Quantitative 3D elemental microtomography of Cyclotella meneghiniana at 400-nm resolution

A New Workflow for x-ray fluorescence tomography: MAPSToTomoPy

X-ray fluorescence tomography involves the acquisition of a series of 2D x-ray fluorescence datasets between which a specimen is rotated. At the Advanced Photon Source at Argonne National Laboratory, the workflow at beamlines 2-ID-E and 21-ID-D (the Bionanoprobe, a cryogenic microscope system) has included the use of the program MAPS for obtaining elemental concentrations from 2D images, and the program TomoPy which was developed to include several tomographic reconstruction methods for x-ray transmission data. In the past, fluorescence projection images from an individual chemical element were hand-assembled into a 3D dataset for reconstruction using interactive tools such as ImageJ. We describe here the program MAPSToTomoPy, which provides a graphical user interface (GUI) to control a workflow between MAPS and TomoPy, with tools for visualizing the sinograms of projection image sequences from particular elements and to use these to help correct misalignments of the rotation axis. The program also provides an integrated output of the 3D distribution of the detected elements for subsequent 3D visualization packages.

Visualising mouse neuroanatomy and function by metal distribution using laser ablation-inductively coupled plasma-mass spectrometry imaging

Studying the neuroanatomy of the mouse brain using imaging mass spectrometry and chemometric analysis.

Metals have a number of important roles within the brain. We used laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to map the three-dimensional concentrations and distributions of transition metals, in particular iron (Fe), copper (Cu) and zinc (Zn) within the murine brain. LA-ICP-MS is one of the leading analytical tools for measuring metals in tissue samples. Here, we present a complete data reduction protocol for measuring metals in biological samples, including the application of a pyramidal voxel registration technique to reproducibly align tissue sections. We used gold (Au) nanoparticle and ytterbium (Yb)-tagged tyrosine hydroxylase antibodies to assess the co-localisation of Fe and dopamine throughout the entire mouse brain. We also examined the natural clustering of metal concentrations within the murine brain to elucidate areas of similar composition. This clustering technique uses a mathematical approach to identify multiple ‘elemental clusters’, avoiding user bias and showing that metal composition follows a hierarchical organisation of neuroanatomical structures. This work provides new insight into the distinct compartmentalisation of metals in the brain, and presents new avenues of exploration with regard to region-specific, metal-associated neurodegeneration observed in several chronic neurodegenerative diseases.

3D imaging of transition metals in the zebrafish embryo by X-ray fluorescence microtomography

Synchrotron X-ray fluorescence (SXRF) microtomography has emerged as a powerful technique for the 3D visualization of the elemental distribution in biological samples. The mechanical stability, both of the instrument and the specimen, is paramount when acquiring tomographic projection series. By combining the progressive lowering of temperature method (PLT) with femtosecond laser sectioning, we were able to embed, excise, and preserve a zebrafish embryo at 24 hours post fertilization in an X-ray compatible, transparent resin for tomographic elemental imaging. Based on a data set comprised of 60 projections, acquired with a step size of 2 μm during 100 hours of beam time, we reconstructed the 3D distribution of zinc, iron, and copper using the iterative maximum likelihood expectation maximization (MLEM) reconstruction algorithm. The volumetric elemental maps, which entail over 124 million individual voxels for each transition metal, revealed distinct elemental distributions that could be correlated with characteristic anatomical features at this stage of embryonic development.

Validation of a Geant4 model of the X-ray fluorescence microprobe at the Australian Synchrotron

A Geant4 Monte Carlo simulation of the X-ray fluorescence microprobe (XFM) end-station at the Australian Synchrotron has been developed. The simulation is required for optimization of the scan configuration and reconstruction algorithms. As part of the simulation process, a Gaussian beam model was developed. Experimental validation of this simulation has tested the efficacy for use of the low-energy physics models in Geant4 for this synchrotron-based technique. The observed spectral distributions calculated in the 384 pixel Maia detector, positioned in the standard back-scatter configuration, were compared with those obtained from experiments performed at three incident X-ray beam energies: 18.5, 11.0 and 6.8 keV. The reduced χ-squared (\chi^{2}_{\rm{red}}) was calculated for the scatter and fluorescence regions of the spectra and demonstrates that the simulations successfully reproduce the scatter distributions. Discrepancies were shown to occur in the multiple-scatter tail of the Compton continuum. The model was shown to be particularly sensitive to the impurities present in the beryllium window of the Maia detector and their concentrations were optimized to improve the \chi^{2}_{\rm{red}} parametrization in the low-energy fluorescence regions of the spectra.

