Even today, the automatic digitisation of scanned documents in general but especially the automatic optical music recognition (OMR) of historical manuscripts still remain an enormous challenge, since both handwritten musical symbols and text have to be identified. This paper focuses on the Medieval so-called square notation developed in the 11th-12th century, which is already composed of staff lines, staves, clefs, accidentals, and neumes, that are roughly spoken connected single notes. The aim is to develop an algorithm that captures both the neume and pitch, that is melody information that can be used to reconstruct the original writing. Our pipeline is similar to the standard OMR approach and comprises a novel staff line and symbol detection algorithm, based on deep Fully Convolutional Networks (FCN), which perform pixel-based predictions for either staff lines or symbols and their respective types. Then, the staff line detection combines the extracted lines to staves and yields an F1-score of over 99% for both detecting lines and complete staves. For the music symbol detection we choose a novel approach that skips the step to identify neumes and instead directly predicts note components (NCs) and their respective affiliation to a neume. Furthermore, the algorithm detects clefs and accidentals. Our algorithm recognises these symbols with an F1-score of over 96% if the type is ignored and predicts the true symbol sequence of a staff with a diplomatic symbol accuracy rate (dSAR) of about 87%. If only the NCs without their respective connection to a neume, all clefs, and accidentals are of interest the algorithm reaches an harmonic symbol accuracy rate (hSAR) of approximately 90%.