Refractive errors and corrections for OCT images in an inflated lung phantom.

Visualization and correct assessment of alveolar volume via intact lung imaging is important to study and assess respiratory mechanics. Optical Coherence Tomography (OCT), a real-time imaging technique based on near-infrared interferometry, can image several layers of distal alveoli in intact, ex vivo lung tissue. However optical effects associated with heterogeneity of lung tissue, including the refraction caused by air-tissue interfaces along alveoli and duct walls, and changes in speed of light as it travels through the tissue, result in inaccurate measurement of alveolar volume. Experimentally such errors have been difficult to analyze because of lack of 'ground truth,' as the lung has a unique microstructure of liquid-coated thin walls surrounding relatively large airspaces, which is difficult to model with cellular foams. In addition, both lung and foams contain airspaces of highly irregular shape, further complicating quantitative measurement of optical artifacts and correction. To address this we have adapted the Bragg-Nye bubble raft, a crystalline two-dimensional arrangement of elements similar in geometry to alveoli (up to several hundred µm in diameter with thin walls) as an inflated lung phantom in order to understand, analyze and correct these errors. By applying exact optical ray tracing on OCT images of the bubble raft, the errors are predicted and corrected. The results are validated by imaging the bubble raft with OCT from one edge and with a charged coupled device (CCD) camera in transillumination from top, providing ground truth for the OCT.

Alignment with sub-pixel accuracy for images of multi-modality microscopes using automatic calibration.

A biological specimen is often imaged with various imaging modalities, and it is crucial that such images are well aligned to best reveal physiological structures and functions of the specimen for in-depth analyses. In this paper, we present a methodology for automatic calibration of multiple optical imaging modalities within the x-y detector plane using a custom chrome-on-glass target and an automatic and accurate registration algorithm. The target contains lines crossing at random angles, and our method of registration is based on the alignment of salient features extracted from the lines within the individual images. Once spatial relationships are found between the various detectors and applied to the resultant images, no further registration is required for all static samples, and the registered images serve as the starting point for registration of dynamic samples, where the remaining misalignment is caused by sample movement. We have validated our algorithm with 40 inter-modal and 30 intra-modal image pairs, and the success rates are 95 and 100%, respectively, with sub-pixel accuracy. This methodology is widely applicable to any multi-modal microscope that combines a number of imaging modalities on a common platform assuming images of the target can be obtained.

Genetics and imaging to assess oocyte and preimplantation embryo health.

Two major criteria are currently used in human assisted reproductive technologies (ART) to evaluate oocyte and preimplantation embryo health: (1) rate of preimplantation embryonic development; and (2) overall morphology. A major gene that regulates the rate of preimplantation development is the preimplantation embryo development (Ped) gene, discovered in our laboratory. In mice, presence of the Ped gene product, Qa-2 protein, results in a fast rate of preimplantation embryonic development, compared with a slow rate of preimplantation embryonic development for embryos that are lacking Qa-2 protein. Moreover, mice that express Qa-2 protein have an overall reproductive advantage that extends beyond the preimplantation period, including higher survival to birth, higher birthweight, and higher survival to weaning. Data are presented that suggest that Qa-2 increases the rate of development of early embryos by acting as a cell-signalling molecule and that phosphatidylinositol-32 kinase is involved in the cell-signalling pathway. The most likely human homologue of Qa-2 has recently been identified as human leukocyte antigen (HLA)-G. Data are presented which show that HLA-G, like Qa-2, is located in lipid rafts, implying that HLA-G also acts as a signalling molecule. In order to better evaluate the second criterion used in ART (i.e. overall morphology), a unique and innovative imaging microscope has been constructed, the Keck 3-D fusion microscope (Keck 3DFM). The Keck 3DFM combines five different microscopic modes into a single platform, allowing multi-modal imaging of the specimen. One of the modes, the quadrature tomographic microscope (QTM), creates digital images of non-stained transparent cells by measuring changes in the index of refraction. Quadrature tomographic microscope images of oocytes and preimplantation mouse embryos are presented for the first time. The digital information from the QTM images should allow the number of cells in a preimplantation embryo to be counted non-invasively. The Keck 3DFM is also being used to assess mitochondrial distribution in mouse oocytes and embryos by using the k-means clustering algorithm. Both the number of cells in preimplantation embryos and mitochondrial distribution are related to oocyte and embryo health. New imaging data obtained from the Keck 3DFM, combined with genetic and biochemical approaches, have the promise of being able to distinguish healthy from unhealthy oocytes and embryos in a non-invasive manner. The goal is to apply the information from our mouse model system to the clinic in order to identify one and only one healthy embryo for transfer back to the mother undergoing an ART procedure. This approach has the potential to increase the success rate of ART and to decrease the high, and undesirable, multiple birth rate presently associated with ART.