Selenium preferentially accumulates in the eye lens following embryonic exposure: a confocal X-ray fluorescence imaging study

Maternal transfer of elevated selenium (Se) to offspring is an important route of Se exposure for fish in the natural environment. However, there is a lack of information on the tissue specific spatial distribution and speciation of Se in the early developmental stages of fish, which provide important information about Se toxicokinetics. The effect of maternal transfer of Se was studied by feeding adult zebrafish a Se-elevated or a control diet followed by collection of larvae from both groups. Novel confocal synchrotron-based techniques were used to investigate Se within intact preserved larvae. Confocal X-ray fluorescence imaging was used to compare Se distributions within specific planes of an intact larva from each of the two groups. The elevated Se treatment showed substantially higher Se levels than the control; Se preferentially accumulated to highest levels in the eye lens, with lower levels in the retina, yolk and other tissues. Confocal X-ray absorption spectroscopy was used to determine that the speciation of Se within the eye lens of the intact larva was a selenomethionine-like species. Preferential accumulation of Se in the eye lens may suggest a direct cause-and-effect relationship between exposure to elevated Se and Se-induced ocular impairments reported previously. This study illustrates the effectiveness of confocal X-ray fluorescence methods for investigating trace element distribution and speciation in intact biological specimens.

Simultaneous cryo X-ray ptychographic and fluorescence microscopy of green algae

Trace metals play important roles in normal and in disease-causing biological functions. X-ray fluorescence microscopy reveals trace elements with no dependence on binding affinities (unlike with visible light fluorophores) and with improved sensitivity relative to electron probes. However, X-ray fluorescence is not very sensitive for showing the light elements that comprise the majority of cellular material. Here we show that X-ray ptychography can be combined with fluorescence to image both cellular structure and trace element distribution in frozen-hydrated cells at cryogenic temperatures, with high structural and chemical fidelity. Ptychographic reconstruction algorithms deliver phase and absorption contrast images at a resolution beyond that of the illuminating lens or beam size. Using 5.2-keV X-rays, we have obtained sub-30-nm resolution structural images and ∼90-nm-resolution fluorescence images of several elements in frozen-hydrated green algae. This combined approach offers a way to study the role of trace elements in their structural context.

Imaging metals in biology: balancing sensitivity, selectivity and spatial resolution

A Tutorial Review to aid in designing the most comprehensive metal imaging experiments for biological samples.

Cryogenic x-ray diffraction microscopy utilizing high-pressure cryopreservation

We present cryo x-ray diffraction microscopy of high-pressure-cryofixed bacteria and report high-convergence imaging with multiple image reconstructions. Hydrated D. radiodurans cells were cryofixed at 200 MPa pressure into ∼10-μm-thick water layers and their unstained, hydrated cellular environments were imaged by phasing diffraction patterns, reaching sub-30-nm resolutions with hard x-rays. Comparisons were made with conventional ambient-pressure-cryofixed samples, with respect to both coherent small-angle x-ray scattering and the image reconstruction. The results show a correlation between the level of background ice signal and phasing convergence, suggesting that phasing difficulties with frozen-hydrated specimens may be caused by high-background ice scattering.

X-ray nanoprobes and diffraction-limited storage rings: opportunities and challenges of fluorescence tomography of biological specimens

X-ray nanoprobes require coherent illumination to achieve optic-limited resolution, and so will benefit directly from diffraction-limited storage rings. Here, the example of high-resolution X-ray fluorescence tomography is focused on as one of the most voracious demanders of coherent photons, since the detected signal is only a small fraction of the incident flux. Alternative schemes are considered for beam delivery, sample scanning and detectors. One must consider as well the steps before and after the X-ray experiment: sample preparation and examination conditions, and analysis complexity due to minimum dose requirements and self-absorption. By understanding the requirements and opportunities for nanoscale fluorescence tomography, one gains insight into the R&D challenges in optics and instrumentation needed to fully exploit the source advances that diffraction-limited storage rings offer.

