getImageData and putImageData calls are relatively slow

You can use i << 2.

const data = context.getImageData(x, y, width, height).data;
const pixels = [];

for (let i = 0, dx = 0; dx < data.length; i++, dx = i << 2) {
    pixels.push({
        r: data[dx  ],
        g: data[dx+1],
        b: data[dx+2],
        a: data[dx+3]
    });
}

Fast and handy

Use following class which implement fast method described in this article and contains all you need: readPixel, putPixel, get width/height. Class update canvas after calling refresh() method. Example solve simple case of 2d wave equation

class Screen{
  constructor(canvasSelector) {
    this.canvas = document.querySelector(canvasSelector);
    this.width  = this.canvas.width;
    this.height = this.canvas.height;
    this.ctx = this.canvas.getContext('2d');
    this.imageData = this.ctx.getImageData(0, 0, this.width, this.height);
    this.buf = new ArrayBuffer(this.imageData.data.length);
    this.buf8 = new Uint8ClampedArray(this.buf);
    this.data = new Uint32Array(this.buf);  
  }
  
  // r,g,b,a - red, gren, blue, alpha components in range 0-255
  putPixel(x,y,r,g,b,a=255) {
    this.data[y * this.width + x] = (a << 24) | (b << 16) | (g <<  8) | r;
  }
  
  readPixel(x,y) {
    let p= this.data[y * this.width + x]
    return [p&0xff, p>>8&0xff, p>>16&0xff, p>>>24];
  }

  refresh() {
    this.imageData.data.set(this.buf8);
    this.ctx.putImageData(this.imageData, 0, 0);
  }
}




// --------
// TEST
// --------

let s=new Screen('#canvas');

function draw() {

  for (var y = 1; y < s.height-1; ++y) {
    for (var x = 1; x < s.width-1; ++x) {      
      let a = [[1,0],[-1,0],[0,1],[0,-1]].reduce((a,[xp,yp])=> 
        a+= s.readPixel(x+xp,y+yp)[0]
      ,0);
      let v=a/2-tmp[x][y];
      tmp[x][y]=v<0 ? 0:v;
    }
  }

  for (var y = 1; y < s.height-1; ++y) {
    for (var x = 1; x < s.width-1; ++x) {  
      let v=tmp[x][y];
      tmp[x][y]= s.readPixel(x,y)[0];
      s.putPixel(x,y, v,v,v);
    }
  }

  s.refresh();
  window.requestAnimationFrame(draw)
}

// temporary 2d buffer ()for solving wave equation)
let tmp = [...Array(s.width)].map(x => Array(s.height).fill(0));

function move(e) { s.putPixel(e.x-10, e.y-10, 255,255,255);}

draw();

<canvas id="canvas" height="150" width="512" onmousemove="move(event)"></canvas>
<div>Move mouse on black box</div>

If you want to extract a particular color of pixel by passing the coordinates of pixel into the function, this will come in handy:

var canvas = document.getElementById("canvas");
var ctx = canvas.getContext("2d");
function detectColor(x, y){
  data=ctx.getImageData(x, y, 1, 1).data;
  col={
    r:data[0],
    g:data[1],
    b:data[2]
  };
  return col;
}

x, y is the coordinate you want to filter out color.

var color = detectColor(x, y)

The color is the object, you will get the RGB value by color.r, color.g, color.b.