We present a novel tunnel magnetoresistance (TMR) scanning microscope set-up capable of quantitatively imaging the magnetic stray field patterns of micron-sized elements in 3D. By incorporating an Anderson loop measurement circuit for impedance matching, we are able to detect magnetoresistance changes of as little as 0.006%/Oe. By 3D rastering a mounted TMR sensor over our magnetic barcodes, we are able to characterize the complex domain structures by displaying the real component, the amplitude and the phase of the sensor's impedance. The modular design, incorporating a TMR sensor with an optical microscope, renders this set-up a versatile platform for studying and imaging immobilised magnetic carriers and barcodes currently employed in biosensor platforms, magnetotactic bacteria and other complex magnetic domain structures of micron-sized entities. The quantitative nature of the instrument and its ability to produce vector maps of magnetic stray fields has the potential to provide significant advantages over other commonly used scanning magnetometry techniques.