Microholography of Living Organisms

A workflow for single-particle structure determination via iterative phasing of rotational invariants in fluctuation X-ray scattering

Fluctuation X-ray scattering (FXS) offers a complementary approach for nano- and bioparticle imaging with an X-ray free-electron laser (XFEL), by extracting structural information from correlations in scattered XFEL pulses. Here a workflow is presented for single-particle structure determination using FXS. The workflow includes procedures for extracting the rotational invariants from FXS patterns, performing structure reconstructions via iterative phasing of the invariants, and aligning and averaging multiple reconstructions. The reconstruction pipeline is implemented in the open-source software xFrame and its functionality is demonstrated on several simulated structures.

Fluorescein dye as a novel cost-effective approach for staining raw specimens in ophthalmic pathology

Purpose:

To study the usefulness of sodium fluorescein dye for staining raw specimens in ophthalmic pathology.

Methods:

Laboratory-based observational study. Eye specimens received in the ocular pathology department of a tertiary eye care center in northeast India were included in the study after obtaining the informed consent. The study period was from 2016 to 2019. Specimens received were a corneal button, lid, orbital tissues, enucleated eyeballs, eviscerated eye, explanted intraocular lens (IOLs), optic nerve and ocular parasites. Sections of the gross specimens were stained with sodium fluorescein (C₂₀H₁₂O₅NA) dye. The average duration of tissue-stain contact time was 45 s. The sections were analyzed under the compound microscope. The intensity of illumination of the microscope was modulated to obtain high contrast digital photographs.

Results:

26 corneal buttons with or without limbal tissue specimens were analyzed with fluorescein staining procedure; limbus with its pigmented cells were seen in the enucleated eyeballs. 33 enucleated eyes (retinoblastoma [RB] (n = 24), phthisical eyes (n = 4), choroidal melanomas (n = 2), and others (n = 3) were included in the study cohort. In these 33 enucleated eyes, vitreous were also examined for the presence of hyalocytes and other pathological cells. Retinal pigment epithelial cells were also seen (n = 11). RB seeds were seen with fluorescein stain and documented in 14 specimens. The RB seeds were mostly in vitreous (n = 9) and subretinal space (n = 5). Fat cells (n = 8) from orbital tissues and sebaceous cells (n = 5) from frozen section specimens were also observed and documented.

Conclusion:

This study highlights a novel method of rapid staining of gross ophthalmic pathology specimens.

X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules

X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.

Intense water-window soft x-ray emission by spectral control using dual laser pulses

We demonstrate intense emission in the water-window soft x-ray spectral region by controlling the spectral behavior through changing the balance between emissivity and self-absorption in an expanding plasma. The number of photons obtained from a dual laser irradiated target with a 150-ps pre-pulse was maximized at 3.8 × 10¹⁴ photons/sr in λ = 2.34 - 4.38 nm at a pulse separation time of 7 - 10 ns. Enhancement of the number of photons is attributed to efficient coupling with the main laser pulse while maintaining a tiny source size.

Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials

Electron and x-ray microscopes allow one to image the entire, unlabeled structure of hydrated materials at a resolution well beyond what visible light microscopes can achieve. However, both approaches involve ionizing radiation, so that radiation damage must be considered as one of the limits to imaging. Drawing upon earlier work, we describe here a unified approach to estimating the image contrast (and thus the required exposure and corresponding radiation dose) in both x-ray and electron microscopy. This approach accounts for factors such as plural and inelastic scattering, and (in electron microscopy) the use of energy filters to obtain so-called "zero loss" images. As expected, it shows that electron microscopy offers lower dose for specimens thinner than about 1 µm (such as for studies of macromolecules, viruses, bacteria and archaebacteria, and thin sectioned material), while x-ray microscopy offers superior characteristics for imaging thicker specimen such as whole eukaryotic cells, thick-sectioned tissues, and organs. The required radiation dose scales strongly as a function of the desired spatial resolution, allowing one to understand the limits of live and frozen hydrated specimen imaging. Finally, we consider the factors limiting x-ray microscopy of thicker materials, suggesting that specimens as thick as a whole mouse brain can be imaged with x-ray microscopes without significant image degradation should appropriate image reconstruction methods be identified.

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.

Conformational landscape of a virus by single-particle X-ray scattering

Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and conformational landscape of the PR772 virus to a detector-limited resolution of 9 nm. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome. These results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes.