A comparison study of linear reconstruction techniques for diffuse optical tomographic imaging of absorption coefficient.

We compare, through simulations, the performance of four linear algorithms for diffuse optical tomographic reconstruction of the three-dimensional distribution of absorption coefficient within a highly scattering medium using the diffuse photon density wave approximation. The simulation geometry consisted of a coplanar array of sources and detectors at the boundary of a half-space medium. The forward solution matrix is both underdetermined, because we estimate many more absorption coefficient voxels than we have measurements, and ill-conditioned, due to the ill-posedness of the inverse problem. We compare two algebraic techniques, ART and SIRT, and two subspace techniques, the truncated SVD and CG algorithms. We compare three-dimensional reconstructions with two-dimensional reconstructions which assume all inhomogeneities are confined to a known horizontal slab, and we consider two 'object-based' error metrics in addition to mean square reconstruction error. We include a comparison using simulated data generated using a different FDFD method with the same inversion algorithms to indicate how our conclusions are affected in a somewhat more realistic scenario. Our results show that the subspace techniques are superior to the algebraic techniques in localization of inhomogeneities and estimation of their amplitude, that two-dimensional reconstructions are sensitive to underestimation of the object depth, and that an error measure based on a location parameter can be a useful complement to mean squared error.

Three-dimensional images generated by quadrature interferometry.

Quadrature detection techniques have been applied to images obtained from a Mach-Zehnder interferometer with differently polarized beams to yield the real and the imaginary parts of the diffracted fields simultaneously. This approach eliminates the need for phase retrieval by providing complete information on the complex amplitude of the diffracted signal. We present results in which we demonstrate our ability to reconstruct two- and three-dimensional microscopic objects from their complex diffraction patterns.

Quadrature detection of a Doppler signal.

We have employed a quadrature detection technique to measure theDoppler signal from a moving target. We mix a circularly polarizedreference with a linearly polarized signal to produce an output thatcontains the real and the imaginary parts of the interference field inthe two output polarizations. We are thus able to measure thein-phase and the quadrature components of an interferometric signalsimultaneously by splitting the output with a polarizing beamsplitter. We present data that demonstrate our ability through thistechnique to obtain both the amplitude and the frequency of vibrationof an audio speaker. We also demonstrate the technique's abilityto give one access to the direction of motion and instantaneousposition of the target.

Light propagation in a planar dielectric waveguide with a gyrotropic layer.

The nature of the magneto-optic Kerr effect in a planar dielectric waveguide geometry has been investigated by calculation of the Jones matrix for a planar waveguide structure with a gyrotropic magnetic material as one wall. The intensity of the component of the field that is in the polarization state orthogonal to the input was calculated as a function of length of the gyrotropic material and input polarization state. The degree of polarization rotation depends on the relative orientation of the magnetization in the magnetic material and the direction of propagation. It is found that there exists an optimal waveguide length and input polarization at which the output signal is maximized and that a significant enhancement in polarization rotation is available with respect to free-space reflection. These results indicate that a magnetic-film-bounded planar waveguide can be used for device applications such as magnetic field sensors or magneto-optic modulators.

Light-guiding effect in a two-fluid model of laser angioplasty.

Mixing and optical characteristics of blood and optical fluid, utilized in laser angioplasty, are investigated with a two-fluid model. Transport equations are solved for the zone-averaged variables of each fluid with allowance for momentum transport at the interface. The predicted volume fractions of the fluids are used as weight functions to calculate the mixture refractive index. A set of light rays are traced through the fluids to the plaque, utilizing the mixture refractive index. The results indicate significant effect of flow characteristics on the focusing of the rays.

Signal-to-noise-ratio equations for a heterodyne laser radar.

We analyze the signal-to-noise-ratio equations for a heterodyne laser radar with identical transmit and receive optics. We defines the beam-profile efficiency, a quantity that must be maximized to optimize a system design. This calculation can be used to evaluate a system in both near and far fields for focused and nonfocused systems. The beam-profile efficiency can be evaluated in many ways, and we describe one possible solution. Using this solution, we present the results of an actual system evaluation.