The DGF Pixie-16 is a scalable 16-channel data acquisition system based on the PCI standard used for nuclear physics and other applications requiring many channels. Originally developed as a digital spectrometer for gamma-ray analysis with high-purity Ge (HPGe) detectors, this system is now being adapted for use with superconducting microcalorimeters. The output signal from each microcalorimeter pixel is read out with a separate channel of the Pixie-16 system. The incoming signal is first adapted for the analog-to-digital converter (ADC) with an analog signal conditioning unit that includes input termination and overvoltage protection circuitry, a user-defined offset adjustment, fixed gain, and a Nyquist filter. Since microcalorimeter pulses have time constants three orders of magnitude greater than HPGe, the ADCs Nyquist filter bandwidth was reduced to remove noise contributions from high frequencies. The signal is digitized using a 12 bit, 100 MHz ADC and read into the digital processing core of the system, which has three major components: (i) four field-programmable gate arrays (FPGA) for filtering, (ii) a digital signal processor (DSP) for pulse height measurements, and (iii) a system interface FPGA.