Laser-pulse compression using magnetized plasmas

Proposals to reach the next generation of laser intensities through Raman or Brillouin backscattering have centered on optical frequencies. Higher frequencies are beyond the range of such methods mainly due to the wave damping that accompanies the higher-density plasmas necessary for compressing higher frequency lasers. However, we find that an external magnetic field transverse to the direction of laser propagation can reduce the required plasma density. Using parametric interactions in magnetized plasmas to mediate pulse compression, both reduces the wave damping and alleviates instabilities, thereby enabling higher frequency or lower intensity pumps to produce pulses at higher intensities and longer durations. In addition to these theoretical advantages, our method in which strong uniform magnetic fields lessen the need for high-density uniform plasmas also lessens key engineering challenges or at least exchanges them for different challenges.

Single-particle structure determination by X-ray free-electron lasers: Possibilities and challenges

Single-particle structure recovery without crystals or radiation damage is a revolutionary possibility offered by X-ray free-electron lasers, but it involves formidable experimental and data-analytical challenges. Many of these difficulties were encountered during the development of cryogenic electron microscopy of biological systems. Electron microscopy of biological entities has now reached a spatial resolution of about 0.3 nm, with a rapidly emerging capability to map discrete and continuous conformational changes and the energy landscapes of biomolecular machines. Nonetheless, single-particle imaging by X-ray free-electron lasers remains important for a range of applications, including the study of large "electron-opaque" objects and time-resolved examination of key biological processes at physiological temperatures. After summarizing the state of the art in the study of structure and conformations by cryogenic electron microscopy, we identify the primary opportunities and challenges facing X-ray-based single-particle approaches, and possible means for circumventing them.

Conformations of macromolecules and their complexes from heterogeneous datasets

We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both discrete and continuous macromolecular conformational spectra. These algorithms naturally incorporate conformational heterogeneity without resort to sorting and classification, or prior knowledge of the type of heterogeneity present. They are applicable to single-particle diffraction and image datasets produced by X-ray lasers and cryo-electron microscopy, respectively, and particularly suitable for systems not easily amenable to purification or crystallization.

Diffraction before destruction

X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.

Opportunities and challenges for time-resolved studies of protein structural dynamics at X-ray free-electron lasers

X-ray free-electron lasers (XFELs) are revolutionary X-ray sources. Their time structure, providing X-ray pulses of a few tens of femtoseconds in duration; and their extreme peak brilliance, delivering approximately 10¹² X-ray photons per pulse and facilitating sub-micrometre focusing, distinguish XFEL sources from synchrotron radiation. In this opinion piece, I argue that these properties of XFEL radiation will facilitate new discoveries in life science. I reason that time-resolved serial femtosecond crystallography and time-resolved wide angle X-ray scattering are promising areas of scientific investigation that will be advanced by XFEL capabilities, allowing new scientific questions to be addressed that are not accessible using established methods at storage ring facilities. These questions include visualizing ultrafast protein structural dynamics on the femtosecond to picosecond time-scale, as well as time-resolved diffraction studies of non-cyclic reactions. I argue that these emerging opportunities will stimulate a renaissance of interest in time-resolved structural biochemistry.

Molecular imaging using X-ray free-electron lasers

The opening of hard X-ray free-electron laser facilities, such as the Linac Coherent Light Source (LCLS) at SLAC National Accelerator Laboratory in the United States, has ushered in a new era in structural determination. With X-ray pulse durations down to 10 fs or shorter, and up to 10(13) transversely coherent photons per pulse in a narrow spectral bandwidth, focused irradiances of 10(18) to 10(21) W cm(-2) or higher can be produced at X-ray energies ranging from 500 eV to 10 keV. New techniques for determining the structure of systems that cannot be crystallized and for studying the time-resolved behavior of irreversible reactions at femtosecond timescales are now available.

Femtosecond nanocrystallography using X-ray lasers for membrane protein structure determination

The invention of free electron X-ray lasers has opened a new era for membrane protein structure determination with the recent first proof-of-principle of the new concept of femtosecond nanocrystallography. Structure determination is based on thousands of diffraction snapshots that are collected on a fully hydrated stream of nanocrystals. This review provides a summary of the method and describes how femtosecond X-ray crystallography overcomes the radiation-damage problem in X-ray crystallography, avoids the need for growth and freezing of large single crystals while offering a new method for direct digital phase determination by making use of the fully coherent nature of the X-ray beam. We briefly review the possibilities for time-resolved crystallography, and the potential for making 'molecular movies' of membrane proteins at work.

