How to indicate that a word / acronym X will refer to Y in academic writing

I have often seen it in brackets, as in your example, with quotation marks and a capital:

Tomatoes ("Toms") are red. This is false, as some Toms are green. I like Toms.

I suppose the capital is not always necessary if the thing referred to isn't a name or a proper noun; however, it is easier to spot that this thing is special later if you use a capital throughout.

In legal texts, they use hereafter or hereinafter:

Tomatoes, hereafter called "Toms", are red. This is false, as some Toms are green. I like Toms.

But this is not recommended in academic writing. You could simply use in this paper and explain what you're going to do:

Tomatoes, which will be referred to as "Toms" in this paper, are red. This is false, as some Toms are green. I like Toms.

Tomatoes, which we will refer to as "Toms" in this paper, are red. This is false, as some Toms are green. I like Toms.