The Experts below are selected from a list of 318 Experts worldwide ranked by ideXlab platform
Gary Brooker - One of the best experts on this subject based on the ideXlab platform.
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high magnification super resolution Finch microscopy using birefringent crystal lens interferometers
Nature Photonics, 2016Co-Authors: Nisan Siegel, Brian Storrie, Vladimir V Lupashin, Gary BrookerAbstract:The use of birefringent crystals improves super-resolution Fresnel incoherent correlation holography (Finch) microscopy.
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cinch confocal incoherent correlation holography super resolution fluorescence microscopy based upon Finch fresnel incoherent correlation holography
Proceedings of SPIE, 2015Co-Authors: Nisan Siegel, Brian Storrie, Marc A Bruce, Gary BrookerAbstract:Finch holographic fluorescence microscopy creates high resolution super-resolved images with enhanced depth of focus. The simple addition of a real-time Nipkow disk confocal image scanner in a conjugate plane of this incoherent holographic system is shown to reduce the depth of focus, and the combination of both techniques provides a simple way to enhance the axial resolution of Finch in a combined method called "CINCH". An important feature of the combined system allows for the simultaneous real-time image capture of widefield and holographic images or confocal and confocal holographic images for ready comparison of each method on the exact same field of view. Additional GPU based complex deconvolution processing of the images further enhances resolution.
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improved axial resolution of Finch fluorescence microscopy when combined with spinning disk confocal microscopy
Optics Express, 2014Co-Authors: Nisan Siegel, Gary BrookerAbstract:Finch holographic fluorescence microscopy creates super-resolved images with enhanced depth of focus. Addition of a Nipkow disk real-time confocal image scanner is shown to reduce the Finch depth of focus while improving transverse confocal resolution in a combined method called “CINCH”.
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faithful reconstruction of digital holograms captured by Finch using a hamming window function in the fresnel propagation
Optics Letters, 2013Co-Authors: Nisan Siegel, Joseph Rosen, Gary BrookerAbstract:Recent advances in Fresnel incoherent correlation holography (Finch) increase the signal-to-noise ratio in hologram recording by interference of images from two diffractive lenses with focal lengths close to the image plane. Holograms requiring short reconstruction distances are created that reconstruct poorly with existing Fresnel propagation methods. Here we show a dramatic improvement in reconstructed fluorescent images when a 2D Hamming window function substituted for the disk window typically used to bound the impulse response in the Fresnel propagation. Greatly improved image contrast and quality are shown for simulated and experimentally determined Finch holograms using a 2D Hamming window without significant loss in lateral or axial resolution.
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reconstruction of objects above and below the objective focal plane with dimensional fidelity by Finch fluorescence microscopy
Optics Express, 2012Co-Authors: Nisan Siegel, Joseph Rosen, Gary BrookerAbstract:Fresnel Incoherent Correlation Holography (Finch) can faithfully reproduce objects above and below the optical plane of focus. However, as in optical imaging, the transverse magnification and optimal reconstruction depth changes based on the longitudinal distance of objects from the focal plane of the input lens with the exception that objects above and below the focal plane are in focus with Finch and out of focus by standard optical imaging. We have analyzed these effects both theoretically and experimentally for two configurations of a Finch fluorescence microscopy system. This information has been used to reconstruct a test planar object placed above or below the optical plane of focus with high dimensional and image fidelity. Because Finch is inherently a super-resolving system, this advance makes it possible to create super-resolved 3D images from Finch holograms.
Nisan Siegel - One of the best experts on this subject based on the ideXlab platform.
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high magnification super resolution Finch microscopy using birefringent crystal lens interferometers
Nature Photonics, 2016Co-Authors: Nisan Siegel, Brian Storrie, Vladimir V Lupashin, Gary BrookerAbstract:The use of birefringent crystals improves super-resolution Fresnel incoherent correlation holography (Finch) microscopy.
