In this article, we investigate short topological decompositions of non-orientable surfaces and provide algorithms to compute them. Our main result is a polynomial-time algorithm that for any graph embedded in a non-orientable surface computes a canonical non-orientable system of loops so that any loop from the canonical system intersects any edge of the graph in at most 30 points. The existence of such short canonical systems of loops was well known in the orientable case and an open problem in the non-orientable case. Our proof techniques combine recent work of Schaefer-Štefankovič with ideas coming from computational biology, specifically from the signed reversal distance algorithm of Hannenhalli-Pevzner. The existence of short canonical non-orientable systems of loops confirms a special case of a conjecture of Negami on the joint crossing number of two embeddable graphs. We also provide a correction for an argument of Negami bounding the joint crossing number of two non-orientable graph embeddings.