Microscopic atom optical devices integrated on atom chips allow to precisely control and manipulate ultra-cold (T < 1 µK) neutral atoms and Bose-Einstein condensates (BECs) close to surfaces. The relevant energy scale of a BEC is extremely small (down to < 10⁻¹¹ eV). Consequently, BECs can be utilized as a sensor for variations of the potential energy of the atoms close to the surface. Here we describe how to use trapped atoms as a measurement device and analyze the performance and flexibility of the field sensor. We demonstrate microscopic magnetic imaging with simultaneous high spatial resolution (3 µm) and high field sensitivity (4 nT). With one dimensional BECs, we probe the magnetic field variations close to the surface at distances down to a few microns. Measurements of the magnetic field of a 100 µm wide current carrying wire imply that the magnetic field variations stem from residual variations of the current flow direction, resulting from local properties of the wire. These disorder potentials found near lithographically fabricated wires are two orders of magnitude smaller than those measured close to electroplated conductors.