Low energy loss electron microscopy of chromophores

Correlative cathodoluminescence electron microscopy bioimaging: towards single protein labelling with ultrastructural context

The understanding of living systems and their building blocks relies heavily on the assessment of structure-function relationships at the nanoscale. Ever since the development of the first optical microscope, the reliance of scientists across disciplines on microscopy has increased. The development of the first electron microscope and with it the access to information at the nanoscale has prompted numerous disruptive discoveries. While fluorescence imaging allows identification of specific entities based on the labelling with fluorophores, the unlabelled constituents of the samples remain invisible. In electron microscopy on the other hand, structures can be comprehensively visualized based on their distinct electron density and geometry. Although electron microscopy is a powerful tool, it does not implicitly provide information on the location and activity of specific organic molecules. While correlative light and electron microscopy techniques have attempted to unify the two modalities, the resolution mismatch between the two data sets poses major challenges. Recent developments in optical super resolution microscopy enable high resolution correlative light and electron microscopy, however, with considerable constraints due to sample preparation requirements. Labelling of specific structures directly for electron microscopy using small gold nanoparticles (i.e. immunogold) has been used extensively. However, identification of specific entities solely based on electron contrast, and the differentiation from endogenous dense granules, remains challenging. Recently, the use of correlative cathodoluminescence electron microscopy (CCLEM) imaging based on luminescent inorganic nanocrystals has been proposed. While nanometric resolution can be reached for both the electron and the optical signal, high energy electron beams are potentially damaging to the sample. In this review, we discuss the opportunities of (volumetric) multi-color single protein labelling based on correlative cathodoluminescence electron microscopy, and its prospective impact on biomedical research in general. We elaborate on the potential challenges of correlative cathodoluminescence electron microscopy-based bioimaging and benchmark CCLEM against alternative high-resolution correlative imaging techniques.

ColorEM: analytical electron microscopy for element-guided identification and imaging of the building blocks of life

Nanometer-scale identification of multiple targets is crucial to understand how biomolecules regulate life. Markers, or probes, of specific biomolecules help to visualize and to identify. Electron microscopy (EM), the highest resolution imaging modality, provides ultrastructural information where several subcellular structures can be readily identified. For precise tagging of (macro)molecules, electron-dense probes, distinguishable in gray-scale EM, are being used. However, practically these genetically-encoded or immune-targeted probes are limited to three targets. In correlated microscopy, fluorescent signals are overlaid on the EM image, but typically without the nanometer-scale resolution and limited to visualization of few targets. Recently, analytical methods have become more sensitive, which has led to a renewed interest to explore these for imaging of elements and molecules in cells and tissues in EM. Here, we present the current state of nanoscale imaging of cells and tissues using energy dispersive X-ray analysis (EDX), electron energy loss spectroscopy (EELS), cathodoluminescence (CL), and touch upon secondary ion mass spectroscopy at the nanoscale (NanoSIMS). ColorEM is the term encompassing these analytical techniques the results of which are then displayed as false-color at the EM scale. We highlight how ColorEM will become a strong analytical nano-imaging tool in life science microscopy.

Application of EELS and EFTEM to the life sciences enabled by the contributions of Ondrej Krivanek

The pioneering contributions of Ondrej Krivanek to the development of electron energy loss spectrometers, energy filters, and detectors for transmission and scanning transmission electron microscopes have provided researchers with indispensible tools across a wide range of disciplines in the physical sciences, ranging from condensed matter physics, to chemistry, mineralogy, materials science, and nanotechnology. In addition, the same instrumentation has extended its reach into the life sciences, and it is this aspect of Ondrej Krivanek's influential contributions that will be surveyed here, together with some personal recollections. Traditionally, electron microscopy has given a purely morphological view of the biological structures that compose cells and tissues. However, the availability of high-performance electron energy loss spectrometers and energy filters offers complementary information about the elemental and chemical composition at the subcellular scale. Such information has proven to be valuable for applications in cell and structural biology, microbiology, histology, pathology, and more generally in the biomedical sciences.

Correlative light and electron microscopy using immunolabeled sections

In correlative microscopy, light microscopy provides the overview and orientation of the complex cells and tissue, while electron microscopy offers the detailed localization and correlation of subcellular structures. In this chapter we offer detailed high-quality electron microscopical preparation methods for optimum preservation of the cellular ultrastructure. From such preparations serial thin sections are collected and used for comparative histochemical, immunofluorescence, and immunogold staining.In light microscopy histological stains identify the orientation of the sample and immunofluorescence labeling facilitates to find the region of interest, namely, the labeled cells expressing the macromolecule under investigation. Sections, labeled with immunogold are analyzed by electron microscopy in order to identify the label within the cellular architecture at high resolution.

Electron energy-loss spectroscopy as a tool for elemental analysis in biological specimens

A transmission electron microscope (TEM) accessory, the energy filter, enables the establishment of a method for elemental microanalysis, the electron energy-loss spectroscopy (EELS). In conventional TEM, unscattered, elastic, and inelastic scattered electrons contribute to image information. Energy-filtering TEM (EFTEM) allows elemental analysis at the ultrastructural level by using selected inelastic scattered electrons. EELS is an excellent method for elemental microanalysis and nanoanalysis with good sensitivity and accuracy. However, it is a complex method whose potential is seldom completely exploited, especially for biological specimens. In addition to spectral analysis, parallel-EELS, we present two different imaging techniques in this chapter, namely electron spectroscopic imaging (ESI) and image-EELS. We aim to introduce these techniques in this chapter with the elemental microanalysis of titanium. Ultrafine, 22-nm titanium dioxide particles are used in an inhalation study in rats to investigate the distribution of nanoparticles in lung tissue.

