We consider the FK-Ising model in two dimensions at criticality. We obtain bounds on crossing probabilities of arbitrary topological rectangles, uniform with respect to the boundary conditions, generalizing results of [DCHN11] and [CS12]. Our result relies on new discrete complex analysis techniques, introduced in [Che12]. We detail some applications, in particular the computation of so-called universal exponents, the proof of quasi-multiplicativity properties of arm probabilities, and bounds on crossing probabilities for the classical Ising model