Minimizing light exposure with the programmable array microscope

The exposure of fluorophores to intense illumination in a microscope often results in photobleaching and phototoxicity, thus constituting a major limiting factor in time lapse live cell or single molecule imaging. Laser scanning confocal microscopes are particularly prone to this problem, inasmuch as they require high irradiances to compensate for the inherently low duty cycle of point scanning systems. In the attempt to maintain adequate speed and signal-to-noise ratios, the fluorophores are often driven into saturation, thereby generating a nonlinear response. One approach for reducing photodegradation in the laser scanning confocal microscope is represented by controlled light exposure microscopy, introduced by Manders and colleagues. The strategy is to reduce the illumination intensity in both background areas (devoid of information) as well as in bright foreground regions, for which an adequate signal-to-noise ratio can be achieved with lower excitation levels than those required for the less intense foreground pixels/voxels. Such a variable illumination scheme can also be exploited in widefield microscopes that employ lower irradiance but higher illumination duty cycles. We report here on the adaptation of the controlled light exposure microscopy principle to the programmable array microscope, which achieves optical sectioning by use of a spatial light modulator (SLM) in an image plane as a programmable mask for illumination and conjugate (and nonconjugate) detection. By incorporating the basic controlled light exposure microscopy concept for minimizing exposure, we have obtained a reduction in the rate of photobleaching of up to ~5-fold, while maintaining an image quality comparable to regular imaging with the programmable array microscope.     

Quantitative determination of the reduction of phototoxicity and photobleaching by controlled light exposure microscopy

Phototoxicity and photobleaching are major limitations in live-cell fluorescence microscopy. They are caused by fluorophores in an excited singlet or triplet state that generate singlet oxygen and other reactive oxygen species. The principle of controlled light exposure microscopy (CLEM) is based on non-uniform illumination of the field of view to reduce the number of excited fluorophore molecules. This approach reduces phototoxicity and photobleaching 2- to 10-fold without deteriorating image quality. Reduction of phototoxicity and photobleaching depends on the fluorophore distribution in the studied object, the optical properties of the microscope and settings of CLEM electronics. Here, we introduce the CLEM factor as a quantitative measure of reduction in phototoxicity and photobleaching. Finally, we give a guideline to optimize the effect of CLEM without compromising image quality.     

Curtailed light sheet microscopy for rapid imaging of macroscopic biological specimens

We study the feasibility of volume imaging from a few angular views/scans in a light sheet fluorescence microscopy. Two‐dimensional (2D) images (angular views) were acquired at an angular separation of 10° and volume images were constructed with merely 18, 9, and 6 views. We study the structural changes in a 5‐day old Zebrafish embryo labeled with Phalloidin TRITC that binds to F‐Actin of embryo cell. To collect the data, the specimen is rotated (for varying sampling angles Δθ) with respect to a fixed vertical axis passing through the volume‐of‐interest (yolk sac). In the proposed realization of selective plane illumination microscopy (SPIM) technique, the translation is completely avoided. Analysis shows rich structural information with marginal reduction in contrast. Comparison with the state‐of‐the‐art SPIM shows appreciable volume reconstruction (from an order less 2D scans) that may be good enough for rapid monitoring of macroscopic specimens. Microsc. Res. Tech. 79:455–458, 2016. © 2016 Wiley Periodicals, Inc.     

Integration of a high‐NA light microscope in a scanning electron microscope

We present an integrated light‐electron microscope in which an inverted high‐NA objective lens is positioned inside a scanning electron microscope (SEM). The SEM objective lens and the light objective lens have a common axis and focal plane, allowing high‐resolution optical microscopy and scanning electron microscopy on the same area of a sample simultaneously. Components for light illumination and detection can be mounted outside the vacuum, enabling flexibility in the construction of the light microscope. The light objective lens can be positioned underneath the SEM objective lens during operation for sub‐10 μm alignment of the fields of view of the light and electron microscopes. We demonstrate in situ epifluorescence microscopy in the SEM with a numerical aperture of 1.4 using vacuum‐compatible immersion oil. For a 40‐nm‐diameter fluorescent polymer nanoparticle, an intensity profile with a FWHM of 380 nm is measured whereas the SEM performance is uncompromised. The integrated instrument may offer new possibilities for correlative light and electron microscopy in the life sciences as well as in physics and chemistry.     

Recording and controlling the 4D light field in a microscope using microlens arrays

By inserting a microlens array at the intermediate image plane of an optical microscope, one can record four-dimensional light fields of biological specimens in a single snapshot. Unlike a conventional photograph, light fields permit manipulation of viewpoint and focus after the snapshot has been taken, subject to the resolution of the camera and the diffraction limit of the optical system. By inserting a second microlens array and video projector into the microscope's illumination path, one can control the incident light field falling on the specimen in a similar way. In this paper, we describe a prototype system we have built that implements these ideas, and we demonstrate two applications for it: simulating exotic microscope illumination modalities and correcting for optical aberrations digitally.     

