Muography is a technique for the imaging of the interior of large size objects, such as volcanoes, mountains, with the measurement of the flux of high energy cosmic muons. The electrons/positrons, high energy hadrons and low energy muons can contaminate the muon signal. These background sources require a good understanding of the creation processes, as well as reliable simulation frameworks with high predictive power. A simulation framework based on GEANT4 has been established to pin down the key features of the background particles. The particle spectra and ratios have been compared to existing other measurements as well as other simulation programs. The correlation between simultaneously arriving particles have also been quantitatively investigated, demonstrating that electrons and positrons tend to arrive close to each other and with low relative angle. This feature, which is highly relevant for counting detectors, has been experimentally verified at shallow depth underground and under open sky using the new variant of MWPC detectors. A low-noise MWPC-based tracking detector (Muographic Observation System, mMOS) has been installed at the Sakurajima volcano. The report on the detector performance and the verification of the applicability of mMOS for long-range muography will be presented.