Malcolm R. Howells

Soft X-ray microscopes and their biological applications

In this review we propose to address the question: for the life-science researcher, what does X-ray microscopy have to offer that is not otherwise easily available?We will see that the answer depends on a combination of resolution, penetrating power, analytical sensitivity, compatibility with wet specimens, and the ease of image interpretation.

X-ray image reconstruction from a diffraction pattern alone

A solution to the inversion problem of scattering would offer aberration-free diffraction-limited three-dimensional images without the resolution and depth-of-field limitations of lens-based tomographic systems. Powerful algorithms are increasingly being used to act as lenses to form such images. Current image reconstruction methods, however, require the knowledge of the shape of the object and the low spatial frequencies unavoidably lost in experiments. Diffractive imaging has thus previously been used to increase the resolution of images obtained by other means. Here we experimentally demonstrate an inversion method, which reconstructs the image of the object without the need for any such prior knowledge.

High-resolution ab initio Three-dimensional X-ray Diffraction Microscopy

Coherent x-ray diffraction microscopy is a method of imaging nonperiodic isolated objects at resolutions limited, in principle, by only the wavelength and largest scattering angles recorded. We demonstrate x-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the three-dimensional diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a nonperiodic object. We also construct two-dimensional images of thick objects with greatly increased depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution with x-ray undulator radiation and establishes the techniques to be used in atomic-resolution ultrafast imaging at x-ray free-electron laser sources.

Biological imaging by soft x-ray diffraction microscopy

We have used the method of x-ray diffraction microscopy to image the complex-valued exit wave of an intact and unstained yeast cell. The images of the freeze-dried cell, obtained by using 750-eV x-rays from different angular orientations, portray several of the cells major internal components to 30-nm resolution. The good agreement among the independently recovered structures demonstrates the accuracy of the imaging technique. To obtain the best possible reconstructions, we have implemented procedures for handling noisy and incomplete diffraction data, and we propose a method for determining the reconstructed resolution. This work represents a previously uncharacterized application of x-ray diffraction microscopy to a specimen of this complexity and provides confidence in the feasibility of the ultimate goal of imaging biological specimens at 10-nm resolution in three dimensions.

High-Resolution Imaging by Fourier Transform X-ray Holography.

Fourier transform x-ray holography has been used to image gold test objects with submicrometer structure, resolving features as small as 60 nanometers. The hologram-recording instrument uses coherent 3.4-nanometer radiation from the soft x-ray undulator beamline X1A at the National Synchrotron Light Source. The specimen to be imaged is placed near the first-order focal spot produced by a Fresnel zone plate; the other orders, chiefly the zeroth, illuminate the specimen. The wave scattered by the specimen interferes with the spherical reference wave from the focal spot, forming a hologram with fringes of low spatial frequency. The hologram is recorded in digital form by a charge-coupled device camera, and the specimen image is obtained by numerical reconstruction.

Massively parallel X-ray holography

Stefano Marchesini, 2 Sébastien Boutet, 4 Anne E. Sakdinawat, Michael J. Bogan, Sas̆a Bajt, Anton Barty, Henry N. Chapman, 6 Matthias Frank, Stefan P. Hau-Riege, Abraham Szöke, Congwu Cui, Malcolm R. Howells, David A. Shapiro, John C. H. Spence, Joshua W. Shaevitz, Johanna Y. Lee, Janos Hajdu, 4 and Marvin M. Seibert Lawrence Livermore National Laboratory, 7000 East Ave., Livermore, CA 94550, USA. Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron rd. Berkeley, CA 94720, USA∗ Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, 2575 Sand Hill Road, Menlo Park, California 94025, USA. Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden. Center for X-ray Optics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. 6 Centre for Free-Electron Laser Science U. Hamburg, DESY, Notkestraße 85, Hamburg, Germany. Department of Physics and Astronomy, Arizona State University, Tempe, AZ 85287-1504, USA Department of Physics and Lewis-Sigler Institute, 150 Carl Icahn Laboratory, Princeton, New Jersey 08544, USA. Department of Plant and Microbial Biology, University of California, Berkeley, 648 Stanley Hall 3220, Berkeley, California 94720, USA. (Dated: February 9, 2008)

Suite of three protein crystallography beamlines with single superconducting bend magnet as the source.