Spectromicroscopy and coherent diffraction imaging: focus on energy materials applications

Current and future capabilities of X-ray spectromicroscopy are discussed based on coherence-limited imaging methods which will benefit from the dramatic increase in brightness expected from a diffraction-limited storage ring (DLSR). The methods discussed include advanced coherent diffraction techniques and nanoprobe-based real-space imaging using Fresnel zone plates or other diffractive optics whose performance is affected by the degree of coherence. The capabilities of current systems, improvements which can be expected, and some of the important scientific themes which will be impacted are described, with focus on energy materials applications. Potential performance improvements of these techniques based on anticipated DLSR performance are estimated. Several examples of energy sciences research problems which are out of reach of current instrumentation, but which might be solved with the enhanced DLSR performance, are discussed.

Soft X-ray spectromicroscopy for speciation, quantitation and nano-eco-toxicology of nanomaterials

There is a critical need for methods that provide simultaneous detection, identification, quantitation and visualization of nanomaterials at their interface with biological and environmental systems. The approach should allow speciation as well as elemental analysis. Using the intrinsic X-ray absorption properties, soft X-ray scanning transmission X-ray spectromicroscopy (STXM) allows characterization and imaging of a broad range of nanomaterials, including metals, oxides and organic materials, and at the same time is able to provide detailed mapping of biological components. Thus, STXM offers considerable potential for application to research on nanomaterials in biology and the environment. The potential and limitations of STXM in this context are discussed using a range of examples, focusing on the interaction of nanomaterials with microbial cells, biofilms and extracellular polymers. The studies outlined include speciation and mapping of metal-containing nanomaterials (Ti, Ni, Cu) and carbon-based nanomaterials (multiwalled carbon nanotubes, C60 fullerene). The benefits of X-ray fluorescence detection in soft X-ray STXM are illustrated with a study of low levels of Ni in a natural river biofilm.

Quantitative chemical imaging of the intracellular spatial distribution of fundamental elements and light metals in single cells

We report a method that allows a complete quantitative characterization of whole single cells, assessing the total amount of carbon, nitrogen, oxygen, sodium, and magnesium and providing submicrometer maps of element molar concentration, cell density, mass, and volume. This approach allows quantifying elements down to 10(6) atoms/μm(3). This result was obtained by applying a multimodal fusion approach that combines synchrotron radiation microscopy techniques with off-line atomic force microscopy. The method proposed permits us to find the element concentration in addition to the mass fraction and provides a deeper and more complete knowledge of cell composition. We performed measurements on LoVo human colon cancer cells sensitive (LoVo-S) and resistant (LoVo-R) to doxorubicin. The comparison of LoVo-S and LoVo-R revealed different patterns in the maps of Mg concentration with higher values within the nucleus in LoVo-R and in the perinuclear region in LoVo-S cells. This feature was not so evident for the other elements, suggesting that Mg compartmentalization could be a significant trait of the drug-resistant cells.

Alignment of low-dose X-ray fluorescence tomography images using differential phase contrast

X-ray fluorescence nanotomography provides unprecedented sensitivity for studies of trace metal distributions in whole biological cells. Dose fractionation, in which one acquires very low dose individual projections and then obtains high statistics reconstructions as signal from a voxel is brought together (Hegerl & Hoppe, 1976), requires accurate alignment of these individual projections so as to correct for rotation stage runout. It is shown here that differential phase contrast at 10.2 keV beam energy offers the potential for accurate cross-correlation alignment of successive projections, by demonstrating that successive low dose, 3 ms per pixel, images acquired at the same specimen position and rotation angle have a narrower and smoother cross-correlation function (1.5 pixels FWHM at 300 nm pixel size) than that obtained from zinc fluorescence images (25 pixels FWHM). The differential phase contrast alignment resolution is thus well below the 700 nm × 500 nm beam spot size used in this demonstration, so that dose fractionation should be possible for reduced-dose, more rapidly acquired, fluorescence nanotomography experiments.