Bayesian algorithms for recovering structure from single-particle diffraction snapshots of unknown orientation: a comparison

The advent of X-ray free-electron lasers promises the possibility to determine the structure of individual particles such as microcrystallites, viruses and biomolecules from single-shot diffraction snapshots obtained before the particle is destroyed by the intense femtosecond pulse. This program requires the ability to determine the orientation of the particle giving rise to each snapshot at signal levels as low as ~10(-2) photons per pixel. Two apparently different approaches have recently demonstrated this capability. Here we show they represent different implementations of the same fundamental approach, and identify the primary factors limiting their performance.

Soft X-ray diffraction microscopy of a frozen hydrated yeast cell

We report the first image of an intact, frozen hydrated eukaryotic cell using x-ray diffraction microscopy, or coherent x-ray diffraction imaging. By plunge freezing the specimen in liquid ethane and maintaining it below -170 degrees C, artifacts due to dehydration, ice crystallization, and radiation damage are greatly reduced. In this example, coherent diffraction data using 520 eV x rays were recorded and reconstructed to reveal a budding yeast cell at a resolution better than 25 nm. This demonstration represents an important step towards high resolution imaging of cells in their natural, hydrated state, without limitations imposed by x-ray optics.

Generation of a coherent x ray in the water window region at 1 kHz repetition rate using a mid-infrared pump source

We demonstrate the generation of a coherent x ray in the water window region in a gas cell filled with neon gas using a wavelength-tunable mid-IR femtosecond laser operating at 1 kHz repetition rate. The cutoff energy and conversion efficiency of the water window x ray can be optimized by tuning gas pressure as well as the focal position.

X-ray imaging beyond the limits

The intense, brief pulses of X-rays from upcoming free-electron lasers will greatly extend X-ray microscopy to the femtosecond time domain and to interatomic length scales. From recent experiments and simulations one can envisage imaging macromolecules with X-rays without the need for crystallization.

Feasibility of imaging living cells at subnanometer resolutions by ultrafast X-ray diffraction

Detailed structural investigations on living cells are problematic because existing structural methods cannot reach high resolutions on non-reproducible objects. Illumination with an ultrashort and extremely bright X-ray pulse can outrun key damage processes over a very short period. This can be exploited to extend the diffraction signal to the highest possible resolution in flash diffraction experiments. Here we present an analysis of the interaction of a very intense and very short X-ray pulse with a living cell, using a non-equilibrium population kinetics plasma code with radiation transfer. Each element in the evolving plasma is modeled by numerous states to monitor changes in the atomic populations as a function of pulse length, wavelength, and fluence. The model treats photoionization, impact ionization, Auger decay, recombination, and inverse bremsstrahlung by solving rate equations in a self-consistent manner and describes hydrodynamic expansion through the ion sound speed. The results show that subnanometer resolutions could be reached on micron-sized cells in a diffraction-limited geometry at wavelengths between 0·75 and 1·5 nm and at fluences of 1011–1012 photons μm−2in less than 10 fs. Subnanometer resolutions could also be achieved with harder X-rays at higher fluences. We discuss experimental and computational strategies to obtain depth information about the object in flash diffraction experiments.

Femtosecond time-delay X-ray holography

Extremely intense and ultrafast X-ray pulses from free-electron lasers offer unique opportunities to study fundamental aspects of complex transient phenomena in materials. Ultrafast time-resolved methods usually require highly synchronized pulses to initiate a transition and then probe it after a precisely defined time delay. In the X-ray regime, these methods are challenging because they require complex optical systems and diagnostics. Here we propose and apply a simple holographic measurement scheme, inspired by Newton's 'dusty mirror' experiment, to monitor the X-ray-induced explosion of microscopic objects. The sample is placed near an X-ray mirror; after the pulse traverses the sample, triggering the reaction, it is reflected back onto the sample by the mirror to probe this reaction. The delay is encoded in the resulting diffraction pattern to an accuracy of one femtosecond, and the structural change is holographically recorded with high resolution. We apply the technique to monitor the dynamics of polystyrene spheres in intense free-electron-laser pulses, and observe an explosion occurring well after the initial pulse. Our results support the notion that X-ray flash imaging can be used to achieve high resolution, beyond radiation damage limits for biological samples. With upcoming ultrafast X-ray sources we will be able to explore the three-dimensional dynamics of materials at the timescale of atomic motion.