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cinch confocal incoherent correlation holography super resolution fluorescence microscopy based upon Finch fresnel incoherent correlation holography
Proceedings of SPIE, 2015Co-Authors: Nisan Siegel, Brian Storrie, Marc A Bruce, Gary BrookerAbstract:Finch holographic fluorescence microscopy creates high resolution super-resolved images with enhanced depth of focus. The simple addition of a real-time Nipkow disk confocal image scanner in a conjugate plane of this incoherent holographic system is shown to reduce the depth of focus, and the combination of both techniques provides a simple way to enhance the axial resolution of Finch in a combined method called "CINCH". An important feature of the combined system allows for the simultaneous real-time image capture of widefield and holographic images or confocal and confocal holographic images for ready comparison of each method on the exact same field of view. Additional GPU based complex deconvolution processing of the images further enhances resolution.
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improved axial resolution of Finch fluorescence microscopy when combined with spinning disk confocal microscopy
Optics Express, 2014Co-Authors: Nisan Siegel, Gary BrookerAbstract:Finch holographic fluorescence microscopy creates super-resolved images with enhanced depth of focus. Addition of a Nipkow disk real-time confocal image scanner is shown to reduce the Finch depth of focus while improving transverse confocal resolution in a combined method called “CINCH”.
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faithful reconstruction of digital holograms captured by Finch using a hamming window function in the fresnel propagation
Optics Letters, 2013Co-Authors: Nisan Siegel, Joseph Rosen, Gary BrookerAbstract:Recent advances in Fresnel incoherent correlation holography (Finch) increase the signal-to-noise ratio in hologram recording by interference of images from two diffractive lenses with focal lengths close to the image plane. Holograms requiring short reconstruction distances are created that reconstruct poorly with existing Fresnel propagation methods. Here we show a dramatic improvement in reconstructed fluorescent images when a 2D Hamming window function substituted for the disk window typically used to bound the impulse response in the Fresnel propagation. Greatly improved image contrast and quality are shown for simulated and experimentally determined Finch holograms using a 2D Hamming window without significant loss in lateral or axial resolution.
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reconstruction of objects above and below the objective focal plane with dimensional fidelity by Finch fluorescence microscopy
Optics Express, 2012Co-Authors: Nisan Siegel, Joseph Rosen, Gary BrookerAbstract:Fresnel Incoherent Correlation Holography (Finch) can faithfully reproduce objects above and below the optical plane of focus. However, as in optical imaging, the transverse magnification and optimal reconstruction depth changes based on the longitudinal distance of objects from the focal plane of the input lens with the exception that objects above and below the focal plane are in focus with Finch and out of focus by standard optical imaging. We have analyzed these effects both theoretically and experimentally for two configurations of a Finch fluorescence microscopy system. This information has been used to reconstruct a test planar object placed above or below the optical plane of focus with high dimensional and image fidelity. Because Finch is inherently a super-resolving system, this advance makes it possible to create super-resolved 3D images from Finch holograms.
Joseph Rosen - One of the best experts on this subject based on the ideXlab platform.
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INDIN - Recent advances in Finch technology
2016 IEEE 14th International Conference on Industrial Informatics (INDIN), 2016Co-Authors: Joseph Rosen, Roy Kelner, Yuval Kashter, Anand VijayakumarAbstract:Incoherent digital holography (IDH) offers the ability to record a complete three-dimensional scene without using lasers. In this review paper, the evolution of a well-established method of IDH, the Fresnel incoherent correlation holography (Finch), is described. Following the Finch development review, several recently developed methods branched out from Finch are discussed.
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faithful reconstruction of digital holograms captured by Finch using a hamming window function in the fresnel propagation
Optics Letters, 2013Co-Authors: Nisan Siegel, Joseph Rosen, Gary BrookerAbstract:Recent advances in Fresnel incoherent correlation holography (Finch) increase the signal-to-noise ratio in hologram recording by interference of images from two diffractive lenses with focal lengths close to the image plane. Holograms requiring short reconstruction distances are created that reconstruct poorly with existing Fresnel propagation methods. Here we show a dramatic improvement in reconstructed fluorescent images when a 2D Hamming window function substituted for the disk window typically used to bound the impulse response in the Fresnel propagation. Greatly improved image contrast and quality are shown for simulated and experimentally determined Finch holograms using a 2D Hamming window without significant loss in lateral or axial resolution.
