Browsing by Subject "Medical Imaging"
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Item Automated counting of cell bodies using Nissl stained cross-sectional images(2009-05-15) D'Souza, Aswin CletusCell count is an important metric in neurological research. The loss in numbers of certain cells like neurons has been found to accompany not only the deterioration of important brain functions but disorders like clinical depression as well. Since the manual counting of cell numbers is a near impossible task considering the sizes and numbers involved, an automated approach is the obvious alternative to arrive at the cell count. In this thesis, a software application is described that automatically segments, counts, and helps visualize the various cell bodies present in a sample mouse brain, by analyzing the images produced by the Knife-Edge Scanning Microscope (KESM) at the Brain Networks Laboratory. The process is described essentially in five stages: Image acquisition, Pre- Processing, Processing, Analysis and Refinement, and finally Visualization. Nissl staining is a staining mechanism that is used on the mouse brain sample to highlight the cell bodies of our interest present in the brain, namely neurons, granule cells and interneurons. This stained brain sample is embedded in solid plastic and imaged by the KESM, one section at a time. The volume that is digitized by this process is the data that is used for the purpose of segmentation. While most sections of the mouse brain tend to be comprised of sparsely populated neurons and red blood cells, certain sections near the cerebellum exhibit a very high density and population of smaller granule cells, which are hard to segment using simpler image segmentation techniques. The problem of the sparsely populated regions is tackled using a combination of connected component labeling and template matching, while the watershed algorithm is applied to the regions of very high density. Finally, the marching cubes algorithm is used to convert the volumetric data to a 3D polygonal representation. Barring a few initializations, the process goes ahead with minimal manual intervention. A graphical user interface is provided to the user to view the processed data in 2D or 3D. The interface offers the freedom of rotating and zooming in/out of the 3D model, as well as viewing only cells the user is interested in analyzing. The segmentation results achieved by our automated process are compared with those obtained by manual segmentation by an independent expert.Item Barium Titanate Nanoparticles as Exogenous Contrast Agents in Second Harmonic Optical Coherence Tomography(2013-05-06) Pearson, Jeremy TI propose and demonstrate a method by which barium titanate nanoparticle clusters can be used as exogenous contrast agents in Second Harmonic Optical Coherence Tomography imaging systems to localize and highlight desired regions of tissue. SH-OCT has previously been used to identify collagen within OCT images. However, SH-OCT signals from collagen are highly susceptible to inferior reflector artifacts because most of the second harmonic generated light is forward scattered. Second harmonic generating nanoparticle clusters exhibit high scattering properties, which can give them the advantage of backscattering a large quantity of second harmonic light while attenuating the forward scattered light. In this research project, a mathematical model is proposed in which the backward to forward scattering ratio of second harmonic generated light from nanoparticle layers is exponentially proportional to the thickness of the layer. This model was supported by measurements of the backward to forward scattering ratio of second harmonic light in barium titanate nanoparticles layers. This indicates that nanoparticle clusters can be designed and manufactured with the proper thickness so that they generate a large second harmonic signal without creating inferior reflector artifacts.Item In vivo blood oxygenation level measurements using photoacoustic microscopy(Texas A&M University, 2007-09-17) Sivaramakrishnan, MathangiWe investigate the possibility of extracting accurate functional information such as local blood oxygenation level using multi-wavelength photoacoustic measurements. Photoacoustic microscope is utilized to acquire images of microvasculature in smallanimal skin. Owing to endogenous optical contrast, optical spectral information obtained from spectral photoacoustic measurements are successfully inverted to yield oxygenation level in blood. Analysis of error propagation from photoacoustic measurements to inverted quantities showed minimum inversion error in the optical wavelength region of 570-600 nm. To obtain accurate and vessel size independent blood oxygenation measurements, transducers with central frequency of more than 25 MHz are needed for the optical region of 570-600 nm used in this study. The effect of transducer focal position on accuracy of blood oxygenation level quantification was found to be negligible. To obtain accurate measurements in vivo, one needs to compensate for factors such as spectral dependent optical attenuation.