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The category of abelian varieties over $\mathbb{F}_q$ is shown to be anti-equivalent to a category of $\mathbb{Z}$-lattices that are modules for a non-commutative pro-ring of endomorphisms of a suitably chosen direct system of abelian varieties over $\mathbb{F}_q$. On full subcategories cut out by a finite set $w$ of conjugacy classes of Weil $q$-numbers, the anti-equivalence is represented by what we call $w$-locally projective abelian varieties., Comment: 41 pages, revised version following advice by the referee

We assign functorially a $\mathbb{Z}$-lattice with semisimple Frobenius action to each abelian variety over $\mathbb{F}_p$. This establishes an equivalence of categories that describes abelian varieties over $\mathbb{F}_p$ avoiding $\sqrt{p}$ as an eigenvalue of Frobenius in terms of simple commutative algebra. The result extends the isomorphism classification of Waterhouse and Deligne's equivalence for ordinary abelian varieties., Comment: Accepted for publication in Algebra & Number Theory

There are many equivalent ways to describe the p-torsion of a principally polarized abelian variety in characteristic p. We briefly explain these methods and then illustrate them for abelian varieties A of arbitrary dimension g in several important cases, including when A has p-rank f and a-number 1 and when A has p-rank f and a-number g-f. We provide complete tables for abelian varieties of dimension up to four.