The Bionanoprobe: hard X-ray fluorescence nanoprobe with cryogenic capabilities

Hard X-ray fluorescence microscopy is one of the most sensitive techniques for performing trace elemental analysis of biological samples such as whole cells and tissues. Conventional sample preparation methods usually involve dehydration, which removes cellular water and may consequently cause structural collapse, or invasive processes such as embedding. Radiation-induced artifacts may also become an issue, particularly as the spatial resolution increases beyond the sub-micrometer scale. To allow imaging under hydrated conditions, close to the `natural state', as well as to reduce structural radiation damage, the Bionanoprobe (BNP) has been developed, a hard X-ray fluorescence nanoprobe with cryogenic sample environment and cryo transfer capabilities, dedicated to studying trace elements in frozen-hydrated biological systems. The BNP is installed at an undulator beamline at sector 21 of the Advanced Photon Source. It provides a spatial resolution of 30 nm for two-dimensional fluorescence imaging. In this first demonstration the instrument design and motion control principles are described, the instrument performance is quantified, and the first results obtained with the BNP on frozen-hydrated whole cells are reported.

Epidermal growth factor receptor targeted nuclear delivery and high-resolution whole cell X-ray imaging of Fe3O4@TiO2 nanoparticles in cancer cells

Sequestration within the cytoplasm often limits the efficacy of therapeutic nanoparticles that have specific subcellular targets. To allow for both cellular and subcellular nanoparticle delivery, we have created epidermal growth factor receptor (EGFR)-targeted Fe3O4@TiO2 nanoparticles that use the native intracellular trafficking of EGFR to improve internalization and nuclear translocation in EGFR-expressing HeLa cells. While bound to EGFR, these nanoparticles do not interfere with the interaction between EGFR and karyopherin-β, a protein that is critical for the translocation of ligand-bound EGFR to the nucleus. Thus, a portion of the EGFR-targeted nanoparticles taken up by the cells also reaches cell nuclei. We were able to track nanoparticle accumulation in cells by flow cytometry and nanoparticle subcellular distribution by confocal fluorescent microscopy indirectly, using fluorescently labeled nanoparticles. More importantly, we imaged and quantified intracellular nanoparticles directly, by their elemental signatures, using X-ray fluorescence microscopy at the Bionanoprobe, the first instrument of its kind in the world. The Bionanoprobe can focus hard X-rays down to a 30 nm spot size to map the positions of chemical elements tomographically within whole frozen-hydrated cells. Finally, we show that photoactivation of targeted nanoparticles in cell nuclei, dependent on successful EGFR nuclear accumulation, induces significantly more double-stranded DNA breaks than photoactivation of nanoparticles that remain exclusively in the cytoplasm.

Rapid and accurate analysis of an X-ray fluorescence microscopy data set through gaussian mixture-based soft clustering methods

X-ray fluorescence (XRF) microscopy is an important tool for studying trace metals in biology, enabling simultaneous detection of multiple elements of interest and allowing quantification of metals in organelles without the need for subcellular fractionation. Currently, analysis of XRF images is often done using manually defined regions of interest (ROIs). However, since advances in synchrotron instrumentation have enabled the collection of very large data sets encompassing hundreds of cells, manual approaches are becoming increasingly impractical. We describe here the use of soft clustering to identify cell ROIs based on elemental contents, using data collected over a sample of the malaria parasite Plasmodium falciparum as a test case. Soft clustering was able to successfully classify regions in infected erythrocytes as “parasite,” “food vacuole,” “host,” or “background.” In contrast, hard clustering using the k-means algorithm was found to have difficulty in distinguishing cells from background.While initial tests showed convergence on two or three distinct solutions in 60% of the cells studied, subsequent modifications to the clustering routine improved results to yield 100% consistency in image segmentation. Data extracted using soft cluster ROIs were found to be as accurate as data extracted using manually defined ROIs, and analysis time was considerably improved.

