Multi-modal diffuse optical tomography and bioluminescence tomography system for preclinical imaging

The development, characterisation and testing of a novel all-optical, multi-modal preclinical biomedical imaging system is presented. The system aims to provide a new way of accurately visualising the spatial distribution and activity of molecular structures and processes in small animals by combining 3D bioluminescence tomography (BLT; reconstruction-based 3D imaging of internal bioluminescent reporter distributions), diffuse optical tomography (DOT; reconstruction-based imaging of optical parameter distributions) and optical surface capture techniques. The key principle of the imaging system is to use surface capture results to enhance the accuracy of DOT image reconstruction, and to use the results of both surface capture and DOT to enhance the accuracy of BLT. Presented experiments show that the developed system can reconstruct luminescent source distributions and optical parameters accurately and that small animal imaging is feasible with the system

Numerical model of light propagation through Fabry-Perot etalons composed of interfaces with non-planar surface topography

We present a model that calculates optical fields reflected and transmitted by a Fabry-Perot (FP) etalon composed of interfaces with non-planar surface topography. The model uses the Rayleigh-Rice theory, which predicts the fields reflected and transmitted by a single interface, to account for the non-planar surface topography of each interface. The Rayleigh-Rice theory is evaluated iteratively to account for all round trips that light can take within the FP etalon. The model predictions can then be used to compute Interferometer transfer function (ITF)s, by performing wavelength or angle resolved simulations enabling predictions of the bandwidth, peak transmissivity, and sensitivity of FP etalons. The model was validated against the Pseudospectral time-domain (PSTD) method, which resulted in good agreement. Since the model accuracy is expected to reduce as the Root mean square (RMS) of the topographic map increases, the error in the model’s predictions was studied as a function of topographic map RMS. Finally, application of the model was exemplified by predicting the impact of roughness on ITFs and computing the changes in FP etalon transmissivity as cavity thickness is modulated by an ultrasonic wave

Time resolved diffuse optical spectroscopy with geometrically accurate models for bulk parameter recovery

A novel straightforward, accessible and efficient approach is presented for performing hyperspectral time-domain diffuse optical spectroscopy to determine the optical properties of samples accurately using geometry specific models. To allow bulk parameter recovery from measured spectra, a set of libraries based on a numerical model of the domain being investigated is developed as opposed to the conventional approach of using an analytical semi-infinite slab approximation, which is known and shown to introduce boundary effects. Results demonstrate that the method improves the accuracy of derived spectrally varying optical properties over the use of the semi-infinite approximation

Novel Myopia Genes and Pathways Identified From Syndromic Forms of Myopia

PURPOSE. To test the hypothesis that genes known to cause clinical syndromes featuring myopia also harbor polymorphisms contributing to nonsyndromic refractive errors. METHODS. Clinical phenotypes and syndromes that have refractive errors as a recognized feature were identified using the Online Mendelian Inheritance in Man (OMIM) database. One hundred fifty-four unique causative genes were identified, of which 119 were specifically linked with myopia and 114 represented syndromic myopia (i.e., myopia and at least one other clinical feature). Myopia was the only refractive error listed for 98 genes and hyperopia and the only refractive error noted for 28 genes, with the remaining 28 genes linked to phenotypes with multiple forms of refractive error. Pathway analysis was carried out to find biological processes overrepresented within these sets of genes. Genetic variants located within 50 kb of the 119 myopia-related genes were evaluated for involvement in refractive error by analysis of summary statistics from genome-wide association studies (GWAS) conducted by the CREAM Consortium and 23andMe, using both single-marker and gene-based tests. RESULTS. Pathway analysis identified several biological processes already implicated in refractive error development through prior GWAS analyses and animal studies, including extracellular matrix remodeling, focal adhesion, and axon guidance, supporting the research hypothesis. Novel pathways also implicated in myopia development included mannosylation, glycosylation, lens development, gliogenesis, and Schwann cell differentiation. Hyperopia was found to be linked to a different pattern of biological processes, mostly related to organogenesis. Comparison with GWAS findings further confirmed that syndromic myopia genes were enriched for genetic variants that influence refractive errors in the general population. Gene-based analyses implicated 21 novel candidate myopia genes (ADAMTS18, ADAMTS2, ADAMTSL4, AGK, ALDH18A1, ASXL1, COL4A1, COL9A2, ERBB3, FBN1, GJA1, GNPTG, IFIH1, KIF11, LTBP2, OCA2, POLR3B, POMT1, PTPN11, TFAP2A, ZNF469). CONCLUSIONS. Common genetic variants within or nearby genes that cause syndromic myopia are enriched for variants that cause nonsyndromic, common myopia. Analysis of syndromic forms of refractive errors can provide new insights into the etiology of myopia and additional potential targets for therapeutic interventions

