Biomedical subjects
Publications and source records attributed to Thomas J Naughton.
We discuss an optical system that encodes an input signal to a polarization state, using a spatial light modulator (SLM). Using two SLMs the optical system multiplexes two 2D signals in the polarization domain, and we demonstrate the multiplexing of two binary images. The encryption and decryption of two binary images using an XOR operation is also presented.
We propose a task-specific digital holographic capture system for three-dimensional scenes, which can reduce the amount of data sent from the camera system to the receiver and can effectively reconstruct partially occluded objects. The system requires knowledge of the object of interest, but it does not require a priori knowledge of either the occlusion or the distance the object is from the camera. Subwindows of the camera-plane Fresnel field are digitally propagated to reveal different perspectives of the scene, and these are combined to overcome the unknown foreground occlusions. The nature of the occlusions and the effect of subwindows are analyzed thoroughly by using the Wigner distribution function. We demonstrate that a careful combination of reconstructions from subwindows can reveal features that are not apparent in a reconstruction from the whole hologram. We provide results by using optically captured digital holograms of real-world objects and simulated occlusions.
BACKGROUND: In recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution models in order to produce accurate phylogenies. In the past, many empirical models of amino acid substitution have been derived using a variety of different methods and protein datasets. These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner. RESULTS: We start by highlighting the potential dangers of arbitrarily choosing protein models by demonstrating an empirical example where a single alignment can produce two topologically different and strongly supported phylogenies using two different arbitrarily-chosen amino acid substitution models. We demonstrate that in simple simulations, statistical methods of model selection are indeed robust and likely to be useful for protein model selection. We have investigated patterns of amino acid substitution among homologous sequences from the three Domains of life and our results show that no single amino acid matrix is optimal for any of the datasets. Perhaps most interestingly, we demonstrate that for two large datasets derived from the proteobacteria and archaea, one of the most favored models in both datasets is a model that was originally derived from retroviral Pol proteins. CONCLUSION: This demonstrates that choosing protein models based on their source or method of construction may not be appropriate.
We compress phase-shift digital holograms (whole Fresnel fields) for the transmission of three-dimensional images. For real-time networking applications, the time required to compress can be as critical as the compression rate. We achieve lossy compression through quantization of both the real and imaginary streams, followed by a bit packing operation. Compression losses in the reconstructed objects were quantified. We define a speedup metric that combines space gains due to compression with temporal overheads due to the compression routine and the transmission serialization. We empirically verify transmission speedup due to compression using a special-purpose Internet-based networking application.
A three-dimensional (3D) object reconstruction technique that uses only phase information of a phase-shifting digital hologram and a phase-only spatial-light modulator is proposed. It is well known that a digital hologram can store both amplitude and phase information of an optical electric field and can reconstruct the original 3D object in a computer. We demonstrate that it is possible to reconstruct optically 3D objects using only phase information of the optical field calculated from phase-shifting digital holograms. The use of phase-only information enables us to reduce the amount of data in the digital hologram and reconstruct optically the 3D objects using a liquid-crystal spatial light modulator without optical power loss. Numerical evaluation of the reconstructed 3D object is presented.
We present the results of applying lossless and lossy data compression to a three-dimensional object reconstruction and recognition technique based on phase-shift digital holography. We find that the best lossless (Lempel-Ziv, Lempel-Ziv-Welch, Huffman, Burrows-Wheeler) compression rates can be expected when the digital hologram is stored in an intermediate coding of separate data streams for real and imaginary components. The lossy techniques are based on subsampling, quantization, and discrete Fourier transformation. For various degrees of speckle reduction, we quantify the number of Fourier coefficients that can be removed from the hologram domain, and the lowest level of quantization achievable, without incurring significant loss in correlation performance or significant error in the reconstructed object domain.