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Muon tomography based on the measurement of multiple scattering of atmospheric cosmic ray muons is a promising technique for detecting and imaging heavily shielded high-Z nuclear materials such as enriched uranium. This technique could complement standard radiation detection portals currently deployed at international borders and ports, which are not very sensitive to heavily shielded nuclear materials. We image small targets in 3D using 2×2×2 mm3 voxels with a minimal muon tomography station prototype that tracks muons with Gas Electron Multiplier (GEM) detectors read out in 2D with x-y microstrips of 400 μm pitch. With preliminary electronics, the GEM detectors achieve a spatial resolution of 130 μm in both dimensions. With the next GEM-based prototype station we plan to probe an active volume of ~27 liters. We present first results on reading out all 1536 microstrips of a 30×30 cm2 GEM detector for the next muon tomography prototype with final frontend electronics and DAQ system. This constitutes the first full-size implementation of the Scalable Readout System (SRS) recently developed specifically for Micropattern Gas Detectors by the RD51 collaboration. Design of the SRS and first performance results when reading out GEM detectors are presented.