Unbiased estimation of particle density in the tandem scanning reflected light microscope

The tandem scanning reflected light microscope has the property of being able to obtain information from ‘inside’ solid objects by taking a thin optical section at the focal plane of the objective lens. This plane can be focused up and down through the specimen. We describe an unbiased 3-D counting rule for the TSRLM, which is applied to the estimation of osteocyte lacunar density in whole bone. This is shown to be an extremely efficient way of making such an estimate. Further possibilities for the application of the microscope in the field of stereology are discussed.     

Reduction of coherent artefacts in super‐resolution fluorescence localisation microscopy

Super‐resolution localisation microscopy techniques depend on uniform illumination across the field of view, otherwise the resolution is degraded, resulting in imaging artefacts such as fringes. Lasers are currently the light source of choice for switching fluorophores in PALM/STORM methods due to their high power and narrow bandwidth. However, the high coherence of these sources often creates interference phenomena in the microscopes, with associated fringes/speckle artefacts in the images. We quantitatively demonstrate the use of a polymer membrane speckle scrambler to reduce the effect of the coherence phenomena. The effects of speckle in the illumination plane, at the camera and after software localisation of the fluorophores, were characterised. Speckle phenomena degrade the resolution of the microscope at large length scales in reconstructed images, effects that were suppressed by the speckle scrambler, but the small length scale resolution is unchanged at ～30 nm.     

New imaging modes for lenslet-array tandem scanning microscopes

The tandem scanning microscope permits confocal images to be obtained in real time and viewed directly by eye. The light budget of these instruments may be increased from a few percent to a few tens of percent by incorporating an array of microlenses so as to increase the amount of illumination light that reaches the specimen. These instruments are configured for fluorescence imaging together with laser illumination. We describe how the versatility of the instrument may be enhanced to permit the use of incoherent light sources as well as extending the imaging modes to include bright‐field reflection.     

Characterization of JEOL 2100F Lorentz-TEM for low-magnification electron holography and magnetic imaging

We present results that characterize the performance and capabilities of the JEOL 2100F-LM electron microscope to carry out holography and quantitative magnetic imaging. We find the microscope is well-suited for studies of magnetic materials, or for semi-conductor dopant profiling, where a large hologram width ( approximately 1 microm) and fine fringe spacing ( approximately 1.5 nm) are obtained with good contrast ( approximately 20%). We present, as well, measurements of the spherical aberration coefficient Cs=(108.7+/-9.6)mm and minimum achievable focal step delta f=(87.6+/-1.4)nm for the specially designed long-focal-length objective lens of this microscope. Further, we detail experiments to accurately measure the optical parameters of the imaging system typical of conventional holography setup in a transmission electron microscope. The role played by astigmatic illumination in the hologram formation is also assessed with a wave-optical model, which we present and discuss. The measurements obtained for our microscope are used to simulate realistic holograms, which we compare directly to experimental holograms finding good agreement. These results indicate the usefulness of measuring these optical parameters to guide the optimization of the experimental setup for a given microscope, and to provide an additional degree of practical experimental possibility.     

An optical sectioning programmable array microscope implemented with a digital micromirror device

The defining feature of a programmable array microscope (PAM) is the presence of a spatial light modulator in the image plane. A spatial light modulator used singly or as a matched pair for both illumination and detection can be used to generate an optical section. Under most conditions, the basic optical properties of an optically sectioning PAM are similar to those of rotating Nipkow discs. The method of pattern generation, however, is fundamentally different and allows arbitrary illumination patterns to be generated under programmable control, and sectioning strategies to be changed rapidly in response to specific experimental conditions. We report the features of a PAM incorporating a digital micromirror device, including the axial sectioning response to fluorescent thin films and the imaging of biological specimens. Three axial sectioning strategies were compared: line scans, dot lattice scans and pseudo-random sequence scans. The three strategies varied widely in light throughput, sectioning strength and robustness when used on real biological samples. The axial response to thin fluorescent films demonstrated a consistent decrease in the full width at half maximum (FWHM), accompanied by an increase in offset, as the unit cells defining the patterns grew smaller. Experimental axial response curves represent the sum of the response from a given point of illumination and cross-talk from neighbouring points. Cross-talk is minimized in the plane of best focus and when measured together with the single point response produces a decrease in FWHM. In patterns having constant throughput, there appears to be tradeoff between the FWHM and the size of the offset. The PAM was compared to a confocal laser scanning microscope using biological samples. The PAM demonstrated higher signal levels and dynamic range despite a shorter acquisition time. It also revealed more structures in x - z sections and less intensity drop-off with scanning depth.     