Correlative light and electron microscopy using immunolabeled resin sections

In correlative microscopy, light microscopy provides the overview and orientation in the complex cells and tissue, whereas electron microscopy offers the detailed localization and correlation to subcellular structures. In this chapter, we offer the detailed high-quality electron microscopical preparation methods for the optimum preservation of the cellular ultrastructure. From such preparations, serial thin sections are collected and used for comparative histochemical, immunofluorescence, and immunogold staining. In light microscopy, histological stains are used to identify the orientation of the sample, and immunofluorescence labeling is used to identify the region of interest, namely, the labeled cells expressing the macromolecule under investigation. Subsequent sections, labeled with immunogold, are analyzed by electron microscopy to identify the label within the cellular architecture at high resolution.

Low-energy-loss electron microscopy of doxorubicin in human breast cancer MCF-7 cells: localization by color

The distribution of the anti-cancer drug doxorubicin (DOX) in human breast cancer MCF-7 cells was imaged directly by low-energy-loss electron microscopy (EM) without specific antibodies or heavy metal stains, using only the electron-induced molecular orbital excitation of the drug. Cells treated with DOX were examined live by confocal fluorescence microscopy and as very thin sections in an electron microscope equipped with an electron energy filter having an energy resolution of 1 eV. The distribution of DOX obtained by EM from pairs of images at energy losses of 3+/-1 eV and 10+/-1 eV agreed with fluorescence microscope observations, but provided much more detail, easily distinguishing localization between nuclear membrane and perimembrane compartments and between vacuolated nucleoli and perinucleolar chromatin. Treatment times up to 1h and DOX concentrations up to 30 microM indicated a progression of DOX ingress from higher concentrations in the nuclear membrane to labeling of the nucleolus. Subsequently DOX moved into perinucleolar chromatin and concentrated in perimembrane chromatin aggregations. Quantification of the DOX signal indicated a decay half-life of 320 e/A2 under electron irradiation, whereas each image at 3000 x required 10 e/A2. The results point to a new field of high resolution microanalysis: color electron microscopy.

Automated most-probable loss tomography of thick selectively stained biological specimens with quantitative measurement of resolution improvement

We describe the technique and application of energy filtering, automated most-probable loss (MPL) tomography to intermediate voltage electron microscopy (IVEM). We show that for thick, selectively stained biological specimens, this method produces a dramatic increase in resolution of the projections and the computed volumes versus standard unfiltered transmission electron microscopy (TEM) methods. This improvement in resolution is attributed to the reduction of chromatic aberration, which results from the large percentage of inelastic electron-scattering events for thick specimens. These improvements are particularly evident at the large tilt angles required to improve tomographic resolution in the z-direction. This method effectively increases the usable thickness of selectively stained samples that can be imaged at a given accelerating voltage by dramatically improving resolution versus unfiltered TEM and increasing signal-to-noise versus zero-loss imaging, thereby expanding the utility of the IVEM to deliver information from within specimens up to 3 microm thick.

New techniques in electron energy-loss spectroscopy and energy-filtered imaging

This article is a survey of hardware and software advances that promise to increase the power and sensitivity of electron energy-loss spectroscopy (EELS) and energy-filtered imaging (EFTEM) in a transmission electron microscope. Recent developments include electron-gun monochromators, lens-aberration correctors, and software for spectral sharpening, spectral processing and interpretation of fine structure. Future improvements could include the deployment of new electron sources. The expected enhancements in energy and spatial resolution are compared with fundamental limitations that arise from the natural widths of spectral peaks, the delocalization of inelastic scattering and the problem of electron-irradiation damage.

Zero-loss image formation and modified contrast transfer theory in EFTEM

For a weak phase/weak amplitude object the information transfer in the imaging process of TEM is described by the common formalism of the contrast transfer function (CTF). So far the effects of inelastic scattering were not accounted for in this formalism. In conventional imaging they were simply neglected. In energy filtering TEM (EFTEM), where removal of inelastic electrons leads to higher specimen contrast, they were modelled by a global increase of the elastic amplitude contrast. Thus, the description of inelastic and elastic scattering was mixed. Here a new ansatz is proposed which treats elastic and inelastic contrast transfer separately by adding an inelastic contribution to the scattering potentials. In EFTEM this has the effect of adding a filter contrast which depends on the characteristics of the inelastic scattering. For samples with dominant plasmon loss the additional filter contrast is restricted to low resolution. Because of its strong dependence on the nature of the inelastic scattering process, the filter contrast cannot in general be unified with the conventional elastic amplitude contrast. The modified CTF theory for EFTEM was tested experimentally on a variety of samples. Images of amorphous layers of copper, aluminium, and carbon films, as well as zero-loss images of proteins embedded in amorphous ice were evaluated. The values of the parameters of the additional filter contrast were determined for carbon film and proteins embedded in vitrified ice. Comparison of different CTF models used to reconstruct 3D volumes from zero-loss images confirmed that best agreement with the atomic model is attained with the new, modified CTF theory.