Imaging Atomic Structure and Dynamics with Ultrafast X-ray Scattering

Measuring atomic-resolution images of materials with x-ray photons during chemical reactions or physical transformations resides at the technological forefront of x-ray science. New x-ray-based experimental capabilities have been closely linked with advances in x-ray sources, a trend that will continue with the impending arrival of x-ray-free electron lasers driven by electron accelerators. We discuss recent advances in ultrafast x-ray science and coherent imaging made possible by linear-accelerator-based light sources. These studies highlight the promise of ultrafast x-ray lasers, as well as the technical challenges and potential range of applications that will accompany these transformative x-ray light sources.

Encapsulation and diffraction-pattern-correction methods to reduce the effect of damage in x-ray diffraction imaging of single biological molecules

Short and intense x-ray pulses may be used for atomic-resolution diffraction imaging of single biological molecules. Radiation damage and a low signal-to-noise ratio impose stringent pulse requirements. In this Letter, we describe methods for decreasing the damage and improving the signal by encapsulating the molecule in a sacrificial layer (tamper) that reduces atomic motion and by postprocessing the pulse-averaged diffraction pattern to correct for ionization damage. Simulations show that these methods greatly improve the image quality.

Subnanometer-scale measurements of the interaction of ultrafast soft x-ray free-electron-laser pulses with matter

At the recently built FLASH x-ray free-electron laser, we studied the reflectivity of Si/C multilayers with fluxes up to 3 x 10(14) W/cm2. Even though the nanostructures were ultimately completely destroyed, we found that they maintained their integrity and reflectance characteristics during the 25-fs-long pulse, with no evidence for any structural changes over lengths greater than 3 A. This experiment demonstrates that with intense ultrafast pulses, structural damage does not occur during the pulse, giving credence to the concept of diffraction imaging of single macromolecules.

Classification of continuous diffraction patterns: A numerical study

The very intense and short pulses of future X-ray free electron lasers may allow the atomic resolution imaging of small, non-periodic objects. Preliminary estimates show that images obtained from single pulses do not contain statistically enough photons to allow successful reconstruction. Therefore multiple exposures of randomly oriented identical replicas have to be taken and the individual images have to be classified according to the object's orientation. The classification has been analytically treated by Huldt et al. [Huldt, G., Szoke, A., Hajdu, J., 2003. J. Struct. Biol. 144, 219.]. In this paper we extend the analytical results with numerical model calculations. This allows us to simulate realistic situations, which we will face in real experiments. We find significant deviations from the analytical expectations, even in the ideal case of spherical particles with random atomic distributions. We introduce a new norm for the individual scattering patterns and describe a criterion to select images belonging to similar orientation, which makes the classification more reliable in practice. We also discuss the effects of particle shape and size, partial orientational ordering, the measurement's resolution and the charge error caused by the Coulomb explosion.

Invited article: a [corrected] unified evaluation of iterative projection algorithms for phase retrieval

Iterative projection algorithms are successfully being used as a substitute of lenses to recombine, numerically rather than optically, light scattered by illuminated objects. Images obtained computationally allow aberration-free diffraction-limited imaging and the possibility of using radiation for which no lenses exist. The challenge of this imaging technique is transferred from the lenses to the algorithms. We evaluate these new computational "instruments" developed for the phase-retrieval problem, and discuss acceleration strategies.

Plasma conditions for improved energy coupling into the gain region of the Ni-like Pd transient collisional x-ray laser

We have directly probed the conditions in which the Ni-like Pd transient collisional x-ray laser is generated and propagates by measuring the near-field image and by utilizing picosecond resolution soft x-ray laser interferometry of the preformed Pd plasma gain medium. The electron density and gain region of the plasma have been determined experimentally and are found to be in good agreement with simulations. We observe a strong dependence of the laser pump-gain medium coupling on the laser pump parameters. The most efficient coupling occurs with the formation of lower density gradients in the preformed plasma and when the duration of the main heating pulse is comparable to the gain lifetime (approximately 10 ps for mid- Z Ni-like schemes). This increases the output intensity by more than an order of magnitude relative to the commonly utilized case where the same pumping energy is delivered within a shorter heating pulse duration (<3 ps) . In contrast, the higher intensity heating pulses are observed to be absorbed at higher electron densities and in regions where steep density gradients limit the effective length of the gain medium.

