Hyperspectral Fourier transform spectrometer for white light reflection spectroscopy and spectral self interference fluorescence microscopy

This dissertation describes the design, build, and test of a hyperspectral Fourier transform spectrometer (HS-FTS) intended for biological imaging and sensing studies on surfaces. The HS-FTS has two modes of operation: a white light reflectance spectroscopy (WLRS) mode and a spectral self interference fluorescence microscopy (SSFM) mode. WLRS is used to determine an optical thickness profile of biological material bound to a multilayer surface by exploiting the spectral content of light reflected from the surface. WLRS can be used on its own as a label-free detection technique. SSFM is used to establish the average height of fluorophores bound to a specific site on the biomolecules immobilized on the surface by making use of the spectral content of light emitted by the fluorophores. The two techniques can be used in concert to predict molecular conformation of the biomolecules.;Prior to the initiation of this research, the WLRS/SSFM hybrid approach had been demonstrated as a single point measurement where spatial information was obtained by laterally scanning the sample. The HS-FTS improves upon the previous work by enabling simultaneous spectral measurement over all spatial resolution elements, thereby increasing the speed at which a surface can be profiled and also minimizing lateral errors due to movement of the sample. The HS-FTS offers a number of advantages over other hyperspectral imaging technologies such as pushbroom gratings, tunable filters, and computed tomography systems. These advantages include the spectral/spatial multiplex which yields a radiometric benefit, ease of spectral band selection, the ability to operate over large spectral ranges without order sorting issues, and superior background rejection owing to the synchronous detection scheme.;This dissertation presents WLRS and SSFM measurement concepts along with background on Fourier transform spectroscopy. The design, build, characterization, and demonstration of the instrument are then described in detail. Characterization includes WLRS and SSFM measurements of photolithographically etched silicon dioxide on silicon substrates. Data reduction techniques in spectral and temporal spaces are presented and demonstrated on these samples. Biological demonstrations include static measurements of protein spots on surfaces in both operating modes as well as dynamic measurements of DNA spots on specialized polymer surfaces in SSFM mode.