Automated Fourier space region-recognition filtering for off-axis digital holographic microscopy

Automated label-free quantitative imaging of biological samples can greatly benefit high throughput diseases diagnosis. Digital holographic microscopy (DHM) is a powerful quantitative label-free imaging tool that retrieves structural details of cellular samples non-invasively. In off-axis DHM, a proper spatial filtering window in Fourier space is crucial to the quality of reconstructed phase image. Here we describe a region-recognition approach that combines shape recognition with an iterative thresholding to extracts the optimal shape of frequency components. The region recognition technique offers fully automated adaptive filtering that can operate with a variety of samples and imaging conditions. When imaging through optically scattering biological hydrogel matrix, the technique surpasses previous histogram thresholding techniques without requiring any manual intervention. Finally, we automate the extraction of the statistical difference of optical height between malaria parasite infected and uninfected red blood cells. The method described here pave way to greater autonomy in automated DHM imaging for imaging live cell in thick cell cultures

Achieving diffraction-limited resolution in soft-X-ray Fourier-transform holography

The spatial resolution of microscopic images acquired via X-ray Fourier-transform holography is limited by the source size of the reference wave and by the numerical aperture of the detector. We analyze the interplay between both influences and show how they are matched in practice. We further identify, how high spatial frequencies translate to imaging artifacts in holographic reconstructions where mainly the reference beam limits the spatial resolution. As a solution, three methods are introduced based on numerical post-processing of the reconstruction. The methods comprise apodization of the hologram, refocusing via wave propagation, and deconvolution using the transfer function of the imaging system. In particular for the latter two, we demonstrate that image details smaller than the source size of the reference beam can be recovered up to the diffraction limit of the hologram. Our findings motivate the intentional application of a large reference-wave source enhancing the image contrast in applications with low photon numbers such as single-shot experiments at free-electron lasers or imaging at laboratory sources.BMBF, 05K10KTB, Verbundprojekt: FSP 301 - FLASH: Nanoskopische Systeme. Teilprojekt 1.1: Universelle Experimentierkammer für Streuexperimente mit kohärenten Femtosekunden-Röntgenpulsen Multi Purpose Coherent Scattering Chamber for FLASH and XFEL 'MPscatt

Holographic opto-fluidic microscopy.

Over the last decade microfluidics has created a versatile platform that has significantly advanced the ways in which micro-scale organisms and objects are controlled, processed and investigated, by improving the cost, compactness and throughput aspects of analysis. Microfluidics has also expanded into optics to create reconfigurable and flexible optical devices such as reconfigurable lenses, lasers, waveguides, switches, and on-chip microscopes. Here we present a new opto-fluidic microscopy modality, i.e., Holographic Opto-fluidic Microscopy (HOM), based on lensless holographic imaging. This imaging modality complements the miniaturization provided by microfluidics and would allow the integration of microscopy into existing on-chip microfluidic devices with various functionalities. Our imaging modality utilizes partially coherent in-line holography and pixel super-resolution to create high-resolution amplitude and phase images of the objects flowing within micro-fluidic channels, which we demonstrate by imaging C. elegans, Giardia lamblia, and Mulberry pollen. HOM does not involve complicated fabrication processes or precise alignment, nor does it require a highly uniform flow of objects within microfluidic channels

The coronagraphic Modal Wavefront Sensor: a hybrid focal-plane sensor for the high-contrast imaging of circumstellar environments

The raw coronagraphic performance of current high-contrast imaging instruments is limited by the presence of a quasi-static speckle (QSS) background, resulting from instrumental non-common path errors (NCPEs). Rapid development of efficient speckle subtraction techniques in data reduction has enabled final contrasts of up to 10-6 to be obtained, however it remains preferable to eliminate the underlying NCPEs at the source. In this work we introduce the coronagraphic Modal Wavefront Sensor (cMWS), a new wavefront sensor suitable for real-time NCPE correction. This pupil-plane optic combines the apodizing phase plate coronagraph with a holographic modal wavefront sensor, to provide simultaneous coronagraphic imaging and focal-plane wavefront sensing using the science point spread function. We first characterise the baseline performance of the cMWS via idealised closed-loop simulations, showing that the sensor successfully recovers diffraction-limited coronagraph performance over an effective dynamic range of +/-2.5 radians root-mean-square (RMS) wavefront error within 2-10 iterations. We then present the results of initial on-sky testing at the William Herschel Telescope, and demonstrate that the sensor is able to retrieve injected wavefront aberrations to an accuracy of 10nm RMS under realistic seeing conditions. We also find that the cMWS is capable of real-time broadband measurement of atmospheric wavefront variance at a cadence of 50Hz across an uncorrected telescope sub-aperture. When combined with a suitable closed-loop adaptive optics system, the cMWS holds the potential to deliver an improvement in raw contrast of up to two orders of magnitude over the uncorrected QSS floor. Such a sensor would be eminently suitable for the direct imaging and spectroscopy of exoplanets with both existing and future instruments, including EPICS and METIS for the E-ELT.Comment: 14 pages, 12 figures: accepted for publication in Astronomy & Astrophysic

Phase Retrieval via Matrix Completion

This paper develops a novel framework for phase retrieval, a problem which arises in X-ray crystallography, diffraction imaging, astronomical imaging and many other applications. Our approach combines multiple structured illuminations together with ideas from convex programming to recover the phase from intensity measurements, typically from the modulus of the diffracted wave. We demonstrate empirically that any complex-valued object can be recovered from the knowledge of the magnitude of just a few diffracted patterns by solving a simple convex optimization problem inspired by the recent literature on matrix completion. More importantly, we also demonstrate that our noise-aware algorithms are stable in the sense that the reconstruction degrades gracefully as the signal-to-noise ratio decreases. Finally, we introduce some theory showing that one can design very simple structured illumination patterns such that three diffracted figures uniquely determine the phase of the object we wish to recover