Three-dimensional distribution of polymorphs and magnesium in a calcified underwater attachment system by diffraction tomography

Biological materials display complicated three-dimensional hierarchical structures. Determining these structures is essential in understanding the link between material design and properties. Herein, we show how diffraction tomography can be used to determine the relative placement of the calcium carbonate polymorphs calcite and aragonite in the highly mineralized holdfast system of the bivalve Anomia simplex. In addition to high fidelity and non-destructive mapping of polymorphs, we use detailed analysis of X-ray diffraction peak positions in reconstructed powder diffraction data to determine the local degree of Mg substitution in the calcite phase. These data show how diffraction tomography can provide detailed multi-length scale information on complex materials in general and of biomineralized tissues in particular.

3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography

We report Fourier transform infrared spectro-microtomography, a nondestructive three-dimensional imaging approach that reveals the distribution of distinctive chemical compositions throughout an intact biological or materials sample. The method combines mid-infrared absorption contrast with computed tomographic data acquisition and reconstruction to enhance chemical and morphological localization by determining a complete infrared spectrum for every voxel (millions of spectra determined per sample).

Opportunities in multidimensional trace metal imaging: taking copper-associated disease research to the next level

Copper plays an important role in numerous biological processes across all living systems predominantly because of its versatile redox behavior. Cellular copper homeostasis is tightly regulated and disturbances lead to severe disorders such as Wilson disease and Menkes disease. Age-related changes of copper metabolism have been implicated in other neurodegenerative disorders such as Alzheimer disease. The role of copper in these diseases has been a topic of mostly bioinorganic research efforts for more than a decade, metal-protein interactions have been characterized, and cellular copper pathways have been described. Despite these efforts, crucial aspects of how copper is associated with Alzheimer disease, for example, are still only poorly understood. To take metal-related disease research to the next level, emerging multidimensional imaging techniques are now revealing the copper metallome as the basis to better understand disease mechanisms. This review describes how recent advances in X-ray fluorescence microscopy and fluorescent copper probes have started to contribute to this field, specifically in Wilson disease and Alzheimer disease. It furthermore provides an overview of current developments and future applications in X-ray microscopic methods.

Fate of intravenously administered gold nanoparticles in hair follicles: follicular delivery, pharmacokinetic interpretation, and excretion

Gold nanoparticles (GNPs) are intravenously administered to mice. Deposition at the pilosebacious unit and whiskers is visualized with X-ray fluorescence after 30 minutes and 14 days. After 30 minutes the dermal papilla, bulge region, and root sheath all contain NPs. GNPs are driven externally out from follicles, counteractive to transfollicular delivery. After 14 days, gold bands in hairs reflect pharmacokinetic profiles indicating blood concentration kinetics. Elimination rate constants infer half-lives from 3 hairs from an individual mouse within reasonable agreement (6.08, 7.15, and 8.66 hours). 3D reconstruction of NP distributions with confocal microscopy identifies aggregates within the medullary canal. Intermittent NP deposition continues randomly over the two week period demonstrating prolonged NP mobility in vivo. NPs are still retained at the hair bulb after 14 days. The observations further account for the excretory mechanisms of NPs and their behavior in the pilosebacous unit, and demonstrate monitoring pharmacokinetic behavior in individual animals.

Manganese enhanced MRI in rat hippocampus: a correlative study with synchrotron X-ray microprobe

Manganese enhanced MRI (MEMRI) offers many possibilities such as tract tracing and functional imaging in vivo. Mn is however neurotoxic and may induce symptoms similar to those associated with Parkinson's disease (manganism). The mechanisms of Mn-induced neurotoxicity are not clear. In this study, we combine synchrotron X-ray fluorescence microprobe (SR-XRF) and MEMRI techniques to investigate spatial distribution of Mn within the rat hippocampus and how Mn interacts with Ca, Fe and Zn at a cellular level. Images were acquired in the rat hippocampus (n=23) and using two injection routes: intra-cerebral (MnCl(2): 50 mM, 10 μL) and intra-peritoneal (MnCl(2): 100 mM, 30 mg/kg). For both injection routes, Mn is found in dentate gyrus and in CA3: control: 2.5 ± 1.6, intra-peritoneal: 5.0 ± 2.4, and intra-cerebral: 25.1 ± 9.2 μg/g. Mn follows Zn distribution and has a negative impact on the total amount of Zn and Fe. The Mn-enhanced MRI contrast is well correlated with the total Mn amount measured with SR-XRF (R(2)=0.93; p<0.002). After intra-cerebral injection, the hippocampal fissure is found to accumulate a large amount of Mn and yields a hypointense MRI signal, which may be ascribed to a reduction in T2. This study shows that SR-XRF is well suited to investigate Mn distribution at a mesoscale and that MRI is sensitive to low Mn concentrations. As perturbations in metal homeostasis may alter brain function, the injected dose of Mn in MEMRI studies needs to be carefully adjusted to obtain reliable functional information.

