Experimental and computational imaging applications: Spectral imaging for brain function, and micromagnetics

This work describes two imaging applications. The first involves optically measuring brain activity in mice. Neural activity in any mammalian brain can be indirectly mapped by measuring related changes in blood flow, volume and oxygenation. Hemodynamic-based "neuroimaging" is widely performed non-invasively in humans using magnetic resonance imaging and positron emission tomography. If the brain is exposed, neuroimaging with much higher temporal and spatial resolution can be performed optically with video recording. This approach currently has limited use with humans, but it is frequently applied to characterize cortical activity in animals. The brain surface is typically illuminated with white light and imaged through an optical filter whose spectral profile emphasizes changes in red blood cell (RBC) oxygenation (red profile) or RBC volume (green profile). This work describes the design, characterization and testing of an instrument built to image the brains of mice with greater spectral resolution. It consists of a fixed magnification "standard" imager, similar to video microscopes used by other researchers, and a type of Fourier transform interferometer called the digital array scanning interferometer (DASI). Both systems view the sample at the same time, permitting direct comparison of the novel DASI approach with techniques typically found in the literature. This instrument was used to measure the response in anesthetized mice to whisker stimulation. The results show that although the DASI is capable of detecting this response, its ability to image the response in two-dimensions is limited.;The second imaging application described in this work involves micromagnetics, which refers to modeling the behavior of magnetic recording media. An implementation of a micromagnetic model is used to simulate recording films, and the simulated response of a magnetic force microscope (MFM) to these films is computed. An MFM is a modified atomic force microscope (AFM) that raster scans a magnetic probe over a sample surface in order to measure the sample's stray field. MFM imagery provides limited information about the sample magnetization. This work outlines a new technique for determining sample magnetization from MFM imagery in the context of the micromagnetic recording model.