Optical sectioning in fluorescence microscopy

We review the origins of optical sectioning in fluorescence microscopy in terms of the structure of the illumination used to generate the fluorescence within the specimen. We note that the conventional microscope using essentially uniform illumination does not exhibit optical sectioning whereas the confocal microscope using point (many spatial frequencies) illumination does. We show that the optical sectioning strength of a confocal microscope is not optimal and discuss the advantages of using a single spatial frequency for the structure of the illumination and the detection. In this case the optical sectioning strength is shown to be up to 25% narrower than in the ideal confocal case.     

Design and performance of a high-resolution photoelectron microscope

The design of a high-resolution photoelectron microscope (photoelectron emission microscope) is described. It is an oil-free ultrahigh-vacuum instrument utilizing electrostatic electron optics. New designs are presented for a specimen translator, cathode stage, aperture stop control, electrostatic hexapole stigmator, beam shutter, and camera system. These components could also be used in a low-energy electron microscope (LEEM). The theoretical resolution of this instrument is 5 nm for UV illumination near the photoemission threshold. The photoelectron microscope is now in operation at the University of Oregon, and it is achieving results within a factor of two of this design limit.     

Development of a standing-wave fluorescence microscope with high nodal plane flatness

This article reports about the development and application of a standing-wave fluorescence microscope (SWFM) with high nodal plane flatness. As opposed to the uniform excitation field in conventional fluorescence microscopes an SWFM uses a standing-wave pattern of laser light. This pattern consists of alternating planar nodes and antinodes. By shifting it along the axis of the microscope a set of different fluorescent structures can be distinguished. Their axial separation may just be a fraction of a wavelength so that an SWFM allows distinction of structures which would appear axially unresolved in a conventional or confocal fluorescence microscope. An SWFM is most powerful when the axial extension of the specimen is comparable to the wavelength of light. Otherwise several planes are illuminated simultaneously and their separation is hardly feasible. The objective of this work was to develop a new SWFM instrument which allows standing-wave fluorescence microscopy with controlled high nodal plane flatness. Earlier SWFMs did not allow such a controlled flatness, which impeded image interpretation and processing. Another design goal was to build a compact, easy-to-use instrument to foster a more widespread use of this new technique. The instrument developed uses a green-emitting helium–neon laser as the light source, a piezoelectric movable beamsplitter to generate two mutually coherent laser beams of variable relative phase and two single-mode fibres to transmit these beams to the microscope. Each beam is passed on to the specimen by a planoconvex lens and an objective lens. The only reflective surface whose residual curvature could cause wavefront deformations is a dichroic beamsplitter. Nodal plane flatness is controlled via interference fringes by a procedure which is similar to the interferometric test of optical surfaces. The performance of the instrument was tested using dried and fluorescently labelled cardiac muscle cells of rats. The SWFM enabled the distinction of layers of stress fibres whose axial separation was just a fraction of a wavelength. Layers at such a small distance would lie completely within the depth-of-field of a conventional or confocal fluorescence microscope and could therefore not be distinguished by these two methods. To obtain futher information from the SWFM images it would be advantageous to use the images as input-data to image processing algorithms such as conceived by Krishnamurthi et al. (Proc. SPIE, 2655, 1996, 18–25). To minimize specimen-caused nodal plane distortion, the specimen should be embedded in a medium of closely matched refractive index. The proper match of the refractive indices could be checked via the method presented here for the measurement of nodal plane flatness. For this purpose the fluorescent layer of latex beads would simply be replaced by the specimen. A combination of the developed SWFM with a specimen embedded in a medium of matched refractive index and further image processing would exploit the full potential of standing-wave fluorescence microscopy.     

Versatile optical access to the tunnel gap in a low-temperature scanning tunneling microscope

We developed a setup that provides three independent optical access paths to the tunnel junction of an ultrahigh vacuum low temperature (4.2 K) scanning tunneling microscope (STM). Each path can be individually chosen to couple light in or out, or to image the tunnel junction. The design comprises in situ adjustable aspheric lenses to allow tip exchange. The heat input into the STM is negligible. We present in detail the beam geometry and the realization of lens adjustment. Measurements demonstrate the characterization of a typical light source exemplified by emission from tip-induced plasmons. We suggest employing the Fourier transforming properties of imaging lenses and polarization analysis to obtain additional information on the light emission process. Performance and future potential of the instrument are discussed.     