Simultaneous X-ray fluorescence and ptychographic microscopy of Cyclotella meneghiniana

Scanning X-ray fluorescence microscopy (XFM) is a particularly useful method for studying the spatial distribution of trace metals in biological samples. Here we demonstrate the utility of combining coherent diffractive imaging (CDI) with XFM for imaging biological samples to simultaneously produce high-resolution and high-contrast transmission images and quantitative elemental maps. The reconstructed transmission function yields morphological details which contextualise the elemental maps. We report enhancement of the spatial resolution in both the transmission and fluorescence images beyond that of the X-ray optics. The freshwater diatom Cyclotella meneghiniana was imaged to demonstrate the benefits of combining these techniques that have complementary contrast mechanisms.

Iron utilization in marine cyanobacteria and eukaryotic algae

Iron is essential for aerobic organisms. Additionally, photosynthetic organisms must maintain the iron-rich photosynthetic electron transport chain, which likely evolved in the iron-replete Proterozoic ocean. The subsequent rise in oxygen since those times has drastically decreased the levels of bioavailable iron, indicating that adaptations have been made to maintain sufficient cellular iron levels in the midst of scarcity. In combination with physiological studies, the recent sequencing of marine microorganism genomes and transcriptomes has begun to reveal the mechanisms of iron acquisition and utilization that allow marine microalgae to persist in iron limited environments.

Fast and accurate X-ray fluorescence computed tomography imaging with the ordered-subsets expectation maximization algorithm

The ordered-subsets expectation maximization algorithm (OSEM) is introduced to X-ray fluorescence computed tomography (XFCT) and studied; here, simulations and experimental results are presented. The simulation results indicate that OSEM is more accurate than the filtered back-projection algorithm, and it can efficiently suppress the deterioration of image quality within a large range of angular sampling intervals. Experimental results of both an artificial phantom and cirrhotic liver show that with a satisfying image quality the angular sampling interval could be improved to save on the data-acquisition time when OSEM is employed. In addition, with an optimum number of subsets, the image reconstruction time of OSEM could be reduced to about half of the time required for one subset. Accordingly, it can be concluded that OSEM is a potential method for fast and accurate XFCT imaging.

Caenorhabditis elegans maintains highly compartmentalized cellular distribution of metals and steep concentration gradients of manganese

Bioinorganic chemistry is critical to cellular function. Homeostasis of manganese (Mn), for example, is essential for life. A lack of methods for direct in situ visualization of Mn and other biological metals within intact multicellular eukaryotes limits our understanding of management of these metals. We provide the first quantitative subcellular visualization of endogenous Mn concentrations (spanning two orders of magnitude) associated with individual cells of the nematode, Caenorhabditis elegans.

X-ray microtomography in biology

Progress in high-resolution X-ray microtomography has provided us with a practical approach to determining three-dimensional (3D) structures of opaque samples at micrometer to submicrometer resolution. In this review, we give an introduction to hard X-ray microtomography and its application to the visualization of 3D structures of biological soft tissues. Practical aspects of sample preparation, handling, data collection, 3D reconstruction, and structure analysis are described. Furthermore, different sample contrasting methods are approached in detail. Examples of microtomographic studies are overviewed to present an outline of biological applications of X-ray microtomography. We also provide perspectives of biological microtomography as the convergence of sciences in X-ray optics, biology, and structural analysis.

