The MATRIX Graphical User Interface has been optimized for improved work flow and consists of control windows (for setting parameters) and display windows (to visualize the data acquisition). The Scan control window provides a quick method of viewing and setting the imaging parameters. Media - like buttons are used to start, stop, pause and restart a scan.

The MATRIX Control System realizes an n-dimensional concept for data acquisition and data handling and is therefore the ideal platform for tunnelling and force spectroscopy. The spectroscopy control window provides a quick method of viewing and setting parameters such as start and end values, number of points, grid settings, slew rates, delay times and the spectroscopy mode. It also provides activation of ramp reversal and repetitions (multiple curve measurement). The MATRIX Automated Task Environment (MATE) allows the user to modify the standard set up for custom experiments. 

The concept of digital control of the MATRIX Control System offers predefined procedures for  manipulation but also the flexibility for user specific programmable interactions. The MATRIX Automated Task Environment (MATE) or the remote access interface give access to more individual manipulation processes, for example lithography experiments.

The MATRIX Control System virtually eliminates sample drift using an image correlation technique with Fast Fourier Analysis. Based on a reference image the MATRIX software continuously calculates and automatically applies drift vectors for x and y after every image is acquired. Two regulation parameters are available for fine-tuning of the drift correction behaviour.

Instead of mixing or switching input signals, the TWIN Regulator has two independent complete feedback loops, allowing for separate but simultaneous optimization of the two regulation signals. Therefore the TWIN Regulator dramatically improves the efficiency of research work by enabling a seamless transition between modes. The TWIN Regulator also opens up chances for unique experiments by combining or mixing different feedback signals.