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reconstruction of objects above and below the objective focal plane with dimensional fidelity by Finch fluorescence microscopy
Optics Express, 2012Co-Authors: Nisan Siegel, Joseph Rosen, Gary BrookerAbstract:Fresnel Incoherent Correlation Holography (Finch) can faithfully reproduce objects above and below the optical plane of focus. However, as in optical imaging, the transverse magnification and optimal reconstruction depth changes based on the longitudinal distance of objects from the focal plane of the input lens with the exception that objects above and below the focal plane are in focus with Finch and out of focus by standard optical imaging. We have analyzed these effects both theoretically and experimentally for two configurations of a Finch fluorescence microscopy system. This information has been used to reconstruct a test planar object placed above or below the optical plane of focus with high dimensional and image fidelity. Because Finch is inherently a super-resolving system, this advance makes it possible to create super-resolved 3D images from Finch holograms.
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enhanced resolution and throughput of fresnel incoherent correlation holography Finch using dual diffractive lenses on a spatial light modulator slm
Optics Express, 2012Co-Authors: Barak Katz, Roy Kelner, Joseph Rosen, Gary BrookerAbstract:Fresnel incoherent correlation holography (Finch) records holograms under incoherent illumination. Finch was implemented with two focal length diffractive lenses on a spatial light modulator (SLM). Improved image resolution over previous single lens systems and at wider bandwidths was observed. For a given image magnification and light source bandwidth, Finch with two lenses of close focal lengths yields a better hologram in comparison to a single diffractive lens Finch. Three techniques of lens multiplexing on the SLM were tested and the best method was randomly and uniformly distributing the two lenses. The improved quality of the hologram results from a reduced optical path difference of the interfering beams and increased efficiency.
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theoretical and experimental demonstration of resolution beyond the rayleigh limit by Finch fluorescence microscopic imaging
Optics Express, 2011Co-Authors: Joseph Rosen, Nisan Siegel, Gary BrookerAbstract:Fresnel Incoherent Correlation Holography (Finch) enables holograms to be recorded from incoherent light with just a digital camera and spatial light modulator. We previously described its application to general three dimensional incoherent imaging and specifically to fluorescence microscopy, wherein one complex hologram contains the three dimensional information in the field of view, obviating the need for scanning or serial sectioning. We have now further analyzed Finch in view of linear system theory and in comparison to conventional coherent and incoherent two dimensional imaging systems. We demonstrate, theoretically and experimentally, improved resolution by Finch, when compared to conventional imaging.
Scott V. Edwards - One of the best experts on this subject based on the ideXlab platform.
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a house Finch haemorhous mexicanus spleen transcriptome reveals intra and interspecific patterns of gene expression alternative splicing and genetic diversity in passerines
BMC Genomics, 2014Co-Authors: Qu Zhang, Scott V. Edwards, Geoffrey E. Hill, Niclas BackstromAbstract:Background: With its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house Finch (Haemorhous mexicanus) is a model species for studying sexual selection, plumage coloration and host-parasite interactions. As part of our ongoing efforts to make available genomic resources for this species, here we report a transcriptome assembly derived from genes expressed in spleen. Results: We characterize transcriptomes from two populations with different histories of demography and disease exposure: a recently founded population in the eastern US that has been exposed to MG for over a decade and a native population from the western range that has never been exposed to MG. We utilize this resource to quantify conservation in gene expression in passerine birds over approximately 50 MY by comparing splenic expression profiles for 9,646 house Finch transcripts and those from zebra Finch and find that less than half of all genes expressed in spleen in either species are expressed in both species. Comparative gene annotations from several vertebrate species suggest that the house Finch transcriptomes contain ~15 genes not yet found in previously sequenced vertebrate genomes. The house Finch transcriptomes harbour ~85,000 SNPs, ~20,000 of which are non-synonymous. Although not yet validated by biological or technical replication, we identify a set of genes exhibiting differences between populations in gene expression ( n= 182; 2% of all transcripts), allele frequencies (76 FST ouliers) and alternative splicing as well as genes with several fixed non-synonymous substitutions; this set includes genes with functions related to double-strand break repair and immune response. Conclusions: The two house Finch spleen transcriptome profiles will add to the increasing data on genome and transcriptome sequence information from natural populations. Differences in splenic expression between house Finch and zebra Finch imply either significant evolutionary turnover of splenic expression patterns or different physiological states of the individuals examined. The transcriptome resource will enhance the potential to annotate an eventual house Finch genome, and the set of gene-based high-quality SNPs will help clarify the genetic underpinnings of host-pathogen interactions and sexual selection.
