Holographic microscopy reconstruction in both object and image half spaces with undistorted 3D grid

We propose an holographic microscopy reconstruction method, which propagates the hologram, in the object half space, in the vicinity of the object. The calibration yields reconstructions with an undistorted reconstruction grid i.e. with orthogonal $x$, $y$ and $z$ axis and constant pixels pitch. The method is validated with an USAF target imaged by a $\times$60 microscope objective, whose holograms are recorded and reconstructed for different USAF locations along the longitudinal axis: -75 to +75 $\mu$m. Since the reconstruction numerical phase mask, the reference phase curvature and MO form an afocal device, the reconstruction can be interpreted as occurring equivalently in the object or in image half space

High numerical aperture holographic microscopy reconstruction with extended z range

An holographic microscopy reconstruction method compatible with high numerical aperture microscope objective (MO) up to NA=1.4 is proposed. After off axis and reference field curvature corrections, and after selection of the +1 grating order holographic image, a phase mask that transforms the optical elements of the holographic setup into an afocal device is applied in the camera plane. The reconstruction is then made by the angular spectrum method. The field is first propagated in the image half space from the camera to the afocal image of the MO optimal plane (plane for which MO has been designed) by using a quadratic kernel. The field is then propagated from the MO optimal plane to the object with the exact kernel. Calibration of the reconstruction is made by imaging a calibrated object like an USAF resolution target for different positions along $z$. Once the calibration is done, the reconstruction can be made with an object located in any plane $z$. The reconstruction method has been validated experimentally with an USAF target imaged with a NA=1.4 microscope objective. Near-optimal resolution is obtained over an extended range ($\pm 50~\mu$m) of $z$ locations

Topological transformations of speckles

Deterministic control of coherent random light is highly important for information transmission through complex media. However, only a few simple speckle transformations can be achieved through diffusers without prior characterization. As recently shown, spiral wavefront modulation of the impinging beam allows permuting intensity maxima and intrinsic $\pm 1$-charged optical vortices. Here, we study this cyclic-group algebra when combining spiral phase transforms of charge $n$, with $D_3$- and $D_4$-point-group symmetry star-like amplitude modulations. This combination allows statistical strengthening of permutations and controlling the period to be 3 and 4, respectively. Phase saddle-points are shown to complete the cycle. These results offer new tools to manipulate critical points in speckles.Comment: 14 pages, 10 figures, 4 table

Heterodyne holographic microscopy of gold particles

We report experimental results on heterodyne holographic microscopy of subwavelength-sized gold particles. The apparatus uses continuous green laser illumination of the metal beads in a total internal reflection configuration for dark-field operation. Detection of the scattered light at the illumination wavelength on a charge-coupled device array detector enables 3D localization of brownian particles in wate

Evolutionary Latent Class Clustering of Qualitative Data

The latent class model or multivariate multinomial mixture is a powerful model for clustering discrete data. This model is expected to be useful to represent non-homogeneous populations. It uses a conditional independence assumption given the latent class to which a statistical unit is belonging. However, whereas a predictive approach of cluster analysis from qualitative data can be easily derived from a fully Bayesian analysis with Jeffreys non informative prior distributions, it leads to a criterion (the integrated completed likelihood derived from the latent class model) that proves difficult to optimize by the standard approach based on the EM algorithm. An Evolutionary Algorithms is designed to tackle this discrete optimization problem, and an extensive parameter study on a large artificial dataset allows to derive stable parameters. A Monte Carlo approach is used to validate those parameters on other artificial datasets, as well as on some well-known real data: the Evolutionary Algorithm seems to repeatedly perform better than other standard clustering techniques on the same data

Parameter Setting for Evolutionary Latent Class Clustering

International audienceThe latent class model or multivariate multinomial mixture is a powerful model for clustering discrete data. This model is expected to be useful to represent non-homogeneous populations. It uses a conditional independence assumption given the latent class to which a statistical unit is belonging. However, it leads to a criterion that proves difficult to optimise by the standard approach based on the EM algorithm. An Evolutionary Algorithms is designed to tackle this discrete optimisation problem, and an extensive parameter study on a large artificial dataset allows to derive stable parameters. Those parameters are then validated on other artificial datasets, as well as on some well-known real data: the Evolutionary Algorithm performs repeatedly better than other standard clustering techniques on the same data

wDBTF: an integrated database resource for studying wheat transcription factor families

<p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) regulate gene expression by interacting with promoters of their target genes and are classified into families based on their DNA-binding domains. Genes coding for TFs have been identified in the sequences of model plant genomes. The rice (<it>Oryza sativa </it>spp. <it>japonica</it>) genome contains 2,384 TF gene models, which represent the mRNA transcript of a locus, classed into 63 families.</p> <p>Results</p> <p>We have created an extensive list of wheat (<it>Triticum aestivum </it>L) TF sequences based on sequence homology with rice TFs identified and classified in the Database of Rice Transcription Factors (DRTF). We have identified 7,112 wheat sequences (contigs and singletons) from a dataset of 1,033,960 expressed sequence tag and mRNA (ET) sequences available. This number is about three times the number of TFs in rice so proportionally is very similar if allowance is made for the hexaploidy of wheat. Of these sequences 3,820 encode gene products with a DNA-binding domain and thus were confirmed as potential regulators. These 3,820 sequences were classified into 40 families and 84 subfamilies and some members defined orphan families. The results were compiled in the Database of Wheat Transcription Factor (wDBTF), an inventory available on the web <url>http://wwwappli.nantes.inra.fr:8180/wDBFT/</url>. For each accession, a link to its library source and its Affymetrix identification number is provided. The positions of Pfam (protein family database) motifs were given when known.</p> <p>Conclusions</p> <p>wDBTF collates 3,820 wheat TF sequences validated by the presence of a DNA-binding domain out of 7,112 potential TF sequences identified from publicly available gene expression data. We also incorporated <it>in silico </it>expression data on these TFs into the database. Thus this database provides a major resource for systematic studies of TF families and their expression in wheat as illustrated here in a study of DOF family members expressed during seed development.</p

One-shot measurement of the three-dimensional electromagnetic field scattered by a subwavelength aperture tip coupled to the environment

International audienceNear-field scanning optical microscopy (NSOM) achieves subwavelength resolution by bringing a nanosized probe close to the surface of the sample. This extends the spectrum of spatial frequencies that can be detected with respect to a diffraction limited microscope. The interaction of the probe with the sample is expected to affect its radiation to the far field in a way that is often hard to predict. Here we address this question by proposing a general method based on full-field off-axis digital holography microscopy which enables to study in detail the far-field radiation from a NSOM probe as a function of its environment. A first application is demonstrated by performing a three-dimensional (3D) tomographic reconstruction of light scattered from the sub-wavelength aperture tip of a NSOM, in free space or coupled to transparent and plasmonic media. A single holographic image recorded in one shot in the far field contains information on both the amplitude and phase of the scattered light. This is sufficient to reverse numerically the propagation of the electromagnetic field all the way to the aperture tip. Finite Difference Time Domain (FDTD) simulations are performed to compare the experimental results with a superposition of magnetic and electric dipole radiation

Anisotropic super-attenuation of capillary waves on driven glass interfaces

Metrological AFM measurements are performed on the silica glass interfaces of photonic band-gap fibres and hollow capillaries. The freezing of attenuated out-of-equilibrium capillary waves during the drawing process is shown to result in a reduced surface roughness. The roughness attenuation with respect to the expected thermodynamical limit is determined to vary with the drawing stress following a power law. A striking anisotropic character of the height correlation is observed: glass surfaces thus retain a structural record of the direction of the flow to which the liquid was submitted