Spatial control of pa-GFP photoactivation in living cells

Photoactivatable green fluorescent protein (paGFP) exhibits peculiar photo-physical properties making it an invaluable tool for protein/cell tracking in living cells/organisms. paGFP is normally excited in the violet range (405 nm), with an emission peak centred at 520 nm. Absorption cross-section at 488 nm is low in the not-activated form. However, when irradiated with high-energy fluxes at 405 nm, the protein shows a dramatic change in its absorption spectra becoming efficiently excitable at 488 nm. Confocal microscopes allow to control activation in the focal plane. Unfortunately, irradiation extends to the entire illumination volume, making impracticable to limit the process in the 3D (three-dimensional) space. In order to confine the process, we used two advanced intrinsically 3D confined optical methods, namely: total internal reflection fluorescence (TIRF) and two-photon excitation fluorescence (2PE) microscopy. TIRF allows for spatially selected excitation of fluorescent molecules within a thin region at interfaces, i.e. cellular membranes. Optimization of the TIRF optical set-up allowed us to demonstrate photoactivation of paGFP fused to different membrane localizing proteins. Exploitation of the penetration depth showed that activation is efficiently 3D confined even if limited at the interface. 2PE microscopy overcomes both the extended excitation volume of the confocal case and the TIRF constraint of operating at interfaces, providing optical confinement at any focal plane in the specimen within subfemtoliter volumes. The presented results emphasize how photoactivation by non-linear excitation can provide a tool to increase contrast in widefield and confocal cellular imaging.     

Optical sectioning microscope with a binary hologram based beam scanning

We describe the development of a beam scanning microscope that can perform optical sectioning based on the principle of confocal microscopy. The scanning is performed by a laser beam diffracted from a dynamic binary hologram implemented using a liquid crystal spatial light modulator. Using the proposed scanning mechanism, unlike the conventional confocal microscopes, scanning over a two-dimensional area of the sample can be obtained without the use of a pair of galvo mirror scanners. The proposed microscope has a number of advantages, such as superior frame to frame repeatability, simpler optical arrangement, increased pixel dwell time relative to the time between two pixels, illumination of only the sample points without pulsing the laser, and absolute control over the amplitude and phase of the illumination beam on a pixel to pixel basis. The proposed microscope can be particularly useful for applications requiring very long exposure time or very large working distance objective lenses. In this paper we present experimental implementation of the setup using a nematic liquid crystal spatial light modulator and proof-of-concept experimental results.     

Single beam optical tweezers setup with backscattered light detection for three-dimensional measurements on DNA and nanopores

We introduce a versatile and high precision three-dimensional optical tweezers setup with minimal optical interference to measure small forces and manipulate single molecules in the vicinity of a weak reflective surface. Our tweezers system integrates an inverted optical microscope with a single IR-laser beam that is spatially filtered in an appropriate way to allow force measurements in three dimensions with remarkably high precision when operated in backscattered light detection mode. The setup was tested by overstretching a lambda-DNA in x and z directions (perpendicular and along the optical axis), and by manipulating individual lambda-DNA molecules in the vicinity of a nanopore that allowed quantitative single molecule threading experiments with minimal optical interference.     

Axial Superresolution by Oblique Two-Dimensional Nondiffracting cos Beam Illumination

Nondiffracting cos beams may be used in the object space of an optical microscope for causing a nonuniform illumination. This irradiance distribution consists in a set of equidistant plane maxima, and therefore the light radiated by the sample decays in its neighborhood. We propose to observe over an object plane coinciding with one of these illumination peaks, which results in a superresolving axial effect. For that purpose, illumination and detection should be oblique processes, and a computer-assisted z-scanning process is needed in order to access the axial structure of a thick object.     

A hybrid scanning force and light microscope for surface imaging and three-dimensional optical sectioning in differential interference contrast

The design of a scanned-cantilever-type force microscope is presented which is fully integrated into an inverted high-resolution video-enhanced light microscope. This set-up allows us to acquire thin optical sections in differential interference contrast (DIC) or polarization while the force microscope is in place. Such a hybrid microscope provides a unique platform to study how cell surface properties determine, or are affected by, the three-dimensional dynamic organization inside the living cell. The hybrid microscope presented in this paper has proven reliable and versatile for biological applications. It is the only instrument that can image a specimen by force microscopy and high-power DIC without having either to translate the specimen or to remove the force microscope. Adaptation of the design features could greatly enhance the suitability of other force microscopes for biological work.     

The “SOMSEM”—An SEM-based scanning optical microscope

No one form of microscopy is ideal for all applications and, in general, significant advances are made by correlating several techniques. In this paper, a scanning optical microscope is discussed which is based on the SEM and is entirely compatible with it. This new hybrid instrument, known as the SOMSEM, has been demonstrated using a converted SEM specimen stage and a standard Cambridge Stereoscan 250 Mk II microscope. The operating principles have been verified, and silicon MOS (metal oxide semiconductor) devices have been successfully imaged using the OBIC (optical beam induced current) mode thus avoiding electron beam damage. Potential applications and future developments are briefly discussed.