  A fully automated linear scanning attenuated total reflection (ATR) accessory
is presented for Fourier transform infrared (FTIR) spectroscopy. The approach
is based on the accurate displacement of a multi-bounce ATR crystal relative to
a stationary infrared beam. To ensure accurate positioning and to provide a
second sample characterization mode, a custom-built microscope was integrated
into the system and the computerized work flow. Custom software includes
automated control and measurement routines with a straightforward user
interface for selecting parameters and monitoring experimental progress. This
cost-effective modular system can be implemented on any research-grade
spectrometer with a standard sample compartment for new bioanalytical chemistry
studies. The system was validated and optimized for use with microfluidic flow
cells containing growing Pseudomonas sp. bacterial biofilms. The
complementarity among the scan positioning accuracy, measurement spatial
resolution and the microchannel dimensions paves the way for parallel
biological assays with real-time control over environmental parameters and
minimal manual labor. By rotating the channel orientation relative to the beam
path, the system could also be used for acquisition of linear biochemical maps
and stitched microscope images along the channel length.