Novel Myopia Genes and Pathways Identified From Syndromic Forms of Myopia

P URPOSE . To test the hypothesis that genes known to cause clinical syndromes featuring myopia also harbor polymorphisms contributing to nonsyndromic refractive errors

Increasing the Q-factor of Fabry-Perot etalons using focused Bessel beam illumination

Sensing and filtering applications often require Fabry-Perot (FP) etalons with an Interferometer Transfer Function (ITF) having high visibility, narrow Full Width at Half Maximum (FWHM), and high sensitivity. For the ITF to have these characteristics, the illumination beam must be matched to the modes of the FP cavity. This is challenging when a small illumination element size is needed, as typical focused beams are not matched to the FP cavity modes. Bessel beams are a potential alternative as their structure resembles the FP cavity modes while possessing a focused core. To study the feasibility of using Bessel beam illumination, in this Letter, ITFs of an FP etalon were measured using Bessel and Gaussian illumination beams. A Bessel beam with core size of 28 µm provided an ITF with visibility 3.0 times higher, a FWHM 0.3 times narrower, and a sensitivity 2.2 times higher than a Gaussian beam with waist 32 µm. The results show that Bessel beam illumination can provide ITFs similar to that of collimated beam illumination while also having with a focused core.</p

Novel Myopia Genes and Pathways Identified From Syndromic Forms of Myopia

Clinical phenotypes and syndromes that have refractive errors as a recognized feature were identified using the Online Mendelian Inheritance in Man (OMIM) database. One hundred fifty-four unique causative genes were identified, of which 119 were specifically linked with myopia and 114 represented syndromic myopia (i.e., myopia and at least one other clinical feature). Myopia was the only refractive error listed for 98 genes and hyperopia and the only refractive error noted for 28 genes, with the remaining 28 genes linked to phenotypes with multiple forms of refractive error. Pathway analysis was carried out to find biological processes overrepresented within these sets of genes. Genetic variants located within 50 kb of the 119 myopia-related genes were evaluated for involvement in refractive error by analysis of summary statistics from genome-wide association studies (GWAS) conducted by the CREAM Consortium and 23andMe, using both single-marker and gene-based tests

Novel Myopia Genes and Pathways Identified From Syndromic Forms of Myopia

Clinical phenotypes and syndromes that have refractive errors as a recognized feature were identified using the Online Mendelian Inheritance in Man (OMIM) database. One hundred fifty-four unique causative genes were identified, of which 119 were specifically linked with myopia and 114 represented syndromic myopia (i.e., myopia and at least one other clinical feature). Myopia was the only refractive error listed for 98 genes and hyperopia and the only refractive error noted for 28 genes, with the remaining 28 genes linked to phenotypes with multiple forms of refractive error. Pathway analysis was carried out to find biological processes overrepresented within these sets of genes. Genetic variants located within 50 kb of the 119 myopia-related genes were evaluated for involvement in refractive error by analysis of summary statistics from genome-wide association studies (GWAS) conducted by the CREAM Consortium and 23andMe, using both single-marker and gene-based tests

ABCD transfer matrix model of Gaussian beam propagation in Fabry-Perot etalons

A numerical model of Gaussian beam propagation in planar Fabry-Perot (FP) etalons is presented. The model is based on the ABCD transfer matrix method. This method is easy to use and interpret, and readily connects models of lenses, mirrors, fibres and other optics to aid simulating complex multi-component etalon systems. To validate the etalon model, its predictions were verified using a previously validated model based on Fourier optics. To demonstrate its utility, three different etalon systems were simulated. The results suggest the model is valid and versatile and could aid in designing and understanding a range of systems containing planar FP etalons. The method could be extended to model higher order beams, other FP type devices such as plano-concave resonators, and more complex etalon systems such as those involving tilted components