Yes, you’ll need to initialize it after rendering. To do that, you can make use of Ember’s didInsertElement event on your view (in conjunction with the Ember Run Loop), but additionally, you’ll want to observe whatever collection is feeding your isotope container.
https://gist.github.com/trabus/8001480
Here’s a working example-
http://emberjs.jsbin.com/oWUZIRuR/3
Edit- I threw together an Isotope component example as well for fun.