When customizing your theme in Online Store > Themes > Customize there's often the option to add/delete images to use in sections of your shop: things like your homepage slideshow.
When you add an image there it is stored under Settings > Files in your Shopify admin.
We optimize all of your other images throughout your shop but cannot optimize the images you have in Files. We'd love to but Shopify doesn't offer access to these files through their API, there is just no technical way to do it.
How to optimize them
Until Shopify open up their API to allow Plug in Speed to optimize them automatically, you will have to unfortunately optimize them manually.
It does take a little more time but the good news is it's free.
- Before adding an image in Themes > Customize, or before uploading it to Settings > Files, run it through an image optimization app like ImageOptim for Mac or FileOptimizer for Windows
Try this and if you get stuck feel free to email us at firstname.lastname@example.org with any questions.
PS: Mention to Shopify you'd like an API for Files! It'd make this much simpler with Plug in Speed.