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Dec 25, 2019 at 1:19 comment added ssx @Manoel: note that $D$ is not a genus $2$ curve or even an irreducible divisor. The point is that one can find non-isomorphic genus $2$ curves $C, C'$ on $E\times E$. In Hayashida's paper one associates a matrix $M(D)$ to every divisor $D$ in $E\times E$ such that $M(D)=M(D')$ if and only if $D$ and $D'$ are algebraically equivalent. He then considers an equivalence relation on the set of all effective divisors on $E\times E$ with self intersection $2$; the relation is such that two genus 2 curves (irreducible effective divisors) are equivalent if and only if they are isomorphic.
Dec 24, 2019 at 22:21 comment added Manoel That is $(E \times E, D)$ and $(J(C), C)$ are not isomorphic as principally polarized abelian varieties. Why does this imply that I cannot recover the curve $C$?
Dec 24, 2019 at 22:21 comment added Manoel Following the reasoning of the first part of your answer, I arrive at the following situation: $(E\times E, C)$ is isomorphic to the Jacobian variety $J(C)$ as principally polarized abelian varieties. On the other hand, for points $a, b \in E$ a divisor $D = a \times E+E \times b$ is effective and $(E \times E, D)$ is also a principally polarized abelian variety. But $(E \times E, C)$ and $(E \times E, D)$ are not isomorphic as principally polarized abelian varieties.
Dec 24, 2019 at 20:59 vote accept Manoel
Dec 24, 2019 at 12:06 history edited ssx CC BY-SA 4.0
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Dec 24, 2019 at 2:38 history answered ssx CC BY-SA 4.0