At the Advanced Light Source, three protein crystallography beamlines have been built that use as a source one of the three 6 T single-pole superconducting bending magnets (superbends) that were recently installed in the ring. The use of such single-pole superconducting bend magnets enables the development of a hard X-ray program on a relatively low-energy 1.9 GeV ring without taking up insertion-device straight sections. The source is of relatively low power but, owing to the small electron beam emittance, it has high brightness. X-ray optics are required to preserve the brightness and to match the illumination requirements for protein crystallography. This was achieved by means of a collimating premirror bent to a plane parabola, a double-crystal monochromator followed by a toroidal mirror that focuses in the horizontal direction with a 2:1 demagnification. This optical arrangement partially balances aberrations from the collimating and toroidal mirrors such that a tight focused spot size is achieved. The optical properties of the beamline are an excellent match to those required by the small protein crystals that are typically measured. The design and performance of these new beamlines are described.

Image reconstruction from electron and X-ray diffraction patterns using iterative algorithms: experiment and simulation

The hybrid input-output iterative algorithm, which solves the phase problem for scattering from non-periodic objects, is reviewed for application to X-ray and electron diffraction data. Desirable convex constraints, including the sign of the scattering potential for electrons, and compact support, are discussed. The cases of complex and real exit-face wavefunctions, strong and weak phase objects, various supports, and the use of coherent focussed radiation are reviewed. Reconstruction of general complex objects requires accurate knowledge of the support, which should consist of two holes or a triangle in an opaque mask. The support boundaries should be as sharp as possible. Strong phase objects without absorption can be recovered if the support consists of one hole, is accurately known and has sufficiently sharp boundaries. Real and weak phase objects with absorption can be recovered without accurate knowledge of the support area if the support boundaries are sufficiently sharp and the support consists of one or more holes. A sign constraint on the scattering potential is used to recover weak phase objects. The experimental realization of theoretically desirable support conditions is discussed. A two-stage method of finding the support for complex objects is proposed. Experimental results from applying the Gerchberg-Saxton-Fienup HiO-algorithm to coherent electron diffraction patterns are presented, using specially made e-beam lithographed support structures. Images with a resolution of about 5 nm are thus recovered from the intensities alone in coherent electron diffraction patterns from non-periodic objects. Limitations of the present experiments are identified and suggestions made for development of both X-ray and electron work.

Three-Dimensional Coherent X-Ray Diffraction Imaging of a Ceramic Nanofoam: Determination of Structural Deformation Mechanisms

Ultralow density polymers, metals, and ceramic nanofoams are valued for their high strength-to-weight ratio, high surface area, and insulating properties ascribed to their structural geometry. We obtain the labrynthine internal structure of a tantalum oxide nanofoam by x-ray diffractive imaging. Finite-element analysis from the structure reveals mechanical properties consistent with bulk samples and with a diffusion-limited cluster aggregation model, while excess mass on the nodes discounts the dangling fragments hypothesis of percolation theory.

Theory and practice of elliptically bent x-ray mirrors

We report the results of our research and development in techniques for producing elliptical x-ray mirrors by controlled bending of a flat substrate. We review the theory and technique of mirror bending with emphasis on the optical engineering issues and describe our design concepts for both metal and ceramic mirrors. We provide analysis of the various classes of error that must be addressed to obtain a high quality elliptical surface and a correspondingly fine focus of the x-ray beam. We describe particular mirrors that have been built, using these techniques, to meet the requirements of the scientific program at the Advanced Light Source at Lawrence Berkeley National Laboratory. For these examples, we show optical metrology results indicating the achievement of surface accuracy values around and, in some cases, below 1 mrad as well as x-ray measurements showing submicrometer focal spots.