In this paper, we study the isotropic Schur roots of an acyclic quiver Q with n vertices. We study the perpendicular category A(d) of a dimension vector d and give a complete description of it when d is an isotropic Schur δ. This is done by using exceptional sequences and by defining a subcategory R(Q, δ) attached to the pair (Q, δ). The latter category is always equivalent to the category of representations of a connected acyclic quiver Q R of tame type, having a unique isotropic Schur root, say δ R . The understanding of the simple objects in A(δ) allows us to get a finite set of generators for the ring of semi-invariants SI(Q, δ) of Q of dimension vector δ. The relations among these generators come from the representation theory of the category R(Q, δ) and from a beautiful description of the cone of dimension vectors of A(δ). Indeed, we show that SI(Q, δ) is isomorphic to the ring of semi-invariants SI(Q R , δ R ) to which we adjoin variables. In particular, using a result of Skowroński and Weyman, the ring SI(Q, δ) is a polynomial ring or a hypersurface. Finally, we provide an algorithm for finding all isotropic Schur roots of Q. This is done by an action of the braid group B n−1 on some exceptional sequences. This action admits finitely many orbits, each such orbit corresponding to an isotropic Schur root of a tame full subquiver of Q.