Examination of trafficking of phagocytosed colloid particles in neutrophils using synchrotron-based X-ray fluorescence microscopy (XFM)

Synchrotron-based X-ray fluorescence microscopy (XFM) can localise chemical elements at a subcellular level. 99mTechnetium stannous (TcSn) colloid is taken up by phagocytes via a Complement Receptor 3 mediated phagocytic process. In the current study, XFM was used to examine the intracellular trafficking of TcSn colloid in neutrophils. XFM was performed on TcSn colloid, and neutrophils labelled with TcSn colloid, in whole blood. We developed a set of pixel by pixel analysis and mapping techniques incorporating cluster analysis that allowed us to differentiate neutrophils and artefactual contaminants, and we examined the changes in element distribution that accompany neutrophil phagocytosis of TcSn colloid. Sn became associated with half the neutrophils. Within cells, Sn colocalised with iron (Fe) and sulphur (S), and was negatively associated with calcium (Ca). Despite the high sensitivity of XFM, Tc was not detected. XFM can help clarify the intracellular processes that accompany neutrophil phagocytosis. The subcellular colocalisation of Sn with Fe is consistent with fusion of the colloid-containing phagosome with neutrophil granules. The association of Sn with S suggests that proteins rich in S-containing amino acids are present in the phagosome. The negative colocalisation with Ca indicates that ongoing maturation of the TcSn colloid phagosome is no longer calcium dependent one hour after phagocytosis.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (doi:10.1007/s10867-011-9233-9) contains supplementary material, which is available to authorized users.

Fast x-ray fluorescence microtomography of hydrated biological samples

Metals and metalloids play a key role in plant and other biological systems as some of them are essential to living organisms and all can be toxic at high concentrations. It is therefore important to understand how they are accumulated, complexed and transported within plants. In situ imaging of metal distribution at physiological relevant concentrations in highly hydrated biological systems is technically challenging. In the case of roots, this is mainly due to the possibility of artifacts arising during sample preparation such as cross sectioning. Synchrotron x-ray fluorescence microtomography has been used to obtain virtual cross sections of elemental distributions. However, traditionally this technique requires long data acquisition times. This has prohibited its application to highly hydrated biological samples which suffer both radiation damage and dehydration during extended analysis. However, recent advances in fast detectors coupled with powerful data acquisition approaches and suitable sample preparation methods can circumvent this problem. We demonstrate the heightened potential of this technique by imaging the distribution of nickel and zinc in hydrated plant roots. Although 3D tomography was still impeded by radiation damage, we successfully collected 2D tomograms of hydrated plant roots exposed to environmentally relevant metal concentrations for short periods of time. To our knowledge, this is the first published example of the possibilities offered by a new generation of fast fluorescence detectors to investigate metal and metalloid distribution in radiation-sensitive, biological samples.

Transmission and emission x-ray microscopy: operation modes, contrast mechanisms and applications

Advances in microscopy techniques based on x-rays have opened unprecedented opportunities in terms of spatial resolution, combined with chemical and morphology sensitivity, to analyze solid, soft and liquid matter. The advent of ultrabright third and fourth generation photon sources and the continuous development of x-ray optics and detectors has pushed the limits of imaging and spectroscopic analysis to structures as small as a few tens of nanometers. Specific interactions of x-rays with matter provide elemental and chemical sensitivity that have made x-ray spectromicroscopy techniques a very attractive tool, complementary to other microscopies, for characterization in all actual research fields. The x-ray penetration power meets the demand to examine samples too thick for electron microscopes implementing 3D imaging and recently also 4D imaging which adds time resolution as well. Implementation of a variety of phase contrast techniques enhances the structural sensitivity, especially for the hard x-ray regime. Implementation of lensless or diffraction imaging helps to enhance the lateral resolution of x-ray imaging to the wavelength dependent diffraction limit.

Hard X-ray fluorescence tomography--an emerging tool for structural visualization

Hard X-ray fluorescence microscopy is well-suited to in-situ investigations of trace metal distributions within whole, unstained, biological tissue, with sub-parts-per-million detection achievable in whole cells. The high penetration of X-rays indicates the use of X-ray fluorescence tomography for structural visualization, and recent measurements have realised sub-500-nm tomography on a 10-μm cell. Limitations of present approaches impact the duration of an experiment and imaging fidelity. Developments in X-ray resolution, detector speed, cryogenic environments, and the incorporation of auxiliary signals are being pursued within the synchrotron community. Several complementary approaches to X-ray fluorescence tomography will be routinely available to the biologist in the near future. We discuss these approaches and review applications of biological relevance.