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  • Aberrations in stimulated emission depletion (STED) microscopy

    14 December 2017

    © 2017 The Authors Like all methods of super-resolution microscopy, stimulated emission depletion (STED) microscopy can suffer from the effects of aberrations. The most important aspect of a STED microscope is that the depletion focus maintains a minimum, ideally zero, intensity point that is surrounded by a region of higher intensity. It follows that aberrations that cause a non-zero value of this minimum intensity are the most detrimental, as they inhibit fluorescence emission even at the centre of the depletion focus. We present analysis that elucidates the nature of these effects in terms of the different polarisation components at the focus for two-dimensional and three-dimensional STED resolution enhancement. It is found that only certain low-order aberration modes can affect the minimum intensity at the Gaussian focus. This has important consequences for the design of adaptive optics aberration correction systems.

  • Snapshot coherence-gated direct wavefront sensing for multi-photon microscopy.

    7 December 2017

    Deep imaging in turbid media such as biological tissue is challenging due to scattering and optical aberrations. Adaptive optics has the potential to compensate the tissue aberrations. We present a wavefront sensing scheme for multi-photon scanning microscopes using the pulsed, near-infrared light reflected back from the sample utilising coherence gating and a confocal pinhole to isolate the light from a layer of interest. By interfering the back-reflected light with a tilted reference beam, we create a fringe pattern with a known spatial carrier frequency in an image of the back-aperture plane of the microscope objective. The wavefront aberrations distort this fringe pattern and thereby imprint themselves at the carrier frequency, which allows us to separate the aberrations in the Fourier domain from low spatial frequency noise. A Fourier analysis of the modulated fringes combined with a virtual Shack-Hartmann sensor for smoothing yields a modal representation of the wavefront suitable for correction. We show results with this method correcting both DM-induced and sample-induced aberrations in rat tail collagen fibres as well as a Hoechst-stained MCF-7 spheroid of cancer cells.

  • Data driven identification and aberration correction for model based sensorless adaptive optics

    27 October 2017

    Wavefront sensorless adaptive optics methodologies are considered in many applications where the deployment of a dedicated wavefront sensor is inconvenient, such as in fluorescence microscopy. In these methodologies, aberration correction is achieved by sequentially changing the settings of the adaptive optical element until a predetermined imaging quality metric is optimised. Reducing the time required for this optimisation is a challenge. In this paper, a two stage data driven optimisation procedure is presented and validated in a laboratory environment. In the first stage, known aberrations are introduced by a deformable mirror and the corresponding intensities are measured by a photodiode masked by a pinhole. A generic quadratic metric is fitted to this collection of aberrations and intensity measurements. In the second stage, this quadratic metric is used in order to estimate and correct for optical aberrations. A closed form expression for the optimisation of the quadratic metric is derived by solving a linear system of equations. This requires a minimum of N +1 pairs of deformable mirror settings and intensity measurements, where N is the number of modes of the aberrations. © 2012 SPIE.

  • Focal-plane wavefront estimation and control using the extended Kalman filter

    27 October 2017

    This paper addresses the problem of disturbance rejection for faint Poisson point-like measurements. The aberration function is approximated with a finite Zernike based expansion. We use nonlinear observers to estimate the aberrations and a linear quadratic regulator to reject the aberrations. Kalman filtering is compared with the phase diversity maximum aposteriori estimation. The approach presented here is beneficial for instance for 2-photon observations, single molecule observations or natural/laser guide star observations in astronomy. © 2012 IEEE.

  • Semidefinite programming for model-based sensorless adaptive optics.

    9 March 2018

    Wavefront sensorless adaptive optics methodologies are widely considered in scanning fluorescence microscopy where direct wavefront sensing is challenging. In these methodologies, aberration correction is performed by sequentially changing the settings of the adaptive element until a predetermined image quality metric is optimized. An efficient aberration correction can be achieved by modeling the image quality metric with a quadratic polynomial. We propose a new method to compute the parameters of the polynomial from experimental data. This method guarantees that the quadratic form in the polynomial is semidefinite, resulting in a more robust computation of the parameters with respect to existing methods. In addition, we propose an algorithm to perform aberration correction requiring a minimum of N+1 measurements, where N is the number of considered aberration modes. This algorithm is based on a closed-form expression for the exact optimization of the quadratic polynomial. Our arguments are corroborated by experimental validation in a laboratory environment.

  • Modal-based phase retrieval for adaptive optics.

