Using Machine-Learning to Optimize phase contrast in a Low-Cost Cellphone Microscope

Cellphones equipped with high-quality cameras and powerful CPUs as well as GPUs are widespread. This opens new prospects to use such existing computational and imaging resources to perform medical diagnosis in developing countries at a very low cost. Many relevant samples, like biological cells or waterborn parasites, are almost fully transparent. As they do not exhibit absorption, but alter the light's phase only, they are almost invisible in brightfield microscopy. Expensive equipment and procedures for microscopic contrasting or sample staining often are not available. By applying machine-learning techniques, such as a convolutional neural network (CNN), it is possible to learn a relationship between samples to be examined and its optimal light source shapes, in order to increase e.g. phase contrast, from a given dataset to enable real-time applications. For the experimental setup, we developed a 3D-printed smartphone microscope for less than 100 \$ using off-the-shelf components only such as a low-cost video projector. The fully automated system assures true Koehler illumination with an LCD as the condenser aperture and a reversed smartphone lens as the microscope objective. We show that the effect of a varied light source shape, using the pre-trained CNN, does not only improve the phase contrast, but also the impression of an improvement in optical resolution without adding any special optics, as demonstrated by measurements

Specific heat of the ideal gas obeying the generalized exclusion statistics

We calculate the specific heat of the ideal gas obeying the generalized exclusion statistics (GES) in the continuum model and the tight binding model numerically. In the continuum model of 3-d space, the specific heat increases with statistical parameter at low temperature whereas it decreases with statistical parameter at high temperature. We find that the critical temperature normalized by $\mu_f$ (Fermi energy) is 0.290. The specific heat of 2-d space was known to be independent of $g$ in the continuum model, but it varies with $g$ drastically in the tight-binding model. From its unique behavior, identification of GES particles will be possible from the specific heat.Comment: 14 pages, 9 figures, to be published in Eur. Phys. J. B, References and figures added, typos corrected, one section removed and two sections merge

Polycomb group protein complexes exchange rapidly in living Drosophila

Fluorescence recovery after photobleaching (FRAP) microscopy was used to determine the kinetic properties of Polycomb group (PcG) proteins in whole living Drosophila organisms (embryos) and tissues (wing imaginal discs and salivary glands). PcG genes are essential genes in higher eukaryotes responsible for the maintenance of the spatially distinct repression of developmentally important regulators such as the homeotic genes. Their absence, as well as overexpression, causes transformations in the axial organization of the body. Although protein complexes have been isolated in vitro, little is known about their stability or exact mechanism of repression in vivo. We determined the translational diffusion constants of PcG proteins, dissociation constants and residence times for complexes in vivo at different developmental stages. In polytene nuclei, the rate constants suggest heterogeneity of the complexes. Computer simulations with new models for spatially distributed protein complexes were performed in systems showing both diffusion and binding equilibria, and the results compared with our experimental data. We were able to determine forward and reverse rate constants for complex formation. Complexes exchanged within a period of 1-10 minutes, more than an order of magnitude faster than the cell cycle time, ruling out models of repression in which access of transcription activators to the chromatin is limited and demonstrating that long-term repression primarily reflects mass-action chemical equilibria

Better than a lens -- Increasing the signal-to-noise ratio through pupil splitting

Lenses are designed to fulfill Fermats principle such that all light interferes constructively in its focus, guaranteeing its maximum concentration. It can be shown that imaging via an unmodified full pupil yields the maximum transfer strength for all spatial frequencies transferable by the system. Seemingly also the signal-to-noise ratio (SNR) is optimal. The achievable SNR at a given photon budget is critical especially if that budget is strictly limited as in the case of fluorescence microscopy. In this work we propose a general method which achieves a better SNR for high spatial frequency information of an optical imaging system, without the need to capture more photons. This is achieved by splitting the pupil of an incoherent imaging system such that two (or more) sub-images are simultaneously acquired and computationally recombined. We compare the theoretical performance of split pupil imaging to the non-split scenario and implement the splitting using a tilted elliptical mirror placed at the back-focal-plane (BFP) of a fluorescence widefield microscope

Using Machine-Learning to Optimize phase contrast in a Low-Cost Cellphone Microscope

