On this page https://www.goodboydigital.com/pixijs/examples/13/?base=pixijs&category=examples&post=13 it is easy to get all objects that you are interested in because they are global - just see source of that page:
<body>
<script>
// create an new instance of a pixi stage
var stage = new PIXI.Stage(0xFFFFFF, true);
stage.setInteractive(true);
var sprite= PIXI.Sprite.fromImage("spinObj_02.png");
//stage.addChild(sprite);
// create a renderer instance
//var renderer = new PIXI.CanvasRenderer(800, 600);//PIXI.autoDetectRenderer(800, 600);
var renderer = PIXI.autoDetectRenderer(620, 380);
// set the canvas width and height to fill the screen
//renderer.view.style.width = window.innerWidth + "px";
//renderer.view.style.height = window.innerHeight + "px";
renderer.view.style.display = "block";
// add render view to DOM
document.body.appendChild(renderer.view);
...
renderer.render(stage);
...
You can try using them via developer tools console (in browser like Firefox or Chrome etc);
For example you can open your devtools and run following line in console:
graphics.position.x+=10;
You should see some objects in canvas moving to right.
Anyway, as i said above: this is the easy case - everything as global variables. When PIXI objects are created inside some other scope (inside some function / class etc) then you will not be able to get them.
About Application: As you see there is no Application here - the "renderer" is used directly - is what you need to render on canvas. Application is just a "helper" object that is not required to work with PIXI - as you my read in its source: https://github.com/pixijs/pixi.js/blob/v5.3.7/packages/app/src/Application.ts.
/**
* Convenience class to create a new PIXI application.
*
* This class automatically creates the renderer, ticker and root container.
...
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