    7 December 2017

    We consider using phase retrieval (PR) to correct phase aberrations in an optical system. Three measurements of the point-spread function (PSF) are collected to estimate an aberration. For each measurement, a different defocus aberration is applied with a deformable mirror (DM). Once the aberration is estimated using a PR algorithm, we apply the aberration correction with the DM, and measure the residual aberration using a Shack-Hartmann wavefront sensor. The extended Nijboer-Zernike theory is used for modelling the PSF. The PR problem is solved using both an algorithm called PhaseLift, which is based on matrix rank minimization, and another algorithm based on alternating projections. For comparison, we include the results achieved using a classical PR algorithm, which is based on alternating projections and uses the fast Fourier transform.

  • Optimization-based wavefront sensorless adaptive optics for multiphoton microscopy.

    28 January 2018

    Optical aberrations have detrimental effects in multiphoton microscopy. These effects can be curtailed by implementing model-based wavefront sensorless adaptive optics, which only requires the addition of a wavefront shaping device, such as a deformable mirror (DM) to an existing microscope. The aberration correction is achieved by maximizing a suitable image quality metric. We implement a model-based aberration correction algorithm in a second-harmonic microscope. The tip, tilt, and defocus aberrations are removed from the basis functions used for the control of the DM, as these aberrations induce distortions in the acquired images. We compute the parameters of a quadratic polynomial that is used to model the image quality metric directly from experimental input-output measurements. Finally, we apply the aberration correction by maximizing the image quality metric using the least-squares estimate of the unknown aberration.

  • Supplementation of iron in pulmonary hypertension: Rationale and design of a phase II clinical trial in idiopathic pulmonary arterial hypertension.

    19 March 2018

    Our aim is to assess the safety and potential clinical benefit of intravenous iron (Ferinject) infusion in iron deficient patients with idiopathic pulmonary arterial hypertension (IPAH). Iron deficiency in the absence of anemia (1) is common in patients with IPAH; (2) is associated with inappropriately raised levels of hepcidin, the key regulator of iron homeostasis; and (3) correlates with disease severity and worse clinical outcomes. Oral iron absorption may be impeded by reduced absorption due to elevated hepcidin levels. The safety and benefits of parenteral iron replacement in IPAH are unknown. Supplementation of Iron in Pulmonary Hypertension (SIPHON) is a Phase II, multicenter, double-blind, randomized, placebo-controlled, crossover clinical trial of iron in IPAH. At least 60 patients will be randomized to intravenous ferric carboxymaltose (Ferinject) or saline placebo with a crossover point after 12 weeks of treatment. The primary outcome will be the change in resting pulmonary vascular resistance from baseline at 12 weeks, measured by cardiac catheterization. Secondary measures include resting and exercise hemodynamics and exercise performance from serial bicycle incremental and endurance cardiopulmonary exercise tests. Other secondary measurements include serum iron indices, 6-Minute Walk Distance, WHO functional class, quality of life score, N-terminal pro-brain natriuretic peptide (NT-proBNP), and cardiac anatomy and function from cardiac magnetic resonance. We propose that intravenous iron replacement will improve hemodynamics and clinical outcomes in IPAH. If the data supports a potentially useful therapeutic effect and suggest this drug is safe, the study will be used to power a Phase III study to address efficacy.

  • Vogels Group

    10 July 2016

    Theoretical and Computational Neuroscience

  • Vyazovskiy Group

    16 December 2013

    Sleep, brain and behaviour laboratory

  • Davies Group

    10 July 2016

    Molecular Analysis of Neurological Disorders

  • Herring Group

    22 January 2015

    Local neuromodulators of cardiac autonomic control

  • Ma Group

    19 January 2016

    The aim of our work is to determine the cellular mechanisms underlying the benefits of traditional multi-herbal Chinese medicines.

  • Threlfell Group

    8 April 2014

    Exploring mechanisms underlying dopamine neuron vulnerability in Parkinson's disease

  • Cantley Group

    10 July 2016

    Beta cell function, obesity and type 2 diabetes

  • Mommersteeg Group

    3 July 2014

    Heart regeneration & development

  • Molnar Group

    10 July 2016

    Cerebral Cortical Development and Evolution

  • de Wet Group

    16 December 2013

    Role of ABC transporters in gut endocrine K-and L-cells

  • Metabolism & Endocrinology

    16 January 2018

    We use the full range of modern molecular genetic and imaging techniques to study a range of metabolic areas.

  • Cardiac Sciences

    5 February 2018

    We are recognised internationally for our pioneering approaches to systems biology and to computational modelling of the heart.

  • Functional Genomics

    16 January 2018

    We play a leading role in the development of more efficient and cost-effective sequencing technologies.

  • Neuroscience

    16 January 2018

    We host a number of internationally recognised neuroscience groups, with expertise in a wide range of experimental and computational methods.

  • Cell Physiology

    16 January 2018

    We study everything from the structure of ion channels and transporters right up to their role in behaviour and human disease.

  • Development & Cell Biology

    16 January 2018

    We dissect the molecular and cellular mechanisms underlying a range of developmental and reproductive processes.