A multichannel acquisition scheme handling 500 MHz data rate will be presented. The input signal is generated by a fast photo detector which can resolve the pulsed time structure of the synchrotron. Single or multiple photon detection is done with an ADC operating at 1 Gsps sampling rate. Dedicated timing hardware provides the synchronization with the RF of the storage ring. Custom counting logics is implemented using a fully reconfigurable FPGA. Low and high level device drivers are based on the VME standard and the EPICS toolkit. A processor core embedded in the FPGA controls the ADC settings and all the tasks of data transfer between the single photon counters and the Input/Output Controller. Basic Functionality of the system includes: full mapping of the filling pattern, gating of empty buckets and the camshaft, and distributing of distinct buckets into dedicated counters. The acquisition card provides timing reference outputs for the diagnostics, as well as for synchronization of other electronics. First application of the acquisition system are measurements of magnetization dynamics at the Scanning Transmission X-ray Microscope at the SLS with 100 ps time resolution.