Cellphones equipped with high-quality cameras and powerful CPUs as well as GPUs are widespread. This opens new prospects to use such existing computational and imaging resources to perform medical diagnosis in developing countries at a very low cost. Many relevant samples, like biological cells or waterborn parasites, are almost fully transparent. As they do not exhibit absorption, but alter the light's phase only, they are almost invisible in brightfield microscopy. Expensive equipment and procedures for microscopic contrasting or sample staining often are not available. By applying machine-learning techniques, such as a convolutional neural network (CNN), it is possible to learn a relationship between samples to be examined and its optimal light source shapes, in order to increase e.g. phase contrast, from a given dataset to enable real-time applications. For the experimental setup, we developed a 3D-printed smartphone microscope for less than 100 \$ using off-the-shelf components only such as a low-cost video projector. The fully automated system assures true Koehler illumination with an LCD as the condenser aperture and a reversed smartphone lens as the microscope objective. We show that the effect of a varied light source shape, using the pre-trained CNN, does not only improve the phase contrast, but also the impression of an improvement in optical resolution without adding any special optics, as demonstrated by measurements

Twin-Photon Confocal Microscopy

A recently introduced two-channel confocal microscope with correlated detection promises up to 50% improvement in transverse spatial resolution [Simon, Sergienko, Optics Express {\bf 18}, 9765 (2010)] via the use of photon correlations. Here we achieve similar results in a different manner, introducing a triple-confocal correlated microscope which exploits the correlations present in optical parametric amplifiers. It is based on tight focusing of pump radiation onto a thin sample positioned in front of a nonlinear crystal, followed by coincidence detection of signal and idler photons, each focused onto a pinhole. This approach offers further resolution enhancement in confocal microscopy

Non-radial oscillations of anisotropic neutron stars in the Cowling approximation

One of the most common assumptions in the study of neutron star models and their oscillations is that the pressure is isotopic, however there are arguments that this may not be correct. Thus in the present paper we make a first step towards studying the nonradial oscillations of neutron stars with an anisotropic pressure. We adopt the so-called Cowling approximation where the spacetime metric is kept fixed and the oscillation spectrum for the first few fluid modes is obtained. The effect of the anisotropy on the frequencies is apparent, although with the present results it might be hard to distinguish it from the changes in the frequencies caused by different equations of state.Comment: 17 pages, 8 figures; title changed, comments adde

Direct simulations of helical Hall-MHD turbulence and dynamo action

Direct numerical simulations of turbulent Hall dynamos are presented. The evolution of an initially weak and small scale magnetic field in a system maintained in a stationary turbulent regime by a stirring force at a macroscopic scale is studied to explore the conditions for exponential growth of the magnetic energy. Scaling of the dynamo efficiency with the Reynolds numbers is studied, and the resulting total energy spectra are found to be compatible with a Kolmogorov type law. A faster growth of large scale magnetic fields is observed at intermediate intensities of the Hall effect.Comment: 13 pages, 17 figures, ApJ (in press

The Emission of Electromagnetic Radiation from Charges Accelerated by Gravitational Waves and its Astrophysical Implications

We provide calculations and theoretical arguments supporting the emission of electromagnetic radiation from charged particles accelerated by gravitational waves (GWs). These waves have significant indirect evidence to support their existence, yet they interact weakly with ordinary matter. We show that the induced oscillations of charged particles interacting with a GW, which lead to the emission of electromagnetic radiation, will also result in wave attenuation. These ideas are supported by a small body of literature, as well as additional arguments for particle acceleration based on GW memory effects. We derive order of magnitude power calculations for various initial charge distributions accelerated by GWs. The resulting power emission is extremely small for all but very strong GWs interacting with large quantities of charge. If the results here are confirmed and supplemented, significant consequences such as attenuation of early universe GWs could result. Additionally, this effect could extend GW detection techniques into the electromagnetic regime. These explorations are worthy of study to determine the presence of such radiation, as it is extremely important to refine our theoretical framework in an era of active GW astrophysics.Comment: Appears in Gravitational Wave Astrophysics, Editor C.F. Sopuerta, Astrophysics and Space Science Proceedings, Volume 40. ISBN 978-3-319-10487-4. Springer International Publishing Switzerland, 2015, p. 30

Comparative performance of airyscan and structured illumination superresolution microscopy in the study of the surface texture and 3D shape of pollen

The visualization of taxonomically diagnostic features of individual pollen grains can be a challenge for many ecologically and phylogenetically important pollen types. The resolution of traditional optical microscopy is limited by the diffraction of light (250 nm), while high resolution tools such as electron microscopy are limited by laborious preparation and imaging workflows. Airyscan confocal superresolution and structured illumination superresolution (SR-SIM) microscopy are powerful new tools for the study of nanoscale pollen morphology and three-dimensional structure that can overcome these basic limitations. This study demonstrates their utility in capturing morphological details below the diffraction limit of light. Using three distinct pollen morphotypes (Croton hirtus, Dactylis glomerata, and Helianthus sp.) and contrast-enhancing fluorescent staining, we were able to assess the effectiveness of the Airyscan and SR-SIM. We further demonstrate that these new superresolution methods can be easily applied to the study of fossil pollen material