Taking X-ray diffraction to the limit: macromolecular structures from femtosecond X-ray pulses and diffraction microscopy of cells with synchrotron radiation

Recent work is extending the methodology of X-ray crystallography to the structure determination of noncrystalline specimens. The phase problem is solved using the oversampling method, which takes advantage of "continuous" diffraction patterns from noncrystalline specimens. Here we review the principle of this newly developed technique and discuss the ongoing experiments of imaging nonperiodic objects, such as cells and cellular structures, using coherent and bright X rays produced by third-generation synchrotron sources. In the longer run, the technique may be applicable to image single biomolecules using anticipated X-ray free electron lasers. Here, computer simulations have so far demonstrated two important steps: (a) by using an extremely intense femtosecond X-ray pulse, a diffraction pattern can be recorded from a macromolecule before radiation damage manifests itself; and (b) the phase information can be retrieved in an ab initio fashion from a set of calculated noisy diffraction patterns of single protein molecules.

Dynamics of biological molecules irradiated by short x-ray pulses

Very short and intense x-ray pulses can be used for diffraction imaging of single biological molecules. Inevitably, x-ray absorption initiates damage that degrades the molecule's image. This paper presents a continuum model of the physics that leads to damage when a small particle absorbs a large x-ray dose. The main processes are found to be ionization and Coulomb-force driven atomic motion. Trapping of electrons, Debye shielding, and nonuniform collisional ionization all have a significant effect on the overall damage kinetics.

Coherent X-ray diffractive imaging: applications and limitations

The inversion of a diffraction pattern offers aberration-free diffraction-limited 3D images without the resolution and depth-of-field limitations of lens-based tomographic systems, the only limitation being radiation damage. We review our experimental results, discuss the fundamental limits of this technique and future plans.

Imaging whole Escherichia coli bacteria by using single-particle x-ray diffraction

We report the first experimental recording, to our knowledge, of the diffraction pattern from intact Escherichia coli bacteria using coherent x-rays with a wavelength of 2 A. By using the oversampling phasing method, a real space image at a resolution of 30 nm was directly reconstructed from the diffraction pattern. An R factor used for characterizing the quality of the reconstruction was in the range of 5%, which demonstrated the reliability of the reconstruction process. The distribution of proteins inside the bacteria labeled with manganese oxide has been identified and this distribution confirmed by fluorescence microscopy images. Compared with lens-based microscopy, this diffraction-based imaging approach can examine thicker samples, such as whole cultured cells, in three dimensions with resolution limited only by radiation damage. Looking forward, the successful recording and reconstruction of diffraction patterns from biological samples reported here represent an important step toward the potential of imaging single biomolecules at near-atomic resolution by combining single-particle diffraction with x-ray free electron lasers.

Methods for imaging the structure and function of living tissues and cells: 2. Fluorescence lifetime imaging

This second article in the series shows how fluorescence lifetime imaging allows natural biochemical and physiological properties of tissues to act as contrast agents and so provide a basis for distinguishing normal and diseased tissue components. When combined with methods for imaging through non-transparent tissues and tomographic reconstruction it shows promise as a new optical biopsy technique. In addition to this, specially designed vital fluorescent probes of specific biochemical, secondary messenger and receptor activity in living cells may be imaged using FLIM. This is the youngest of the techniques covered in these review articles on imaging, the first FLIM images of cells having been produced in 1994.

Fast numerical reconstruction technique for high-resolution hybrid holographic microscopy

A numerical reconstruction method believed to be new is proposed for hybrid holographic microscopy in which the hologram of a microscopic object is recorded by an image sensor and is then reconstructed by a computer. Because the Fresnel-Kirchhoff integral must be used for numerical reconstruction to achieve high resolution, we propose an approximation technique for reducing the calculation time. This approximation technique is suitable for microscopic application. The numerical reconstruction of 1-microm-sized objects was demonstrated with a He-Ne laser (lambda = 0.6328 microm).

