Magnetic source imaging (MSI) involves the reconstruction of the current sources in a portion of a body, such as an organ, from measured magnetic field data. The measured magnetic field data may be from one-dimensional or three-dimensional sensors. Aspects of the present invention include systems and methods for reconstructing the electrical current of an organ given magnetic data. In embodiments, reconstruction of three-dimensional current sources is accomplished knowing or estimating the position, or offset, of the sensor plane with respect to the patient in order to form a set of linear equations. Alternatively, reconstruction of three-dimensional current sources is accomplished without knowing the offset of the sensor plane with respect to the patient. In embodiments, the linear and nonlinear systems of equations are iteratively used to obtain the current source information. In embodiments, multi-scale strategies are employed.