Supplementary Figure 7: Synchronization scheme of the fast scanning axis with the timing signal of LCLS.

Once the goniometer is in the right position to perform a line scan a TTL “scanner ready” signal is sent from the goniometer controller to the LCLS control system. When the signal is received by the LCLS control systems it starts sending a predefined sequence of TTL signals co-incident to the X-ray pulse arrival times with a frequency of 120 Hz. At the beginning the pulse picker at XPP is blocking the beam and no X-ray pulses are delivered to the sample. These first timing pulses are used for acceleration of the sample scanner and to synchronize the position of the pores with the beam position and arrival time of the X-ray pulses. Once the pore position is in phase with the arrival of the X-ray pulses the pulse picker opens and X-rays are hitting the crystals located in the pores of the chip and diffraction images are recorded. Once the end of a line is reached, the pulse picker closes and the X-rays are blocked. A few more timing signals are sent out for deceleration of the chip. After no signals are received by the goniometer controller anymore, the goniometer moves to the starting position of the next scan line, sends out the “scanner ready” signal to the controller, which then continues scanning the line in reverse direction and so on. After the number of predefined lines are scanned in a meander-like fashion no “scanner ready’ signal is sent out anymore and data collection is finished.