Biomedical three-dimensional holographic microimaging at visible, ultraviolet and X-ray wavelengths

A new imaging technology is under advanced development that has several key advantages over conventional forms of microimaging performed with standard light microscopes, confocal light microscopes, and electron microscopes. The image created by this microscope possesses several unique features: It is intrinsically three-dimensional; it can be formed with very high contrast, a characteristic of the phase-sensitive nature of the recording; the information contained in the image is obtained in a single exposure of the specimen, a feature that eliminates the accumulation of damage to living systems that can occur with techniques utilizing multiple exposures; the method of image construction is fundamentally free from aberration (distortion), thereby obviating the need to employ complex procedures for correction; the exact focal plane of any optical section is digitally determined through computation and is not based on any mechanical adjustments; and the principles of operation, including the computational processes and modalities of image presentation, are uniform over the full range of spectral coverage spanning from the visible (approximately 500 nm) to the X-ray (approximately 0.3 nm) regions. The application of this new technology is expected to open new cost-effective avenues to the understanding, prevention and treatment of broad areas of human disease.

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.

Chemical contrast in X-ray microscopy and spatially resolved XANES spectroscopy of organic specimens

The scanning transmission x-ray microscope at the National Synchrotron Light Source has been used to record x-ray absorption near-edge structure (XANES) spectra from 0.01-square-micrometer regions of organic specimens. The spectral features observed reflect the molecular structure of the dominant absorbing atoms and provide the contrast mechanism for high-resolution imaging with chemical sensitivity. This technique was used with x-ray energies near the carbon K absorption edge to identify and map separate phases in various polymer blends and to map the DNA distribution in chromosomes with a spatial resolution of 55 nanometers.

Method of concentration of power in materials for x-ray amplification

Recent experimental and theoretical results indicate that a new technique for the controlled concentration of power in materials may be feasible. The power levels that are potentially achievable are sufficient for the generation of amplification of x-ray wavelengths in the kilovolt range. The method of power concentration involves the combination of (1) a new ultrahigh brightness subpicosecond laser technology, (2) multiphoton coupling to atoms and molecules, and (3) a new channeled mode of electromagnetic propagation. The energy scaling of this approach is the most important consideration, and it is shown that the control of the propagation is the key factor that enables high levels of amplification in the kilovolt regime to be achieved with a total excitation energy of ~1 J.

Wavelength choice for soft x-ray laser holography of biological samples

The choice of an optimal wavelength for soft x-ray holography is discussed, based on a description of scattering by biological structures within an aqueous environment. We conclude that wavelengths slightly longer than the 43.7-A carbon K-edge provide a good trade off between minimizing the necessary source power and the dose absorbed by the sample and maximizing the penetrability of the x-rays through wet samples. This differs from the previous notion that wavelengths within the water window (between 23.2 A and 43.7 A) would be the best for holography. The problem of motion resulting from the absorption of x rays during a short exposure is described. The possibility of using ultrashort exposures in order to capture the image before motion can compromise the resolution is explored. The impact of these calculations on the question of the feasibility of using an x-ray laser for holography of biological structures is discussed.

A 3D display with a linearly moving mirror to reflect a series of 2D cross sections and its application to noninvasive angiography

A 3D display equipped with a linearly moving mirror reflecting a series of 2D cross sections pictures has been devised. The pictures were displayed by a CRT in perfect synchronization with the back-and-forth movements of the mirror. The 80x80x80 mm(3) 3D space contained 128x128 pixels; with each pixel having 256 grades of intensity, enough to produce a satisfactory 3D image of an ultrasonic echogram of hepatic vessels. The images can be observed from different angles by changing the observer's position or by prompt rotation of the image through a console. Mechanical problems inherent in using moving parts have been solved.

X-ray holograms at improved resolution: a study of zymogen granules

X-ray holography offers the possibility of three-dimensional microscopy with resolution higher than that of the light microscope and with contrast based on x-ray edges. In principle, the method is especially advantageous for biological samples if x-rays in the wavelength region between the carbon and oxygen K edges are used. However, until now the achieved resolution has not exceeded that of the light microscope because of the poor coherence properties of the x-ray sources and the low resolution of the detectors that were available. With a recently developed x-ray source based on an undulator on an electron storage ring, and high resolution x-ray resist, a hologram has been recorded at about 400-angstrom resolution. The experiment utilized x-rays with wavelengths of 24.7 angstroms and required a 1-hour exposure of the pancreatic zymogen granules under study.