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Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma Gallisepticum
PLoS Genetics, 2012Co-Authors: Nigel F. Delaney, Susan Balenger, Christopher J. Marx, Naola Ferguson-noel, Allen Rodrigo, Geoffrey E. Hill, Camille Bonneaud, Peter Tsai, Scott V. EdwardsAbstract:Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house Finches (Carpodacus mexicanus), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups. Using whole-genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only ∼2% of ancestral poultry strains and a nucleotide substitution rate of 0.8-1.2×10(-5) per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only ∼50% of the CRISPR repertoire founding (1994-95) strains and have lost the CRISPR-associated genes required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs.
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nucleotide variation linkage disequilibrium and founder facilitated speciation in wild populations of the zebra Finch taeniopygia guttata
Genetics, 2009Co-Authors: Christopher N Balakrishnan, Scott V. EdwardsAbstract:The zebra Finch has long been an important model system for the study of vocal learning, vocal production, and behavior. With the imminent sequencing of its genome, the zebra Finch is now poised to become a model system for population genetics. Using a panel of 30 noncoding loci, we characterized patterns of polymorphism and divergence among wild zebra Finch populations. Continental Australian populations displayed little population structure, exceptionally high levels of nucleotide diversity (π = 0.010), a rapid decay of linkage disequilibrium (LD), and a high population recombination rate (ρ ≈ 0.05), all of which suggest an open and fluid genomic background that could facilitate adaptive variation. By contrast, substantial divergence between the Australian and Lesser Sunda Island populations (KST = 0.193), reduced genetic diversity (π = 0.002), and higher levels of LD in the island population suggest a strong but relatively recent founder event, which may have contributed to speciation between these populations as envisioned under founder-effect speciation models. Consistent with this hypothesis, we find that under a simple quantitative genetic model both drift and selection could have contributed to the observed divergence in six quantitative traits. In both Australian and Lesser Sundas populations, diversity in Z-linked loci was significantly lower than in autosomal loci. Our analysis provides a quantitative framework for studying the role of selection and drift in shaping patterns of molecular evolution in the zebra Finch genome.
Jon Slate - One of the best experts on this subject based on the ideXlab platform.
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a comparison of snps and microsatellites as linkage mapping markers lessons from the zebra Finch taeniopygia guttata
BMC Genomics, 2010Co-Authors: A H Ball, Jessica Stapley, T R Birkhead, Terry Burke, Deborah A Dawson, Jon SlateAbstract:Background Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four zebra Finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled zebra Finch genome sequence.
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a linkage map of the zebra Finch taeniopygia guttata provides new insights into avian genome evolution
Genetics, 2008Co-Authors: Jessica Stapley, T R Birkhead, Terry Burke, Jon SlateAbstract:Passeriformes are the largest order of birds and one of the most widely studied groups in evolutionary biology and ecology. Until recently genomic tools in passerines relied on chicken genomic resources. Here we report the construction and analysis of a whole-genome linkage map for the zebra Finch (Taeniopygia guttata) using a 354-bird pedigree. The map contains 876 SNPs dispersed across 45 linkage groups and we found only a few instances of interchromosomal rearrangement between the zebra Finch and the chicken genomes. Interestingly, there was a greater than expected degree of intrachromosomal rearrangements compared to the chicken, suggesting that gene order is not conserved within avian chromosomes. At 1068 cM the map is approximately only one quarter the length of the chicken linkage map, providing further evidence that the chicken has an unusually high recombination rate. Male and female linkage-map lengths were similar, suggesting no heterochiasmy in the zebra Finch. This whole-genome map is the first for any passerine and a valuable tool for the zebra Finch genome sequence project and for studies of quantitative trait loci.